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Analysis of the Arabidopsis fatty acyl-CoA synthetase5 gene and co-expressed genes reveals an ancient.. 2011

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  Analysis of the Arabidopsis fatty acyl-CoA synthetase5 gene and co- expressed genes reveals an ancient biochemical pathway required for pollen development and sporopollenin biosynthesis  by  Sung Soo Kim    A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF    DOCTOR OF PHILOSOPHY   in    THE FACULTY OF GRADUATE STUDIES (Botany)     THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver)  June 2011  ©  Sung Soo Kim, 2011 ii ABSTRACT   The structure of the sporopollenin polymer that is the major constituent of exine, the outer pollen wall, remains poorly understood. In flowering plants, sporopollenin precursors are known to be produced in the tapetum and must be deposited and polymerized on the developing microspore during exine formation. Recent characterization of Arabidopsis thaliana genes and corresponding enzymes involved in exine formation has demonstrated the role of fatty acid derivatives as precursors of sporopollenin building units. In collaboration with other research groups, we discovered that the Arabidopsis ACOS5 gene is transiently and exclusively expressed in tapetum cells and that an Arabidopsis acos5 mutant is completely male sterile with pollen grains that are apparently devoid of sporopollenin. In this thesis, Arabidopsis genes encoding potential enzymes that could work with ACOS5 in a common biosynthetic pathway were identified by in silico co-expression analyses and functionally characterized. Previous studies and my reverse genetic analyses of selected co-expressed genes including POLYKETIDE SYNTHASE A and POLYKETIDE SYNTHASE B (PKSA/B), and TETRAKETIDE α-PYRONE REDUCTASE1 and TETRAKETIDE α-PYRONE REDUCTASE2 (TKPR1/2) revealed that mutants in these genes are also compromised in male fertility and sporopollenin deposition. In vivo biochemical assays by heterologous expression of PKSA in the yeast Saccharomyces cerevisiae showed that the enzyme catalyzes condensation of endogenous fatty acyl-CoAs with malonyl-CoA to generate α- pyrone triketides. Moreover, in vitro assays performed by collaborators revealed that the sequential actions of ACOS5, PKSA/B, and TKPR1/2 enzymes on fatty acid substrates generate polyhydroxylated long-chain α-pyrones, suggesting that these novel coumpounds are building units of sporopollenin. Phylogenetic analyses showed that these genes are highly conserved in land plants including the moss Physcomitrella patens. This work has illuminated the outlines of a conserved novel biosynthetic pathway involved in generating monomer constituents of the sporopollenin biopolymer component of the pollen wall. iii  PREFACE  Chapter 2 is part of a recently published research paper: de Azevedo Souza C, Kim SS, Koch S, Kienow L, Schneider K, McKim SM, Haughn GW, Kombrink E, Douglas CJ. (2009) A novel fatty Acyl-CoA Synthetase is required for pollen development and sporopollenin biosynthesis in Arabidopsis. Plant Cell 21:507-525.  All experiments and data reported in the Results section of this chapter were designed, performed and analyzed by me. All data including figures and tables are extracted from the above paper and reprinted with permission of the American Society of Plant Biologists.  Chapter 3 is part of a recently published research paper: Kim SS*, Grienenberger E*, Lallemand B, Colpitts CC, Kim SY, de Azevedo Souza C, Geoffroy P, Heintz D, Krahn D, Kaiser M, Kombrink E, Heitz T, Suh DY, Legrand M and Douglas CJ (2010) LAP6/POLYKETIDE SYNTHASE A and LAP5/POLYKETIDE SYNTHASE B Encode Hydroxyalkyl α-Pyrone Synthases Required for Pollen Development and Sporopollenin Biosynthesis in Arabidopsis thaliana. Plant Cell 22: 4045-4066 (* These authors contributed equally to this work)  All experiments and data reported in the Results section of this chapter were designed, performed and analyzed by me. All data including figures and tables are extracted from the above paper and reprinted with permission of the American Society of Plant Biologists.  Chapter 4 is part of a recently published research paper: Grienenberger E*, Kim SS*, Lallemand B, Geoffroy P, Heintz D, de Azevedo Souza C, Heitz T, Douglas CJ and Legrand M. (2010) Analysis of TETRAKETIDE α-PYRONE REDUCTASE Function in Arabidopsis thaliana Reveals a Previously Unknown, but Conserved, Biochemical Pathway in Sporopollenin Monomer Biosynthesis. Plant Cell 22: 4067-4083 (* These authors contributed equally to this work)  All experiments and data reported in the Results section of this chapter were designed, performed and analyzed by me and the results in sections 4.4.1, 4.4.2 and 4.4.5 are extracted from the above paper and reprinted with permission of the American Society of Plant Biologists.  iv  TABLE OF CONTENTS TABLE OF CONTENTS ABSTRACT ................................................................................................................................... ii PREFACE ..................................................................................................................................... iii TABLE OF CONTENTS ............................................................................................................. iv LISTS OF FIGURES .................................................................................................................... ix LIST OF ABBREVIATIONS ...................................................................................................... xii ACKNOWLEDGEMENTS ....................................................................................................... xiv Chapter 1. General introduction and literature review ..............................................................1 1.1 Anther development and microsporogenesis ..........................................................................1 1.2 Related biopolymers: suberin, cutin and sporopollenin .........................................................6 1.3 Mutants showing male sterility in Arabidopsis ................................................................... 10 1.4 Phenylpropanoid metabolism-like enzymes ........................................................................ 16 1.5 Research objectives ............................................................................................................. 18 Chapter 2. A novel fatty acyl-CoA synthetase (ACOS5) is required for pollen development and sporopollenin biosynthesis in Arabidopsis thaliana ............................................................19 2.1 Summary ............................................................................................................................. 19 2.2 Introduction ......................................................................................................................... 20 2.2.1 4-coumarate:CoA ligase-like (4CL-like) and acyl-CoA synthetase (ACOS) genes ...... 20 2.3 Materials and methods ......................................................................................................... 23 2.3.1 Plant material and growth conditions ........................................................................... 23 2.3.2 Complementation of acos5 mutants ............................................................................. 23 2.3.3 Nucleic acid methods.................................................................................................... 23 2.3.4 Phenotypic analyses ...................................................................................................... 23 2.3.5 Accession number ........................................................................................................ 24 2.3.6 Sequences of primers .................................................................................................... 24 2.4 Results ................................................................................................................................. 25 2.4.1 The ability of the ACOS5 gene to complement the male sterile phenotype ................. 25 2.4.2 Anther and microspore development in the acos5-1 mutant ........................................ 26 2.5 Discussion ........................................................................................................................... 29 Chapter 3. LAP6/POLYKETIDE SYNTHASE A and LAP5/POLYKETIDE SYNTHASE B encode hydroxyalkyl α-pyrone synthases required for pollen development and sporopollenin v  biosynthesis in Arabidopsis thaliana ............................................................................................34 3.1 Summary ............................................................................................................................. 34 3.2 Introduction ......................................................................................................................... 35 3.2.1 Polyketides and type III polyketide synthases (PKS) ................................................... 35 3.3 Materials and methods ......................................................................................................... 37 3.3.1 Plant material and growth conditions ........................................................................... 37 3.3.2 Phylogenetic and bioinformatic analyses ..................................................................... 38 3.3.3 RT-PCR ........................................................................................................................ 38 3.3.4 Phenotypic analyses ...................................................................................................... 39 3.3.5 In situ hybridization and validation of RNA probes ..................................................... 39 3.3.6 Cloning for PKSA and PKSB protein expression ........................................................ 41 3.3.7 Accession number ........................................................................................................ 41 3.3.8 Sequences of primers .................................................................................................... 42 3.4 Results ................................................................................................................................. 44 3.4.1 Analysis of ACOS5 co-expression genes ...................................................................... 44 3.4.2 PKSA and PKSB-like genes are conserved in land plant lineage .................................. 44 3.4.3 Tapetum-specific expression of PKSA and PKSB proteins ......................................... 47 3.4.4 Identification and phenotypic analysis of PKSA and PKSB loss-of-function alleles.... 50 3.4.5 PKSA and PKSB have partially redundant function in male fertility .......................... 52 3.4.6 Anther and microspore development in the pksa-1 pksb-3 double mutant ................... 54 3.5 Discussion ........................................................................................................................... 60 Chapter 4. Analysis of TETRAKETIDE -PYRONE REDUCTASE (TKPR) function in Arabidopsis thaliana reveals a novel and conserved biochemical pathway in sporopollenin monomer biosynthesis ..................................................................................................................67 4.1 Summary ............................................................................................................................. 67 4.2 Introduction ......................................................................................................................... 68 4.2.1 DIHYDROFLAVONOL 4-REDUCTASE (DFR) and DIHYDROFLAVONOL 4- REDUCTASE-LIKE1 (DRL1).............................................................................................. 68 4.3 Materials and methods ......................................................................................................... 71 4.3.1 Plant material and growth conditions ........................................................................... 71 4.3.2 Identification and characterization of TKPR1 insertion mutant ................................... 71 4.3.3 Complementation of tkpr1 mutant ................................................................................ 72 vi  4.3.4 Phylogenetic studies ..................................................................................................... 72 4.3.5 Microscopy ................................................................................................................... 73 4.3.6 RT-PCR ........................................................................................................................ 73 4.3.7 In situ hybridization and validation of RNA probes ..................................................... 74 4.3.8 Production of TKPR1 recombinant proteins and activity assay in vitro ...................... 74 4.3.9 Identification of products by GC-MS ........................................................................... 75 4.3.10 Accession numbers ..................................................................................................... 75 4.3.11 Sequences of primers .................................................................................................. 76 4.4 Results ................................................................................................................................. 76 4.4.1 Genes involved in pollen cell wall formation are tightly co-regulated ......................... 76 4.4.2 At4g35420 and At1g68540 expression profiles during flower development ............... 78 4.4.3 Genetic and phenotypic analysis of tkpr1-1 ................................................................. 81 4.4.4 Complementation analysis ............................................................................................ 83 4.4.5 Anther and microspore development in the tkpr1 mutant ............................................ 84 4.4.6 Testing TKPR1 enzymatic function in vitro ................................................................. 88 4.4.7 Phylogenetic analysis of TKPR genes .......................................................................... 91 4.5 Discussion ........................................................................................................................... 94 Chapter 5. The introduction of sporopollenin biosynthesis enzymes CYP703A2, ACOS5, PKSA and TKPR1 into the yeast Saccharomyces cerevisiae in different combinations .........99 5.1 Summary ............................................................................................................................. 99 5.2 Introduction ....................................................................................................................... 100 5.3 Materials and methods ....................................................................................................... 102 5.3.1 Construction of CYP703A2, ACOS5, PKSA and TKPR1 in pESC vector ............... 102 5.3.2 Yeast strains, culture and heterologous expression in yeast ....................................... 102 5.3.3 SDS-PAGE and immuno-blotting .............................................................................. 104 5.3.4 Chemical analysis of yeast expression product .......................................................... 104 5.4 Results ............................................................................................................................... 105 5.4.1 CYP703A2 and/or ACOS5 expression in yeast ......................................................... 105 5.4.2 Triple and quadruple expression in yeast ................................................................... 109 5.4.3 PKSA and/or TKPR1 expression in yeast .................................................................. 114 5.5 Discussion ......................................................................................................................... 119 Chapter 6. Conclusion and future directions ...........................................................................123 vii  References ...................................................................................................................................127 Appendices ..................................................................................................................................142 Appendix A. Amino acid sequences used in construction of the phylogenetic tree shown in Figure 3.2. ................................................................................................................................ 142 Appendix B. Alignment of amino acid sequences used to generate the phylogenetic tree shown in Figure 3.2. ........................................................................................................................... 145 Appendix C. Amino acid sequences used in construction of the phylogenetic tree shown in Figure 4.14. .............................................................................................................................. 152 Appendix D. Alignment of amino acid sequences used to generate the phylogenetic tree shown in Figure 4.14. ......................................................................................................................... 158  viii  LIST OF TABLES  Table 1.1 Summary of major events during Arabidopsis anther and pollen development…1 Table 1.2 Summary of common cutin, suberin and sporopollenin monomers, identified by functional group and possible biosynthetic reactions for each biopolymer…………………7 Table 1.3 Summary of male sterile Arabidopsis mutants……………………………………12 Table 2.1 Primers used in this study……………………………………………………………24 Table 3.1 Primers used in this study……………………………………………………………42 Table 3.2 Putative PKSA and PKSB orthologs and expression in other species……………45 Table 3.3 Quantification of seed set in plants with different PKSA and PKSB allelic combinations……………………………………………………………………………………54 Table 4.1 Primers used in this study……………………………………………………………76 Table 4.2 Putative TKPR orthologs and expression in other species…………………………93   ix  LISTS OF FIGURES   Figure 1.1 Anther cell differentiation………………………………………………………… 4 Figure 1.2 Arabidopsis (Col-0) pollen wall structure (A and B), schematic diagram of the main features of a mature pollen grain wall (C) and of exine formation (D)………………5 Figure 1.3 Model of the role of CYP703A2 in sporopollenin formation……………………10 Figure 2.1 Phylogenetic relationships of plant-specific acyl-CoA synthetases (ACSs, ACOSs) from three fully sequenced angiosperm genomes……………………………………………22 Figure 2.2 The construct used for acos5 complementation…………………………………26 Figure 2.3 Transmission electron micrographs of wild-type (Col-0) and acos5 mutant anthers, pollen grains, and pollen walls………………………………………………………28 Figure 2.4 Model for the role of ACOS5 in sporopollenin monomer biosynthesis in developing anthers……………………………………………………………………………32 Figure 3.1 Diverse cyclization strategies employed by type III PKSs………………………36 Figure 3.2 Phylogenetic analysis of CHS and CHS-like (CHSL) protein sequences from land plants……………………………………………………………………………………………47 Figure 3.3 Developmental expression profiles of PKSA and PKSB…………………………48 Figure 3.4 DNA gel blot showing specificity of PKSA or PKSB RNA probes used for in situ hybridization……………………………………………………………………………………49 Figure 3.5 Transient tapetum-specific expression of PKSA and PKSB………………………50 Figure 3.6 Molecular characterization of pksa, pksb and pksa pksb insertion alleles and effects on gene expression………………………………………………………………………51 Figure 3.7 Phenotypic characterization of plants segregating for pksa and pksb alleles……53 Figure 3.8 Phenotypic characterization of anther and microspore development in wild-type (Col-0) and pksa-1 pksb-3 flowers………………………………………………………………55 Figure 3.9 Anther development in the double mutant pksa-1 pksb-3………………………57 Figure 3.10 Transmission electron micrographs of wild-type (Col-0) and pksa-1 pksb-3 anthers and pollen………………………………………………………………………………59 Figure 4.1 Overview of the flavonoid biosynthesis pathway…………………………………69 x  Figure 4.2 Developmental expression profile of TKPR1, TKPR2 and At1g25460……………78 Figure 4.3 Transient tapetum-specific expression of TKPR1 and TKPR2…………………80 Figure 4.4 Specificity of TKPR nucleotidic probes……………………………………………81 Figure 4.5 Molecular characterization of tkpr1 insertion alleles and effects on gene expression………………………………………………………………………………………82 Figure 4.6 Phenotypic characterization of tkpr1 plant………………………………………83 Figure 4.7 Schematic representations of the construct for tkpr1 complementation test……84 Figure 4.8 Phenotypic characterization of anther and microspore development in wild-type (Col-0) and tkpr1 flowers………………………………………………………………………85 Figure 4.9 Exine formation is impaired in tkpr1-1 anthers…………………………………86 Figure 4.10 Analysis of recombinant protein preparations at different steps of purification………………………………………………………………………………………88 Figure 4.11 Structure of a synthetic alkyl phloroglucinol tested as a TKPR1 substrate and predicted MS fragmentation patterns…………………………………………………………89 Figure 4.12 GC analysis of reaction products generated by TKPR1 incubation with a synthetic alkyl phloroglucinol…………………………………………………………………89 Figure 4.13 Mass spectra of a peak indicated by arrowhead in the GC chromatogram of Figure 4.12 ………………………………………………………………………………………90  Figure 4.14 Phylogenetic analysis of DFR and DFR related protein sequences in Arabidopsis, poplar, rice, and Physcomitrella………………………………………………………………92  Figure 5.1 A putative scheme of sporopollenin biosynthesis………………………………100 Figure 5.2 Immunoblot detection of CYP703A2 and ACOS5 proteins in transgenic yeast strains…………………………………………………………………………………………105 Figure 5.3 GC analysis of fatty acid metabolites produced by vector control and transgenic yeast strains……………………………………………………………………………………107 Figure 5.4 Immunoblot detection of CYP703A2, ACOS5 and TKPR1 proteins in transgenic yeast strains……………………………………………………………………………………109 Figure 5.5 GC analysis of fatty acid metabolites produced by vector control and transgenic yeast strains……………………………………………………………………………………111 Figure 5.6 Mass spectra of two novel metabolites found in yeast strains expressing CYP703A2/ACOS5/PKSA or CYP703A2/ACOS5/PKSA/TKPR1……………………………112 xi  Figure 5.7 Immunoblot detection of TKPR1 proteins in transgenic yeast strains…………114 Figure 5.8 GC analysis of fatty acid metabolites produced by vector control and PKSA/TKPR1 expressing yeast strains………………………………………………………115 Figure 5.9 Mass spectra of novel peaks from the GC chromatogram obtained from the yeast strain expressing PKSA/TKPR1………………………………………………………………116 Figure 5.10 Predicted GC-MS fragmentation patterns and estimated molecular weights of α-pyrones containing various alkyl chain lengths……………………………………………118  xii  LIST OF ABBREVIATIONS   AHCT Anthocyanin O-hydroxycinnamoyltransferase AMP Adenosine monophosphate ATP Adenosine triphosphate BCIP 5-Bromo-4-chloro-3-indolyl phosphate BEAT Benzylalcohol O-acetyltransferase bp Base pair cDNA Complementary deoxyribonucleic acid CER Eceriferum CoA Coenzyme A CYP Cytochrome P450 DAT Deacetylvindoline 4-O-acetyltransferase DNA Deoxyribonucleic acid DTT Dithiothreitol EDTA Ethylenediaminetetraacetic acid EMBL European Molecular Biology Laboratory FID Flame ionization detector GC Gas chromatography HCBT Anthranilate N-hydroxycinnamoyl/benzoyltransferase HCT Hydroxycinnamoyltransferase HCT/HQT Hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase His Histidine IPTG  Isopropyl β-D-1-thiogalactopyranoside JA Jasmonic Acid Km Michaelis-Menten constant LAP Less adhesive pollen LB Luria-Bertani Leu Leucine MADS MCM1, AGAMOUS, DEFICIENS, SRF MS Mass spectrometry NADH Nicotinamide adenine dinucleotide NADPH Nicotinamide adenine dinucleotide phosphate NBT Nitro blue tetrazolium chloride NTA Nitrilotriacetic acid PAGE Polyacrylamide gel electrophoresis PCR Polymerase chain reaction PHD Plant Homeo Domain PMSF  Phenylmethylsulfonyl fluoride xiii  RNA Ribonucleic acid RT Reverse transcription SDS  Sodium dodecyl sulfate SSC Saline sodium citrate TEM Transmission electron microscopy TF Transcription factor TMS Trimethylsilyl group Trp Tryptophan Ura Uracil UV Ultraviolet   xiv  ACKNOWLEDGEMENTS   This thesis could not been completed without the guidance and the support of many people. First and foremost, I wish to express my appreciation to my supervisor, Dr. Carl J Douglas, who offered invaluable assistance, support, training, guidance, and hours of academically stimulating conversation and meeting. I would also like to thank my committee members, Dr. George Haughn, Dr. Reinhard Jetter, Dr. Jin-Gui Chen and Dr. Lacey Samuels for their advice on this research project.  I would like to thank all my lab mates, including the past members: Dr. Michael Friedmann, Dr. Björn Hamberger, Dr. Clarice Souza, Dr. June Kim, Dr. Eryang Li, Dr. Apruva Bhargava, Dr. Etienne Grienenberger, Yuanyuan Liu, Teagan Quilichini for sharing their knowledge and experience as well as providing extremely valuable assistance. I also would like to thank Dr. Zhonghua Wang, Dr. Christopher Buschhaus and Yan Cao in Dr. Jetter’s lab for their help in chemical analyses and GC maintenance, together with Derrick Horne and Brad Ross in the UBC Bioimaging facility for TEM support. Special thanks to Dr. Santokh Singh and Jarnail Mehroke for thoughtful guidance to improve intellectual communication and teaching skills with various levels of undergraduate students in class.  I am grateful to my collaborators, members of Dr. Michel Legrand's research group in IBMP, France and of Dr. Dae-Yeon Suh's in University of Regina to help make this study successful. I am especially appreciated Che C. Colpitts and Dr. Etienne Grienenberger and for insightful and helpful discussion of biochemistry.  I wish to express my love and gratitude to my beloved family, especially thanks to my wife, KyungHee for her positive thoughts, encouragement and support through the duration of my studies. And finally, I am very happy to complete this thesis, seeing a big and innocent smile of my son, Se-hun.  1  Chapter 1. General introduction and literature review  1.1 Anther development and microsporogenesis  Microsporogenesis and pollen development are complex processes that take place during flower development, starting with theinitiation of stamen primordia and leading to the formation of two microgametes per mature pollen grain. These developmental events involve precisely controlled cellular processes, such as cell division, cell differentiation, and cell death (Sanders et al., 1999; Scott et al., 2004; Ma, 2005). In Arabidopsis thaliana, anther development has been divided into stages based  on anatomical, morphological, cellular, and molecular events (Table 1.1; Sanders et al., 1999; Scott et al., 2004; Ma, 2005). At the beginning of anther cell differentiation (Stage 5 in Figure 1.1), four clearly defined locules are established and visible pollen mother cells appear. Subsequent to this, the pollen mother cells undergo meiosis and tetrads are formed, connected by a callose wall (Stage 7 in Figure 1.1). Once the  callose wall degenerates to release free microspores (Stage 8 in Figure 1.1), they become vacuolated, and the pollen wall becomes visible. Microspores  continue to enlarge and develop, and the tapetum layer, a maternal cell layer that surrounds the inner side of the anther locules, starts to degenerate. At the end of anther development (Stage 10 in Figure 1.1), the tapetum cell layer completely degenerates, and mature pollen  grains fill the locules and are released by anther dehiscence (Sanders et al., 1999; Ma, 2005).  Table 1.1 Summary of major events during Arabidopsis anther and pollen development.  Anther stage Major event/ landmark Pollen wall development TEM images 1  for Col-0 pollen wall TEM images 1  for Col-0 pollen Stage 5 Anther morphogenesis is complete.  Epidermis, endothecium, middle layer, tapetum and microsporocyte are visible    2  Table 1.1 Summary of major events during Arabidopsis anther and pollen development. (cont.)  Anther stage Major event/ landmark Pollen wall development TEM images 1  for Col-0 pollen wall TEM images 1  for Col-0 pollen Stage 6 MMC enters Meiosis I.  Callose is deposited. Meiotic cell dissociated from each other and from tapetum.  Stage 7 Meiosis is completed.  Tetrad stage (haploid microspore)  Primexine formation (Black arrow)  Probacular formation (White)  Stage 8 Microspore is released.  Callose wall is degenerated.   Exine formation is initiated  Intine, tectum , nexine,  and bacular are visible  Stage 9 - 10 Tapetum degeneration initiated at stage 10.     3  Table 1.1 Summary of major events during Arabidopsis anther and pollen development. (cont.)  Anther stage Major event/ landmark Pollen wall development TEM images 1  for Col-0 pollen wall TEM images 1  for Col-0 pollen Stage 11 Pollen mitotic division occurs (vegetative and generative cell stage).  Tapetum degeneration Completion of exine formation  Intine is thicker than previously  Stage 12 Tricelluar haploid pollen grain develops. Deposition of extracellular pollen coat  Stage 13 Anther dehiscence occurs. Stage 14 Senescence of stamen occurs.  1  All TEM images are adapted and reprinted from (Ariizumi et al., 2008), with permission of Oxford University Press (Copyright ©  2008 Oxford University Press). The major events in each anther developmental stages are described based on Sanders et al. (1999). Bar = 500nm for pollen wall and 5µm for pollen. Ba, bacula; In, intine; MSp, microspores; Ne, nexine; Tc, tectum.  A critical event during pollen maturation is the formation of the pollen surface structure. The pollen wall represents one of the most complex plant cell walls, with contributions from both the sporophyte and gametophyte generations (Figure 1.2). The major pollen wall components are a microspore-derived cellulosic primexine synthesized by the developing haploid microspores themselves at the tetrad stage (Blackmore et al., 2007), a thick exine deposited on the outer surface of the primexine largely after the release of free microspores, and a pectocellulosic intine produced by developing 4  microspores and male gametophytes (Figure 1.2D). In contrast with the primexine and intine, the exine is maternally derived, and exine constituents are produced in the sporophytic tapetum cell layer (Piffanelli et al., 1998). These exine constituents are secreted into the locules and incorporated  into the exine by polymerization on the surface    Figure 1.1 Anther cell differentiation. The flower sections were stained in toluidine blue and anthers were photographed by bright-field microscopy. C, connective; E, epidermis; En, endothecium; Fb, fibrous bands; MC, meiotic cell; ML, middle layer; MMC, microspore mother cells; MSp, microspores; PG, pollen grains; Sm, septum; St, stomium; StR, stomium region; T, tapetum; Tds, 5  tetrads; V, vascular region. Bar= 50µm (Sanders et al., 1999). Images are adapted and reprinted with permission of Springer (Copyright ©  1999, Springer)   of the primexine (Piffanelli et al., 1998; Scott et al., 2004; Ma, 2005), where it often assumes a characteristic reticulate pattern, consisting of baculae and tecta (Figure 1.2B and 1.2C). The final component of the pollen wall is the lipid-rich pollen coat, or tryphine, which is deposited onto the exine surface. Pollen coat components accumulate in tapetum cells and are released into locules during the course of tapetum cell degeneration (Ma, 2005).    Figure 1.2 Arabidopsis (Col-0) pollen wall structure (A and B), schematic diagram of the main features of a mature pollen grain wall (C) and of exine formation (D).  (A) and (B) Scanning electron micrograph, kindly provided by Dr. Etienne Grienenberger. (C) and (D) Diagrams are modified and adapted based on Suzuki et al., (2008). 6  The pollen wall consists essentially of two layers: the intine and the exine. The intine is mostly synthesized by the haploid microspore itself. However, the tapetum is responsible for the production and secretion of the exine, generally known as a mixture of protein, lipids and aromatic molecules (Sanders et al., 1999; Ma, 2005). After synthesis and deposition of the pollen wall, the tapetum cells are degraded via programmed cell death, and pollen grains continue to develop and mature. Although the exact composition of the exine and other components of the pollen wall are not completely understood, it is known that functional tapetum cells are essential for the development of viable pollen grains (Zhang and Chiang, 1997; Vizcay-Barrena and Wilson, 2006). The major component of the exine is termed sporopollenin, a complex biopolymer which is composed of long-chain fatty acids and poorly characterized phenolic molecules coupled by ester and ether bonds (Scott et al., 2004; Blokker et al., 2006).  1.2 Related biopolymers: suberin, cutin and sporopollenin  Land plants have evolved aliphatic biopolymers that protect their cell surfaces against dehydration, pathogens, and chemical and physical damage. Moreover, to adapt rapid barriers to new physiological and environmental conditions, they have evolved elaborate regulatory networks (Pichersky and Gang, 2000; Bowman et al., 2007; Franke and Schreiber, 2007). Land plants have three types of lipid-based polyesters: cutin, suberin and sporopollenin. They are composed of both fatty acid- and glycerol-based extracellular polymers with phenolic components that represent a barrier of resistance to both water and solutes (Hose et al., 2001; Beisson et al., 2007). Cutin and suberin are better characterized than sporopollenin. The cuticle, which consists of cutin and waxes, is deposited at the outermost area of the epidermis cell wall as a thin membrane-like layer. On the other hand, the location of suberin deposition in plants is highly variable. For example, the outer bark of trees, the outer tissues of stems, the outer and inner sealing tissues of primary roots, and seed coat are known to contain the polymer suberin (Beisson et al., 2007; Soler et al., 2007). Moreover, suberin is located in the Casparian strip, a waterproof band of wall material in the radial (anticlinal) cell walls of the endodermis which has various chemical components described as composed of lignin or suberin or 7  both (Kolattukudy, 2001). Cutin is a biopolymer containing mainly ω-hydroxylated and epoxy hydroxylated fatty acids 16 to 18 carbons in length ester-linked into a polymer (Table 1.2; Kolattukudy, 2001). On the other hand, suberin has distinctive domains composed of aliphatic and aromatic constituents (Table 1.2; Kolattukudy, 2001; Soler et al., 2007; Pollard et al., 2008). The aliphatic domain of suberin is a polyester polymer, comprised of mainly ω- hydroxy fatty acids and α,ω-dicarboxylic acids as very long aliphatic constituents with over 20 carbon chain-length (Kolattukudy, 2001; Pollard et al., 2008). Hydroxycinnamic acids in aromatic domains are proposed to covalently link the aliphatic suberin polyester to the cell wall, possibly some monolignols (Kolattukudy, 2001). A recent macromolecular structure model for suberin proposed that the monomeric blocks contain long-chain α,ω-dicarboxyolic acids esterified to glycerol at both ends as the core of the suberin macromolecule (Franke and Schreiber, 2007). These polyol glycerols provide a cross-linked two- and three-dimensional network by the formation of ester linkages to additional α,ω-dicarboxylic acids and ω-hydroxy fatty acids, leading to a rigid and insoluble polymer (Franke and Schreiber, 2007).   Table 1.2 Summary of common cutin, suberin and sporopollenin monomers, identified by functional group and possible biosynthetic reactions for each biopolymer.  Common monomer type Cutin Suberin Sporopollenin LCFA (C16 ~ C18) Yes Yes Yes (C10~) VLCFA No Yes (~C30) Yes Fatty alcohols CH3(CH2)mOH Yes Yes N/A Hydroxy fatty acid Yes Yes  Yes α,ω-dicarboxylic fatty acid Yes Yes N/A    8  Table 1.2 Summary of common cutin, suberin and sporopellenin monomers, identified by functional group and possible biosynthetic reactions for each biopolymer. (cont.)  Common monomer type Cutin Suberin Sporopollenin Phenolics N/A Ferulic acid / p-hydroxy cinammate Oxygenated phenylpropanoid (p-coumaric, caffeic acid) Glycerol Yes Yes N/A Funtional group Cutin Suberin Sporopollenin Ketones Yes N/A Yes Epoxide Yes N/A N/A Ester Yes Yes Yes Ether N/A N/A Yes Possible enzyme reaction Cutin Suberin Sporopollenin Reduction (carboxylic acid to aldehyde) N/A Yes N/A Reduction (aldehyde to alcohol) N/A Yes N/A Esterification (carboxylic acid and alcohol) Yes Yes Yes Etherification  N/A N/A Yes Hydroxylation by P450 Yes Yes Yes Oxidation by dehydrogenase (alcohol to aldehyde) N/A Yes N/A Oxidation ) by dehydrogenase  (aldehyde to carboxylic acid) N/A Yes N/A Epoxidation Yes Yes N/A N/A, No information available VLCFA, Very long chain (longer than 22C) fatty acids  The main constituent of the pollen exine layer is sporopollenin, an extremely robust and durable biopolymer found in the spores of bryophytes and ferns and in pollen exine of seed plants (Bohne et al., 2003). The chemical composition of sporopollenin remains poorly  characterized because it is extremely resistant to chemical and biological 9  degradation procedures (Bubert et al., 2002; Vizcay-Barrena and Wilson, 2006). However, available data are consistent with a sporopollenin polymer consisting of phenolic and fatty acid–derived constituents that are covalently coupled by ether and ester linkages (Table 1.2; Ahlers et al., 2000; Rozema et al., 2001; Bubert et al., 2002; Ahlers et al., 2003; Scott et al., 2004). Recently, a partially male sterile mutant phenotype was described for Arabidopsis CYP703A2, a member of cytochrome P450 gene family, and a possible substrate of the CYP703A2 enzyme was reported (Morant et al., 2007). The mutant plants showed impaired pollen wall development with defective exine. Additionally, CYP703A2 hydroxylated medium-chain saturated fatty acids to the corresponding mono-hydroxy fatty acids, with a preferential hydroxylation of lauric acid (C12:0) in vitro and in vivo. A model for the role of CYP703A2 was proposed to explain its involvement of sporopollenin formation (Figure 1.3). According to the model, monomeric hydroxy fatty acid units generated by CYP703A2 and phenylpropanoid derived molecules like p-coumaric acid and caffeic acid are connected by ether and ester linkages, and they give rise to the backbone structure of the sporopollenin polymer. However, to form a three-dimensional network or cross-linked polymer, additional ether or ester linkages may be needed. This could mean that currently unknown enzymes co- expressed with CYP703A2 contribute to further strengthening of the sporopollenin polymer.  10   Figure 1.3 Model of the role of CYP703A2 in sporopollenin formation. Monomeric units derived from CYP703A2-catalyzed hydroxylation of lauric acids are shown in red. The participation of oxygen atoms within these units in ether and ester linkages in the formation of the sporopollenin biopolymer is illustrated by circles and squares, respectively. The p-coumaric and caffeic acid units illustrate the presence of phenylpropanoids in the sporopollenin polymer (Morant et al., 2007). Image was reprinted with permission of American Society of Plant Biologists (Copyright © American Society of Plant Biologists).   1.3 Mutants showing male sterility in Arabidopsis  Numerous male sterile or partially sterile mutants that have been isolated and characterized in Arabidopsis define some of the key processes in anther and male gametophyte development. Table 1.3 shows some examples of male sterile Arabidopsis 11  mutants that have been characterized. Male sterile mutants displaying apparently normal microspore and tapetum development, but with defects in pollen wall formation and pollen maturation, have started to shed light on the cell  biology and biochemistry of pollen wall, exine, and sporopollenin  development and biosynthesis. For example, the Arabidopsis MALE STERILITY (MS2) gene, defined by the ms2 male-sterile  mutation, is required for exine formation and encodes a predicted  fatty acyl-CoA reductase (Aarts et al., 1997). Expression of  MS in Escherichia coli results in the production of alcohols  from endogenous E. coli fatty acids (Doan et al., 2009), supporting  a function in fatty acid metabolism. Loss of function of the FACELESS POLLEN1/WAX2/YRE/CER3 gene results in defects in both  exine and epicuticular wax deposition, and the gene encodes  a putative enzyme of unknown function presumably involved in  both wax biosynthesis and pollen wall formation (Ariizumi et al., 2003; Chen et al., 2003; Rowland et al., 2007). Recently, Arabidopsis genes encoding the cytochrome P450 enzymes CYP704B1, as well as CYP703A2 described above, have been shown to be involved in the biosynthesis of sporopollenin, since mutants show severe to moderate defects in exine deposition and pollen grain development  (Morant et al., 2007; Dobritsa et al., 2009). In vitro assays indicate that the enzymes catalyze hydroxylation of medium- to long-chain fatty acid substrates. While CYP703A2 is an in-chain  hydroxylase with substrate preference for lauric acid (C12:0), CYP704B1 catalyzes the ω-hydroxylation of long-chain fatty acids (Morant et al., 2007; Dobritsa et al., 2009). 12  Table 1.3 Summary of male sterile Arabidopsis mutants. Mutant name Stages of gene expression Defective main event Encoding / related metabolism Phenotype Reference spl/nzz (SPOROCYTLESS/NOZZ LE) Stage 3, 4 and 5 Sporogenesis TF (MADS box) Possession of AGAMOUS binding site Fail to differentiation to male and female sporocyte (Yang et al., 1999) ems1/exs (EXCESS MALE SPOROCYTES /EXTRA SPOROGENOUS CELL) Stage 3, 4 and 5 Tapetum differentiation  Putative leucine-rich repeat receptor protein kinase (LRR-RPK) A tapetum is absent in anther and extra microsporocytes are present (Zhao et al., 2002) tpd1 (TAPETUM DETERMINANT 1) Unknown protein of 176 amino acids (Yang et al., 2003a) mmd1/duet (MALE MEIOCYTE DEATH1) Stage 6 and 7 Defective meiosis PHD-finger Nuclear Protein Aberrant tetrad  (Yang et al., 2003b) ams (ABORTED MICROSPORES) Stage 7 and 8 Tapetum and microspore development  MYC TF (basic helix-loop- helix (bHLH)) The complete absence of pollen grains due to both the microspores and tapetum disintegration (Sorensen et al., 2003) dex1 (DEFECTIVE IN EXINE PATTERN FORMATION) Low and relatively equal amounts throughout the plant Defective primexine Membrane protein containing several potential calcium-binding domains Normal primexine development is disrupted, which affects the conformation of the plasma membrane and sporopollenin deposition. (Paxson-Sowders et al., 2001)  13  Table 1.3 Summary of male sterile Arabidopsis mutants. (cont.) Mutant name Stages of gene expression Defective main event Encoding / related metabolism Phenotype Reference myb103 (R2R3 MYB GENE FAMILY) N.A. Defective exine formation Action of upstream of MS2  Tapetum Development, callose dissolution and exine formation  Premature degeneration of the tapetum  (Zhang et al., 2007) ms1 (MALE STERILITY 1) Stage 7 and 8 Defective exine formation Tapetum specific TF, PHD finger motif Abnormal pollen wall with aberrant deposition of the exine due to defective development of the tapetum (Wilson et al., 2001) myb32 myb4 N.A. Pollen development Tapetum specific  Phenylpropanoid and flavonoid Aberrant pollen grain due to absence of cytoplasm  (Preston et al., 2004) ms2 (MALE STERILITY 2) Stage 8, 9, and 10 Defective exine formation Tapetum specific  Fatty acid reductase involved in the synthesis of sporopollenin No exine in pollen wall  (Aarts et al., 1997) CYP703A2  Stage 7, 8 and 9 (closed buds) Defective exine formation Tapetum specific  The conversion of medicum-chain saturated fatty acids to corresponding monohydroxylated fatty acid Defective exine in pollen wall  (Morant et al., 2007)  14  Table 1.3 Summary of male sterile Arabidopsis mutants. (cont.) Mutant name Stages of gene expression Defective main event Encoding / related metabolism Phenotype Reference nef1 (NO EXINE FORMATION1) N.A. Lipid accumulation in the plastid Tapetum specific  Plastid integral membrane protein Growth defect  Aberrant lipid accumulation of the plastid in tapetum  (Ariizumi et al., 2004) cer1  N.A. The aberrant pollen coat structure Conversion of stem wax C30 aldehydes to C29 alkanes The rehydration deficiency by depleting pollen coat lipids leading to a pollen-stigma signaling failure (Aarts et al., 1995) cer6-2 N.A. Lipid elongation in production >28 Carbons long Unevenly distributed pollen coat (Fiebig et al., 2000) flp1 (FACELESS POLLEN-1) N.A. Allelic to CER3, unknown function  The smooth appearance of the pollen surface is due to excess tryphine.  Reduced cuticular wax in stems and siliques  (Ariizumi et al., 2003; Rowland et al., 2007) scp (SIDECAR POLLEN)  N.A. Defective mitosis in pollen grain Gametophytic mutation  Asymmetric cell division of pollen development No cell wall separating the two vegetative-like nuclei  (Chen and McCormick, 1996)    15  Table 1.3 Summary of male sterile Arabidopsis mutants. (cont.) Mutant name Stages of gene expression Defective main event Encoding / related metabolism Phenotype Reference myb26/ms35 (MALE STERILE 35) N.A. No anther dehiscence Endothecial wall thickenings Disruption of the development of lignified, cellulosic secondary thickenings in the anther endothecium, preventing anther dehiscence. (Yang et al., 2007b) myb26 N.A.  Endothecial wall thickenings (allelic to ms35) No dehiscence process due to the failure that endothecial cell undergo the lignification (Steiner-Lange et al., 2003) fad3fad7fad8 N.A. Deficiency in synthesis of jasmonic acid (JA) No dehiscence process due to the failure of controlling water transport in the anther (McConn and Browse, 1996) dde1 (DELAYED DEHISCENCE 1) Stage 10 and 11 12-oxophytodienoate (OPDA) reductase, in the JA biosynthesis No dehiscence process due to the failure of controlling water transport in the anther (Sanders et al., 2000) dad1 (DEFECTIVE IN ANTHER DEHISCENCE1) N.A. Chloroplastic phospholipase A1 in JA biosynthesis Anthers do not dehisce at flower opening (Ishiguro et al., 2001) N.A., No information available 16  1.4 Phenylpropanoid metabolism-like enzymes  The genes encoding enzymes in phenylpropanoid, flavonoid, and monolignol metabolism have been identified and characterized in many species. Following the generation of complete genome sequence data from Arabidopsis, the full set of phenylpropanoid and lignin biosynthetic genes was identified (Costa et al., 2003; Raes et al., 2003; Ehlting et al., 2005). Moreover, the likely sets of true Arabidopsis phenylpropanoid gene family members were annotated by sequence similarity searches and gene expression profiling (Raes et al., 2003; Costa et al., 2005; Ehlting et al., 2005). Whereas these phenylpropanoid-like genes are closely related to true phenylpropanoid genes, they likely encode enzymes of unknown specific biochemical function in diverse metabolic pathways in natural product biosynthesis. Plant adaptation relies on significant metabolic changes that are reflected by the evolution of large gene families. The elaborate decoration of a basic carbon skeleton structure, by using enzymes that catalyze oxidation, reduction, hydroxylation, decarboxylation, glycosylation, and acylation reactions generates the large diversity in plant secondary metabolites. These reactions are well known in phenylpropanoid metabolism, but phenylpropanoid-like enzymes may catalyze similar reactions using different starter carbon skeletons. A well-studied example would be the large family of acyl transferases, BAHD, which is an acronym composed of the first letter from biochemically characterized enzymes of this family (BEAT, AHCT, HCBT, and DAT) (D'Auria, 2006). The HCT enzyme involved in monolignol biosynthesis is part of a large family of “BAHD” acyl tranferases. The BAHD members share sequence identity, conserved motifs and catalytic mechanisms (D'Auria, 2006). The distinct classes of BAHD enzymes are identified by phylogenetic analysis. One subgroup consists of enzymes including HCT/HQT enzymes which are responsible for the formation of hydroxycinnamoyl quinate/shikimate esters in Nicotiana tabacum and Arabidopsis (D'Auria, 2006). The absence of this enzyme activity results in severe phenotype changes, such as dwarfed plants and deficiency in syringyl lignin units (Hoffmann et al., 2004). Coumaroyl-shikimate esters formed by the action of HCT are known to be intermediates in P450-mediated hydroxylation of coumaric acid to yield caffeic acid (Schoch et al., 17  2001). BAHD enzymes in other clades are involved in modification of other secondary metabolites (D'Auria, 2006). Recently, a function of SHT (Spermidine Hydroxycinnamoyl Transferase, At2g19070), one member of the BAHD family was characterized (Grienenberger et al., 2009). SHT is specifically expressed in tapetum cells at early flower development stages. SHT catalyzes acylation using hydroxycinnamoyl- CoAs as donor and spermidine as acceptor substrates, generating mono- to trihydroxycinnamoyl spermidine, which is involved in the formation of the pollen coat (Grienenberger et al., 2009). A key enzyme in phenylpropanoid metabolism is 4-coumarate:CoA ligase (4CL; (Hahlbrock and Scheel, 1989), which generates hydroxycinnamoyl-CoA esters that are central intermediates in the biosynthesis of lignin monomers, flavonoids and other secondary metabolites (Hahlbrock and Scheel, 1989). Previous work in the Douglas lab identified a large set of plant-specific 4CL-like enzymes of mostly unknown function (Souza et al., 2008). The Arabidopsis 4CL-like enzyme most closely related to true 4CLs is ACYL-COA SYNTHETASE5 (ACOS5; At1g62940). ACOS5 is a single copy gene that has homologs in all plants investigated, and such homologs are expressed specifically in anthers (Souza Cde et al., 2008; de Azevedo Souza et al., 2009). The function of ACOS5 was investigated using a reverse genetic approach which showed that an acos5 loss of function mutant is male sterile, with complete loss of pollen grain formation. The acos5 mutation co-segregated with the male sterile phenotype. Normal development of microspores is arrested in the acos5 mutant at anther development stage 9, and they have apparently defective exine (de Azevedo Souza et al., 2009). A transmission electron microscopy (TEM) of developing acos5 pollen grains suggests a complete deficiency of sporopollenin and exine. Moreover, the results of in situ hybridization experiments demonstrated that ACOS5 has a transient and tapetum preferred expression pattern and is most highly expressed in the stages immediately preceding the appearance of the visible mutant phenotype. In this thesis, I report and discuss the further characterization of the acos5 phenotype and the characterization of a total of five phenylpropanoid-like genes and the corresponding enzymes, which are co-expressed with ACOS5 and are required for pollen wall formation. Additionally a potential pathway of sporopollenin biosynthesis catalyzed 18  by these enzymes will be explored in more detail in Chapters 5 and 6.  1.5 Research objectives  1. Determine if enzymes encoded by genes co-expressed with ACOS5 are required for male fertility. 2. Characterize ACOS5 co-expressed genes and enzymes that are required for male fertility, and determine possible roles in sporopollenin biosynthesis. 3. Test whether ACOS5 co-expressed enzymes work in the same biochemical pathway. 4. Investigate the evolutionary conservation of the set of ACOS5 co-expressed genes in land plants using bioinformatics tools.  19  Chapter 2. A novel fatty acyl-CoA synthetase (ACOS5) is required for pollen development and sporopollenin biosynthesis in Arabidopsis thaliana  2.1 Summary  Acyl-CoA Synthetase (ACOS) genes are related to 4-coumarate:CoA ligase (4CL) but have distinct functions. The Arabidopsis thaliana ACOS5 protein is in clade A of Arabidopsis ACOS proteins, the clade most closely related to true 4CL proteins. This clade contains putative non-peroxisomal ACOS enzymes conserved in several angiosperm lineages and in the moss Physcomitrella patens. Although its function is unknown, ACOS5 is preferentially expressed in the flowers of all angiosperms examined. Together with genetic, phenotypic, bioinformatic experiments performed by a previous student, Dr. Clarice de Azevedo Souza, my data show that an acos5 mutant produces no pollen in mature anthers, no seeds by self-fertilization, and is severely compromised in pollen wall formation, apparently lacking sporopollenin or exine. Moreover, data from in vitro enzymes assays provided by a collaborator, Dr. Erich Kombrink, indicate that recombinant ACOS5 enzyme has a broad in vitro preference for medium-chain fatty acids. Based on this work, I propose that ACOS5 encodes an enzyme that participates in a conserved and ancient biochemical pathway required for sporopollenin monomer biosynthesis that may also include the Arabidopsis CYP703A2 and MS2 enzymes.  20  2.2 Introduction  2.2.1 4-coumarate:CoA ligase-like (4CL-like) and acyl-CoA synthetase (ACOS) genes  The enzyme 4-coumarate:CoA ligase (4CL) plays important roles in phenylpropanoid metabolism by generating CoA esters of p-coumaric acid and its derivatives. These activated CoA esters are precursors utilized for the biosynthesis of various plant secondary metabolites such as lignin, flavonoids, suberin and signal molecules in plant-microbe interactions (Hahlbrock and Scheel, 1989). Many adenylate- forming enzymes related to 4CL were identified by sequence homology searches in plant and other genomes. In spite of the remarkable diversity of their substrates, adenylate- forming enzymes use the same two-step catalytic reaction to activate carboxylate substrates. In the first step, adenylation of the carbonyl group of substrates takes place by condensation with ATP to release pyrophosphate (Schneider et al., 2005). The resulting carboxylate adenylate (acyl-AMP) intermediate is very reactive. Thus, it is necessary that this intermediate react with either a thiol, amide or alcohol in the next step to generate the corresponding product by releasing AMP. Adenylate-forming enzymes contain highly conserved putative AMP-binding domains and the adenylate-forming enzyme superfamily is divided into diverse clades containing enzymes such as fatty acyl-CoA synthetases, acetyl-CoA synthetases, 4-coumarate:CoA ligases, chlorobenzoate:CoA ligase, non-ribosomal polypeptide synthetases, and firefly luciferases (Stuible et al., 2000). In Arabidopsis, 44 genes have been identified that encode proteins containing the AMP-binding domain (Shockey et al., 2002; Shockey et al., 2003). Among these proteins, several fatty acyl-CoA synthetases, four 4-coumarate:CoA ligases (4CLs), and one acetyl- CoA synthetase have been identified (Ehlting et al., 1999; Fulda et al., 2002; Schnurr et al., 2002; Hamberger and Hahlbrock, 2004). The four isoforms of 4-coumarate:CoA ligase (4CL) presumably constitute the complete enzyme family (Raes et al., 2003), but represent only a portion of the diversity of enzymes related to 4CL in plant genomes. Using an in silico similarity search based on the amino-acid sequences of known Arabidopsis genes encoding 4-coumarate:CoA ligase (4CL), the Douglas lab and other labs (Raes et al., 2003; Costa et al., 2005; Ehlting et al., 2005; Souza Cde et al., 2008) identified nine putative genes as members of an Arabidopsis 4CL-like gene family which 21  encode a plant-specific clade of enzymes closely related to true 4CLs. Previous studies have shown that some enzymes encoded by this family of 4CL-like genes activate cinnamic, benzoic, or fatty acid derivatives in vitro including precursors of jasmonic acid (JA) (Costa et al., 2005; Schneider et al., 2005). Additionally, recent data indicate that many 4CL-like proteins accept a relatively broad and overlapping range of various medium- and long-chain fatty acid as substrates, instead of the hydroxycinnamate substrates accepted by true 4CL enzymes to form the corresponding CoA esters (Kienow et al., 2008). Based on their activities towards acyl substrates, we have designated those 4CL-like genes with unknown in vivo substrates as Acyl-CoA Synthetase (ACOS; formerly referred to as the ACS genes; Souza Cde et al., 2008). Phylogenetic analysis of amino-acid sequences revealed five ACOS subclades, each containing at least one ACOS member from each species, suggesting conserved biochemical functions for ACOS enzymes (Figures 2.1). In four of five subclades, almost all proteins contain the PTS1 (peroxisomal target sequence) in their C-termini. On the other hand, subclade A, which includes the Arabidopsis gene ACOS5 (At1g62940), is most closely related to bona fide 4CLs and contains single copy genes from Arabidopsis, poplar, and rice, which all encode enzymes without predicted PTS1 (Souza Cde et al., 2008). Expression analysis revealed that ACOS5 is preferentially expressed in flowers, whereas expression of the poplar ortholog is specific to male flowers (Souza Cde et al., 2008). Thus, a function for ACOS5 in anther and/or pollen development has been proposed (Souza Cde et al., 2008). In this chapter, I further analyzed acos5-1, a loss-of-function allele of the Arabidopsis ACOS5 gene, which was first characterized by a previous student, Dr. Clarice de Azevedo Souza, using light and transmission electron microscopy. In addition, the ability of ACOS5 to complement the male sterile phenotype in the acos5-1 background was tested. 22    Figure 2.1 Phylogenetic relationships of plant-specific acyl-CoA synthetases (ACSs, ACOSs) from three fully sequenced angiosperm genomes.  Translated nucleotide sequences corresponding to ACS (ACOS5) genes from Arabidopsis, poplar and rice were aligned and an unrooted phylogenetic tree generated. Nodes with bootstrap values above 70% are shown by stars. The 4-coumarate:CoA ligase (4CL) and ACS (ACOS) clades A–E discussed in the text are circled and contain at least one representative of each plant species. Protein names in shaded boxes contain the PTS1 peroxisomal target signal. Bar represents 0.1 amino acid changes (Souza Cde et al., 2008). Image was reprinted with permission of New Phytologist (Copyright ©  New Phytologist (2008)).   23  2.3 Materials and methods  2.3.1 Plant material and growth conditions  Arabidopsis thaliana wild-type (Col-0) and mutant plants were grown in soil (Sunshine mix 5; Sungrow Horticulture) in controlled environment chambers at 20°C under long-day conditions (18 h light).  2.3.2 Complementation of acos5 mutants  A 4368-bp ACOS5 genomic fragment was amplified using the Plantinum Taq DNA polymerase High Fidelity (Invitrogen) with gene-specific primers (Table 2.1) and cloned into pCR8/GW/TOPO (Invitrogen). After verification by sequencing, the fragment was subcloned into the pGWB1 Gateway binary vector (Nakagawa et al., 2007) and introduced into Agrobacterium tumefaciens. Then, acos5-1 heterozygous plants were transformed using the floral dip method (Clough and Bent, 1998). T1 seeds were sown in half-strength Murashige and Skoog salts (Sigma-Aldrich), supplemented with 1% sucrose and 0.6% agar medium containing 25 mg/L hygromycin. Individual T1 lines were allowed to self pollinate and progeny genotypes were tested with respect to the ACOS5 locus. The presence of respective transgenes was tested using PCR with the primers given in Table 2-1.  2.3.3 Nucleic acid methods  Genomic DNA extraction was performed using young leaf tissue ground in a bead beater at 4℃, with the use of the Nucleon PhytoPure Kit (Amersham-Pharmacia), according to the manufacturer’s instructions. Arabidopsis RNA was isolated from tissues frozen in liquid nitrogen and ground to a fine powder by using RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.  2.3.4 Phenotypic analyses  To obtain cross sections of developing anthers, wild-type and homozygous 24  double mutant inflorescences were fixed in 20ml fixative mixture (4% paraformaldehyde, 2.5% glutaraldehyde and 0.05M sodium phosphate) overnight and directly dehydrated through an aqueous alcohol series (30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% and 100% three times) for 30 min each, without postfixation. Samples were first transferred to a propylene oxide solution in 50% (v/v) ethanol and then two-time washed in only propylene oxide for 30 min. For infiltration of Spurr's epoxy resin (Canemco), propylene oxide solution was replaced with following resin series for 4 hr each: 10%, 25%, 50%, 75%, and 100% twice. For  bright-field microscopy, 1 µm sections were cut with  glass knives (Leica) on a microtome, mounted on  glass slides, heat fixed to the slides and stained with toluidine blue. Sections were photographed using  a light microscope. For TEM, Arabidopsis wild-type and acos5 mutant inflorescences were postfixed in 1% osmium tetraoxide 0.05M sodium cacodylate (pH 6.9) for 30 min and rinsed twice in distilled water. Thin sections (70 nm) were taken using a Leica Ultracut T and Druuker diamond Histoknife. Sections were placed on 100-mesh copper grids and stained for 15 min with 2% uranyl acetate in 70% (v/v) methanol, rinsed thoroughly with water, and stained for 10 min with lead citrate (Sato’s Lead). Sections were visualized using a Hitachi H7600 transmission electron microscope.  2.3.5 Accession number  Sequence data from this chapter can be found in the Arabidopsis Genome Initiative or GenBank/EMBL databases under the following accession numbers: Arabidopsis ACOS5, At1g62940.  2.3.6 Sequences of primers  Table 2.1 Primers used in this study.   Genotyping Gene Primer name Sequence (5' → 3') At1g62940 CLL4F TTTGGTACCGTTTAAAAATGGAGTCAAAAG  EcoR1 reverse  AAAGAATTCCATTGCGGTATCTCCGCA  dspn1  CTTATTTCAGTAAGAGTGTGGGGTTTTG  25  Table 2.1 Primers used in this study. (cont.)   Complementation construct Gene Primer name Sequence (5' → 3') At1g62940 ACLL5F GATTGGTTAAGTTCATACGTTC  ACLL5R GCATGAGAAAGCAGCGTG   Checking complementation Gene Primer name Sequence (5' → 3') At1g62940 F CompACLL5 GAG CAA CCA TCT TCC CTT GTG ATT GC  R CompACLL5 AGA AGC AGG AGA CAA ATG CGG AGA  2.4 Results  2.4.1 The ability of the ACOS5 gene to complement the male sterile phenotype  To test the ability of the ACOS5 gene to complement the male sterile phenotype in the acos5-1 background, I introduced an about 4.4-kb DNA region from an Arabidopsis wild-type (Columbia-0 [Col-0]) plant, containing 1.9 kb of the promoter sequence and the complete transcribed region of ACOS5 (Figure 2.2), into ACOS5 acos5- 1 heterozygote plants by Agrobacterium tumefaciens–mediated transformation. Four T1 lines harbouring the ACOS5 transgene were subjected to PCR-aided genotyping, and one was established as being ACOS5/ACOS5, one as being ACOS5/acos5-1, and two as being acos5-1 acos5-1. All plants were fully fertile, suggesting that the introduced ACOS5 transgene had complemented the acos5-1 mutation in the two homozygous lines. We further determined the genotypes and phenotypes of 18 T2 progeny from each T1 line that had inherited the ACOS5 transgene (i.e., that was either homozygous or hemizygous for the ACOS5 transgene, based on hygromycin resistance specified by the T-DNA insertion). For each T1 line, including the two that were homozygous for the acos5-1 allele and gave rise only to acos5-1/acos5-1 T2 progeny, all 18 T2 plants were fully fertile, confirming the ability of ACOS5 to complement the male sterile mutant phenotype.  26    Figure 2.2 The construct used for acos5 complementation.  Schematic representation of the construct used for the acos5 complementation test. Shaded boxes show the ACOS5 transgene, containing 1.9 kb of the promoter sequence, the 3’ untranslated region/terminator regions (light gray), and the transcribed region between the start and stop codons (thick black arrow). Primers used to amplify genomic DNA are indicated with arrows above and below the diagram and are shown in Table 2.1 (de Azevedo Souza et al., 2009). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   2.4.2 Anther and microspore development in the acos5-1 mutant  To further pinpoint the stage of anther development defective in the acos5 mutant, I used transmission electron microscopy to gain higher-resolution images of developing anthers in the acos5 mutant and compared these to the corresponding images from wild- type plants. Figures 2.3A to 2.3D show that, at stage 7, characterized by the presence of tetrads that form after meiosis, wild-type and acos5 mutant microspores were similar in morphology, with characteristic callose walls. At this stage, tapetal cells in the mutant appeared normal. At stage 8, when free microspores had been released from tetrads following callose wall hydrolysis, massive deposition of a thick sporopollenin-containing exine on the nexine layer was evident in the wild-type anthers (Figures 2.3E and 2.3F). The exine had started to develop into a thick, reticulated wall characteristic of pollen grains, residual primexine was visible in spaces of exine baculae, which are characteristic of this stage (Goldberg et al., 1993; Sanders et al., 1999; Scott et al., 2004; Ma, 2005), and microspores were nonvacuolated. In comparison with the wild type, free acos5 mutant microspores at stage 8 had a similar nonvacuolated morphology but contained thinner walls that were devoid of the pronounced reticulate exine wall seen in the wild 27  type (Figures 2.3G and 2.3H). In place of a well-defined exine, these microspores contained an amorphous substance adhering to the nexine that could be residual primexine or unpolymerized sporopollenin precursors. Again, tapetal cells at this stage appeared normal. At stage 9, wild-type pollen grains contained thick, reticulated exine walls and an intine layer. In stage 9 of the acos5 mutant, many pollen grains were in various stages of lysis and degradation (Figure 2.3K) and had thin cell walls that were devoid of a characteristic exine layer (Figure 2.3L) but often retained amorphous wall material outside the intine and apparent nexine. In other cases, relatively intact pollen grains were observed in acos5 anthers at stage 9 (Figure 2.3M), but in many cases, pollen walls were completely devoid of wall material outside the intine (Figure2.3N). Again, tapetal cells in the acos5 mutant anthers appeared normal at this stage (Figures 2.3K and 2.3M), suggesting that the defect in acos5 pollen development is primarily due to the lack of sporopollenin deposition and exine formation, rather than a general defect in tapetal cell development. This analysis pinpoints the defect in microspore development in the acos5 mutant to the deposition of the sporopollenin-rich exine wall at stages 8 and 9 of anther development, while other aspects of anther development, including tapetal cell development, appear normal. 28    Figure 2.3 Transmission electron micrographs of wild-type (Col-0) and acos5 mutant anthers, pollen grains, and pollen walls.  (A), (B), (E), (F), (I) and (J) Microspore and pollen wall development in Col-0 wild-type 29  plants. (C), (D), (G), (H) and (K) to (N) Microspore and pollen wall development in acos5 mutant anthers. (A) to (D) Stage 7 anthers; (E) to (H) Stage 8 anthers; (I) to (N) Stage 9 anthers White arrows in (F) indicate residual primexine in developing baculae of the exine. CW, callose wall; Ex, exine; In, intine; Lo, locule; Msp, microspore; Ne, nexine; Nu, nucleus; PM. Plasma membrane; T, tapetum cell; Td, tetrad. Bars = 2 µm in (A), (C), (E), (G), (I), (K), and (M) and 500 nm in (B), (D), (F), (H), (J), (L), and (N) (de Azevedo Souza et al., 2009). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   2.5 Discussion  In this chapter, I showed that pollen development in the acos5 loss-of-function mutant is arrested after release from tetrads and free microspores are devoid of exine (Figure 2.3). Since only one acos5 allele was available, I used a complementation approach to show that the male sterile and pollen development phenotypes observed are indeed due to loss of function of the ACOS5 gene. A unique feature of the mutant is the complete absence of pollen grains at anther maturity and consequent complete male sterility. While a number of other Arabidopsis male sterile or partial sterile mutants with impaired exine and pollen wall development have been described (Aarts et al., 1997; Morant et al., 2007; Persson et al., 2007), such mutants typically retain variable amounts of abnormal pollen grains at anther maturity and corresponding low levels of fertility and seed development. By contrast, the acos5 homozygote line never produced even partially fertile siliques, necessitating maintenance of the mutant lines as heterozygote. The exceptionally strong male sterile phenotype and lack of exine formation (Figure 2.3) suggests that ACOS5 plays a crucial role in exine formation and sporopollenin biosynthesis. Previous analysis of the recombinant ACOS5 protein suggested a lack of activity against hydroxycinnamic acids, substrates typically used by 4CLs (Costa et al., 2005; Kienow et al., 2008). In addition, biochemical assay results from the group of Dr. Kombrink demonstrated ACOS5 in vitro activity against oleic acid (C18:1) with kinetic constants comparable to those of other fatty acyl-CoA synthetases (de Azevedo Souza et al., 2009). Hydroxycinnamic acids failed to compete with oleic acid as ACOS5 substrates, 30  verifying that ACOS5 is not a 4CL. Thus, these data suggest that the in vivo substrate of ACOS5 is a fatty acid, consistent with a role for ACOS5 in the biosynthesis of an aliphatic sporopollenin monomeric constituent (de Azevedo Souza et al., 2009). Moreover, competition assay data from Dr. Kombrink showed an in vitro preference of ACOS5 for medium-chain fatty acids, including hydroxy fatty acids (de Azevedo Souza et al., 2009). Such hydroxy fatty acids appear to be important sporopollenin constituents, since they provide the second functional group required for the formation of the extensive ether crosslinks in the sporopollenin polymer (Ahlers et al., 2003; Morant et al., 2007). Based on competition assays, the best ACOS5 substrates among those tested were 16- hydroxy hexadecanoic acid (16OH-C16), 8-hydroxy octanoic acid (8OH-C8), and 12- hydroxy octadecanoic acid (12OH-C18) (de Azevedo Souza et al., 2009). The tapetum contribution to exine synthesis and sporopollenin deposition starts while the microspores are still attached in tetrads and continues through the vacuolated stages until the first pollen mitosis is almost completed (Blackmore et al., 2007). My collaborators showed that the spatio-temporal patterns of ACOS5 gene expression, revealed by in situ hybridization and promoter-reporter fusion expression (de Azevedo Souza et al., 2009), are consistent with transient, tapetum-localized functions (occurring maximally at around stage 7 of anther development) at the time of tetrad formation and microspore release, when biosynthesis and secretion of sporopollenin precursors is required. Furthermore, the phenotype associated with loss of ACOS5 function in the acos5 mutant first appears at stage 8 (Figure 2.3), consistent with defects in deposition of a critical secreted sporopollenin component(s), leading to defective microspores. These microspores, when released from tetrads in stage 8 anthers, fail to develop normal exine and are aborted in development by stage 9 (Figure 2.3). Taken together, these data support the hypothesis that the enzyme encoded by ACOS5 is required for production of sporopollenin constituents in the early steps of exine formation. The combination of our functional data for ACOS5 (de Azevedo Souza et al., 2009) and similar data for CYP703A2 and MS2 (Aarts et al., 1997; Morant et al., 2007) provides further insight into potential pathway(s) for generation of sporopollenin monomeric units. Based on these data, I propose a working model for the biosynthesis of sporopollenin monomers (Figure 2.4). According to this model, the fatty acyl-CoA ester 31  product of the ACOS5-catalyzed reaction is a central intermediate used to generate sporopollenin monomers in tapetal cells for export to the locule. Consistent with a central role for ACOS5 in one or more biochemical pathways leading to sporopollenin monomer biosynthesis is the strong sterility phenotype of the acos5 mutant, and the highly correlated coexpression of ACOS5 with Arabidopsis genes encoding enzymes that could act in the same pathway(s), including CYP703A2 and MS2. As shown in Figure 2.4, one function of ACOS5 could be to regenerate the CoA ester of the proposed hydroxylated fatty acid generated by CYP703A2 (7-hydroxylauryl-CoA). Another possibility is that ACOS5 could function as a plastid-localized acyl-CoA synthetase required to generate a fatty acyl-CoA ester for export into the cytoplasm. However, there is no in silico evidence for such localization and also transient ACOS5:YFP fusion protein expression data from collaborator suggest that  ACOS5 is localized to cytoplasm rather than  plastid (de Azevedo Souza et al., 2009). In biochemical pathways downstream of ACOS5, reduction and/or modification of the ACOS5-generated fatty acyl-CoA could be required to generate sporopollenin monomers (Figure 2.4). For example, MS2 or other tapetum-expressed reductases could generate fatty aldehyde or alcohol monomeric constituents of sporopollenin from the ACOS5-derived CoA ester, which could then be exported into the locule for incorporation into the sporopollenin polymer. Alternatively, the ACOS5-derived fatty acyl CoA ester could also be used as a starter molecule for incorporation into potentially more complex sporopollenin monomeric constituents, analogous to the incorporation of 4CL- derived p-coumaryl-CoA into flavonoids. In this way, the function of ACOS5 in tapetal cells could be analogous to that of 4CL, which generates hydroxycinnamyl-CoA esters used in distinct branch pathways.  32   Figure 2.4 Model for the role of ACOS5 in sporopollenin monomer biosynthesis in developing anthers (de Azevedo Souza et al., 2009).  Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   Both CYP703A2 and ACOS5 are conserved in land plant lineages, including Physcomitrella, but are absent in Chlamydomonas (Morant et al., 2007; Souza Cde et al., 2008). Thus, acquisition of an ACOS5- and CYP703A2-dependent sporopollenin biosynthetic pathway appears to be an adaptation that was shared by the common terrestrial ancestor of bryophytes and vascular plants. The ability to generate sporopollenin was likely a key land plant innovation essential for protection of haploid spores from desiccation, UV irradiation, and other stresses of the terrestrial environment, and its evolution likely predated vascular system development and the ability to produce lignin (Bowman et al., 2007). Thus, it is conceivable that the repertoire of 4CL and 4CL- related enzymes now found in land plants (Souza Cde et al., 2008) arose from an ACOS5- 33  like ancestral enzyme. Further definition of the biochemical pathway involving ACOS5 should not only reveal the nature of sporopollenin monomeric constituents and the sporopollenin polymer but also shed light on the evolution of the diverse polyether and polyester polymers now found in plants.   34  Chapter 3. LAP6/POLYKETIDE SYNTHASE A and LAP5/POLYKETIDE SYNTHASE B encode hydroxyalkyl α-pyrone synthases required for pollen development and sporopollenin biosynthesis in Arabidopsis thaliana  3.1 Summary  Plant type III polyketide synthases (PKSs) catalyze the condensation of malonyl- CoA units with various CoA ester starter molecules to generate a diverse array of natural products. The fatty acyl-CoA esters synthesized by Arabidopsis thaliana ACYL-COA SYNTHETASE5 (ACOS5) are key intermediates in the biosynthesis of sporopollenin, the major constituent of exine in the outer pollen wall. By coexpression analysis, I identified two Arabidopsis PKS genes, POLYKETIDE SYNTHASEA (PKSA) and PKSB (also known as LAP6 and LAP5, respectively) that are tightly coexpressed with ACOS5. PKSA and PKSB are specifically and transiently expressed in tapetal cells during microspore development in Arabidopsis anthers. Mutants compromised in expression of the PKS genes displayed pollen exine layer defects, and a double pksa pksb mutant was completely male sterile, with no apparent exine. The biochemical results provided by collaborators indicate that hydroxylated α-pyrone polyketide compounds are the products of sequential action of anther-specific fatty acid hydroxylases, an acyl-CoA synthetase (ACOS5) and two polyketide synthases (PKSA/B).   35  3.2 Introduction 3.2.1 Polyketides and type III polyketide synthases (PKS)  Polyketide synthases (PKSs) generate a vast array of natural products and are classified as type I, II and III enzymes based on their architectures (Austin and Noel, 2003). Type I PKSs are large multi-domain enzymes consisting of several modules that are comprised of catalytic domains with diverse functions in bacteria and fungi (Austin and Noel, 2003; Watanabe et al., 2007). Type II PKSs, primarily found in bacteria, are separable multi-enzyme complexes that carry out a single set of repeating activities. Each type II PKS contains a minimal set of three subunits containing two β-ketoacyl synthase subunits and an acyl carrier protein subunit to which the growing chain is attached (Austin and Noel, 2003; Watanabe et al., 2007). In addition to being found in bacteria and fungi, type III PKSs are also very common in plants. As homodimers, each subunit of a type III PKS iteratively carries out polyketide synthesis at a single active site (Watanabe et al., 2007). Regardless of their structural differences, all PKSs use a common chemical strategy; they catalyze chain elongation by a decarboxylative condensation reaction, followed by cyclization to generate the final polyketide products (Austin and Noel, 2003). The type III PKS enzyme superfamily generates a remarkable diversity of polyketide products, due to their ability to accept a broad range of starter-CoA units (Figure 3.1). The best-studied plant type III PKS, chalcone synthase (CHS), as well as CHS-related enzymes such as stilbene synthases, can utilize a wide range of phenylpropanoid-CoAs that are condensed with malonyl-CoAs to generate phloroglucinol-type products with variable functional groups (Austin and Noel, 2003). Moreover a fungal type III polyketide synthase, 2’-oxoalkylresorcylic acid synthase (ORAS) in Neurospora crassa as well as a bacterial type III polyketide synthase, alkylresorcinol synthases (ARS) in Azotobacter vinelandii are able to generate alkylresorcinols, alkylresorcylic acids and alkylpyrones using a broad range of medium- and long-chain fatty acyl-CoAs as starter units (Funa et al., 2006; Funa et al., 2007). These long-chain alkylresorcinols have been found to be essential for mature cyst formation in A. vinelandii by generating an exine structure (Funa et al., 2006).  36   Figure 3.1 Diverse cyclization strategies employed by type III PKSs. Image was reprinted with permission of Che Caswell Colpitts (Copyright ©  2009 C.C. Colpitts).  Type III PKSs are ubiquitous in vascular plants as well as non-vascular plants such as Physcomitrella patens (Austin and Noel, 2003; Koduri et al., 2010), and plant- specific type III PKSs synthesize diverse natural products that play import roles in UV photoprotection, anthocyanin flower pigmentation, antimicrobial defense, and pollen fertility. The completed Arabidopsis thaliana genome project identified three type III CHS gene homologs, At1g02050, At4g34850 and At4g00040 as well as the originally described bona fide CHS gene, At5g13930 (Tsai et al., 2006; Wang et al., 2007). Phylogenetic analysis suggested that the two CHS homologs At1g02050 and At4g34850 could have undergone functional divergence (Wang et al., 2007), however, until recently little was known about the functions of these CHS-like genes. The first biochemical study of the proteins encoded by At1g02050 (POLYKETIDE SYNTHASE A, PKSA) and At4g34850 (POLYKETIDE SYNTHASE B, PKSB) was performed by Mizuuchi et al., 37  (2008) and revealed they can catalyze the unusual formation of alkyl α-pyrones by utliziting fatty acyl-CoAs of up to C20 chain lengths as substrates in vitro. Also, a recent genetic study demonstrated mutations in At1g02050 (LAP6) and At4g34850 (LAP5) led to defective exine formation and they are specifically expressed in anthers of stage 9 and 10 buds (Dobritsa et al., 2010). In this study, I now significantly extend a previous study (Dobritsa et al., 2010) to show that the plant-specific CHS-like type III PKSs LAP6/PKSA and LAP5/PKSB are coexpressed with ACOS5, are specifically and transiently expressed in tapetum cells, are required for exine formation and development, and function at specific stages of microspore development. Genetic analyses also showed that LAP6/PKSA and LAP5/PKSB have overlapping but partially distinct functions in exine development. Furthermore, my collaborators show that LAP6/PKSA and LAP5/PKSB encode enzymes that catalyze the condensation of hydroxy fatty acyl-CoA esters synthesized by ACOS5 with malonyl-CoAs to yield triketide and tetraketide α-pyrones and that PKSA has a strong in vitro preference for medium-chain hydroxy fatty acyl-CoAs that, based on in vitro data, may be preferentially synthesized by ACOS5. Combined with the finding that PKSA and PKSB preferentially localize to the endoplasmic reticulum (ER), where they may form part of a metabolon with upstream and downstream enzymes, these data illuminate the important role played by these enzymes in an ancient and evolutionarily conserved biochemical pathway or pathways required for the biosynthesis of polyketide sporopollenin precursors.  3.3 Materials and methods  3.3.1 Plant material and growth conditions  Arabidopsis thaliana Columbia (Col-0) seeds were sterilized and after a cold treatment (2 days at 4°C in the dark) and germinated at 20°C under 70 µmol m -2  s -1  fluorescent lighting. Twelve days later, the plants were transferred to a growth chamber with a light/dark cycle of 16 hr/8 hr. T-DNA insertion mutants were obtained from SALK (Alonso et al., 2003), and Gabi-Kat (Rosso et al., 2003) collections via The Arabidopsis Information Resource and the Nottingham Arabidopsis Stock Centre. In progeny, 38  homozygous insertion lines SALK_134643 for pksa-1and GK_089C04 for pksb-3 were identified by PCR using gene-specific and T-DNA specific primers (Table 3.1).  3.3.2 Phylogenetic and bioinformatic analyses  All aligned sequences obtained are given in Appendix A. Protein sequences were aligned using MUSCLE 3.6 using the default parameters (sequencing clustering; UPGMA, objective score; classic sum-of-pairs score) (Edgar, 2004), and the multiple protein sequence alignments were manually optimized. Aligned sequences are available in Appendix B. To reconstruct phylogenetic trees, maximum likelihood analyses with 1000 bootstrap replicates were performed using PhyML v2.4.4 and default settings (Guindon and Gascuel, 2003) with the JTTmodel of amino acid substitution.  3.3.3 RT-PCR  RNA quality was assessed by visual inspection of rRNA on a 1.2% formaldehyde-agarose (FA) gel and quantified spectrophotometrically, and 2.5 μg RNA/ 20 µL reaction was used to generate first strand cDNA using Superscript II Reverse Transcriptase (Invitrogen) following the manufacturer’s protocol. For RT-PCR, gene- specific and intron-spanning primers (Table 3.1) were used in PCR reactions to amplify corresponding cDNA sequences under the following PCR conditions: 95°C for 3 min, followed by 35 cycles of (94°C for 30 s, 56°C for 30 s, 72°C 1 min) followed by 72°C for 10 min, using Taq polymerase in a 50 µL total reaction. Actin2 was used as control. For quantitative RT-PCR analysis of PKSA and PKSB expression, 10 ng of cDNA was incubated with 10 µL iQ SYBR Green Supermix (Bio-Rad) and 5 pmol of each forward and reverse primer (Table 3.1) in a total volume of 20 µL. After an initial denaturation step at 95°C for 3 min, 40 cycles at 95°C for 15 s, 60°C for 15 s, and 72°C for 30 s were followed by a fluorescence reading. A melting curve was generated ranging from 95°C to 60°C. Threshold cycles (CT) were adjusted manually, and the CT values for a housekeeping control Actin2 amplified in parallel on each plate were subtracted from CT values obtained for each gene of interest, thus generating normalized CT values (∆CT). The relative starting quantities of each gene were determined by setting as a base 39  value the gene with the highest CT value within a tissue panel or treatment series, and relative quantities were calculated using the ∆∆CT method as described in (Hietala et al., 2003). ∆∆CT was calculated using immature flower buds as the highest expressing tissue.  3.3.4 Phenotypic analyses  Tissue fixation, embedding, and sectioning of Arabidopsis wild type (Col-0) and pksa-1 pksb-3 double mutant inflorescences were performed as described in section 2.3.4.  3.3.5 In situ hybridization and validation of RNA probes  Arabidopsis Col-0 inflorescences of different developmental stages were fixed in 20 mL scintillation vials in FAA (3.7% formaldehyde, 5% acetic acid, 50% ethanol and 41.3% distilled water) for 3 hr to 4.5 hr. The samples were then dehydrated by immersion in the following ethanol series for 30 min each: 50% twice, 60%, 70%, 85%, 95%, and 100% twice. After ethanol dehydration, 75:25, 50:50, 25:75 ethanol/xylene, and two times of 100% xylene were applied to the samples. The vials containing samples were filled half way with xylene and topped up with paraffin (Paraplast Plus, Sigma) for incubation at 55°C overnight. Molten paraffin was used to replace the xylene/paraffin solution, and after that, paraffin was replaced at least six times at least 6 hr intervals. Embedded samples were sectioned with a microtome to 8 μm. Sections were floated onto precharged slides using distilled water, dried at 42°C overnight, and affixed to the slides by raising the temperature of the hot plate to 56 °C for 4 hr. For sense and antisense PKSA and PKSB probe synthesis, 1209 bp and 1200 bp DNA template corresponding to the PKSA and PKSB coding region, respectively, were PCR amplified from flower cDNA using gene-specific forward and reverse primers (Table 3.1). A T7 polymerase binding site was incorporated into the forward primer for sense probe amplification and in the reverse primer for antisense probe amplification. In vitro transcription was carried out at 37°C for 2 hr, and then the RNA was precipitated by adding 2.5 μL of 4 M LiCl and 75 μL of 100% ethanol, and kept at -80°C for 2 hr. RNA was spun down at 4°C at maximum speed of microcentrifuge and resuspended in 100 μL 40  of DEPC-treated water. The RNA probe was then hydrolyzed into fragments between 100 and 150 base pairs long by adding 60 μL 200 mM Na2CO3 and 40 μL 200 mM NaHCO3 followed by incubation at 60°C for 30 min. The mixture was neutralized by the addition of 10 μL of 20% acetic acid. The probe was precipitated using 21 μL of 3 M NaOAC, 2 volumes of 100% ethanol and 1 μL of 20 mg/ml oyster glycogen as carrier at -20°C for 2- 3 hr. 100 μL of 50% deionized formamide was used to dissolve the pelleted probe and then the probe was quantified against digoxygenin (DIG) standard according to manufacturer’s instructions. For hybridization of probes into sections on slides, first paraffin was removed by immersing slides in xylene twice for 10 min, and 100% ethanol twice for 2 min each. Sections were hydrated by immersion in 95%, 90%, 80%, 60%, and 30% ethanol, 0.85% NaCl, and then 1X PBS (0.13 M NaCl, 3 mM NaH2PO4, 7 mM Na2HPO4) for 2 min each. Slides were incubated for exactly 30 min at 37°C with 1 μg/mL proteinase K in 100 mM Tris-HCl, pH 7.5, and 50 mM EDTA, and washed with 1x PBS again at the end. Slides were then dehydrated in 0.85% NaCl, 30%, 60%, 80%, 90%, 95%, and 100% ethanol for 1 min each and stored at 4°C in a closed box with a few drops of ethanol soaking the paper until further processing. Hybridization was done overnight at 55°C with a DIG- labeled RNA probe (10-50 ng) in 200 μL of hybridization buffer (10 mM Tris-HCl, pH7.5, 1 mM NaCl, 50% deionized formamide, 7% dextransulfate, 1x Denhardt’s solution (Sigma), 50 mg/mL yeast tRNA (Roche)). Slides were washed in 2x SSC (1x SSC is 0.15 M NaCl, 0.015 M sodium citrate) for 5 min, four times in 0.2X SSC at 55°C for 30 min each, once at 37°C and then in 1x PBS for 5 min at RT. Immunological detection of the hybridization probe was performed as follows: slides were covered for 45 min with 1 mL of 1% blocking reagent (Boehringer Mannheim) in 100 mM maleic acid, pH 7.5, and 150 mM NaCl, then incubated for 45 min in 1 mL of BSA solution (1% BSA, 0.3% Triton X-100, 100 mM Tris-HCl, pH 7.5, and 150 mM NaCl) after washing with 2 mL of fresh BSA solution. The slides were then incubated for 1.5 hr with 1 mL of diluted (1:1250) antibody conjugated in BSA solution, followed by three washes in BSA solution for 20 min each. For color reaction, the slides were washed in TNM-50 (100 mM Tris-HCl pH 9.5, 100 mM NaCl, 50 mM MgCl2) twice for 15 min each. To activate the color reaction, slides were incubated overnight with 20 uL of the 41  BCIP/NBT (Roche) per 1ml of TMN-50 in substrate buffer in the dark. 10 mM Tris-HCl, pH 8.0, and 5mM EDTA were added to stop the color reaction. To validate specificity of RNA antisense probes, I performed DNA gel blotting. PCR-amplified cDNA clones of PKSA and PKSB (Table 3.1) were blotted to positively charged nylon membranes, Hybond-XL (GE Healthcare Life Sciences), using 10x SSC as the transfer buffer. Transfer of cDNA to the nylon membrane was  monitored via ethidium bromide. The digoxigenin-labeled probes were prehybridized and hybridized using 1x Denhardt's solution, 50% deionized formamide, 10% dextran sulfate, 0.2 mg/mL of salmon sperm DNA. The blots were washed twice using 2x SSC and 0.1% SDS at 55°C for 10 min each, three times using 2x SSC at 55°C for 30 min each, and twice using 0.2x SSC at 55°C for 10 min each. The hybridized probes were detected by the addition of BCIP/NBT color reagent (Roche).  3.3.6 Cloning for PKSA and PKSB protein expression  Arabidopsis total RNA was extracted from flower buds with the RNeasy Plant Mini kit (Qiagen) following the manufacturer’s protocol. First strand cDNA was generated from RNA (2.5 μg) using SuperScript II reverse transcriptase (Invitrogen), and PCR-amplification of PKSA and PKSB was carried out with the primers containing NcoI and EcoRI sites (Table 3.1). Because PKSA coding sequence contains EcoRI restriction enzyme site, both the 3 rd  (AAT) and 4 th (TCT) codon sequences from start codon (ATG) were replaced with AAC encoding Asn and TCG encoding Ser in PKSA forward primer, FCHSL1NcoI (Table 3.1), respectively, based on codon usage table for E. coli W3110 (http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=316407). The PCR products were digested with restriction enzymes and subcloned into pET-32a(+) or pET- 28a(+) expression vector (Novagen) for further heterologous expression in E. coli.  3.3.7 Accession number  Sequence data from this article can be found in the Arabidopsis Genome Initiative, GenBank/EMBL, or other databases under the following accession numbers: Arabidopsis PKSA, At1g02050; Arabidopsis PKSB, At4g34850; Arabidopsis Actin2, 42  At3g18780; Arabidopsis CHSL2, At4g00040; Oryza sativa CHSL1,LOC_Os10g34360 (http://rice.plantbiology.msu.edu/index.shtml);  O. sativa CHSL2, LOC_Os07g22850 (http://rice.plantbiology.msu.edu/index.shtml);  Physcomitrella patens CHS10, protein ID 149790 (http://genome.jgi-psf.org/Phypa1_1/Phypa1_1.home.html); Pinus radiata CHS1, AAB80804; Nicotiana sylvestris CHSLK, CAA74847; Silene latifolia Chs, AB182106; Populus trichocarpa CHSL4, protein ID 551991 (http://genome.jgi- psf.org/poplar/poplar.home.html); P. trichocarpa CHSL5, protein ID 591704 (http://genome.jgi-psf.org/poplar/poplar.home.html); P. trichocarpa CHSL6, protein ID 556583 (http://genome.jgi-psf.org/poplar/poplar.home.html); and P. trichocarpa CHSL, protein ID 200918 (http://genome.jgi-psf.org/poplar/poplar.home.html).  3.3.8 Sequences of primers  Table 3.1 Primers used in this study. Genotyping Gene allele Primer Name Sequence (5' → 3') PKSA(At1g02050) pksa-1 PKSa1F GCA TCC ACC ATC TTT CTT CC   PKSa1R GGG GTT GTT CTC AGC AAT GT PKSB(At4g34850) pksb-1 PKSb1F GAG GAA TTC AAT GGG AAG CAT CGA TGC TGC   PKSb1R AAC CCG TTA TGA GAA GAT CCA A  pksb-3 CHSL3LP TGT AAC ACC AGG TCC AAA AGC   CHSL3RP TGA AGG AGG ATC CAC AGT GAC T-DNA specific  GK specific ATA TTG ACC ATC ATA CTC ATT GC   LBb1.3 ATTTTGCCGATTTCGGAAC  RT-PCR Gene allele Primer Name Sequence (5' → 3') PKSA(At1g02050) pksa-1 RCHSL1 RT TTA GGA AGA GGT GAG GCT GCG G   FCHSL1 RT ATG TCG AAT TCT AGG ATG AAT GGT GTT G PKSB(At4g34850) pksb-1 FPKSB RT GAG GAA TTC AAT GGG AAG CAT CGA TGC TGC   RPKSB RT CTC AAG CTT TCA GAC ATC AAG GTT TCG AG  pksb-3 FCHSL3 RT ACT CGT CTC TGC AAG ACA   RCHSL3 RT TGT AAC ACC AGG TCC AAA AGC Actin2  Actin2-RT-FW CCAGAAGGATGCATATGTTGGTGA   Actin2-RT-RW GAGGAGCCTCGGTAAGAAGA    43  Table 3.1 Primers used in this study. (cont.) Quantitative RT-PCR Gene  Primer name Sequence (5' → 3') PKSA(At1g02050)  FCHSL1-qRT TAA GCA GCA AAT CCA CAA GGC GTG   RCHSL1-qRT CGT TTT GCA CAA GTG TTC PKSB(At4g34850)  FCHSL3-qRT TGT TCT GGG CGG TTC AT   RCHSL3-qRT CCT CAC TTT CTT GCT CTC CT Actin2  Actin2-RT-FW CCAGAAGGATGCATATGTTGGTGA   Actin2-RT-RW GAGGAGCCTCGGTAAGAAGA -tubulin  tubulin-RT-F CGT GGA TCA CAG CAA TAC AGA GCC   tubulin-RT-R CCT CCT GCA CTT CCA CTT CGT CTT C  In situ hybridization Gene  Primer name Sequence (5' → 3') PKSA(At1g02050)  CHSL1F-Sense CAT AAT ACG ACT CAC TAT AGG ATG TCG AAT TCT AGG ATG AAT G   CHSL1R-Sense GGA AGA GGT GAG GCT GCG   CHSL1R-Anti CAT AAT ACG ACT CAC TAT AGG TTA GGA AGA GGT GAG GCT GCG   CHSL1F-Anti A TGT CGA ACT CGA GGA TGA ATG PKSB(At4g34850)  CHSL3F-Sense CAT AAT ACG ACT CAC TAT AGG ATG GGA AGC ATC GAT GCT G   CHSL3R-Sense GAC ATC AAG GTT TCG AGC GAT   CHSL3R-Anti CAT AAT ACG ACT CAC TAT AGG TCA GAC ATC AAG GTT TCG AGC GAT   CHSL3F-Anti A TGG GAA GCA TCG ATG CTG  Cloning Gene  Primer name Sequence (5' → 3') PKSA(At1g02050)  F CHSL1 NcoI CCA TGG CTA TGT CGA ACT CGA GGA TGA ATG   R CHSL1 EcoRI GAA TTC TTA GGA AGA GGT GAG GCT GCG PKSB(At4g34850)  F CHSL3 NcoI CCA TGG CTA TGG GAA GCA TCG ATG CTG   R CHSL3 EcoRI GAA TTC TCA GAC ATC AAG GTT TCG AGC GAT  DNA blotting Gene  Primer name Sequence (5' → 3') PKSA(At1g02050)  FPKSABlot ATGTCGAATTCTAGGATGA   RPKSABlot AGGAAGAGGTGAGGCT PKSB(At4g34850)  FPKSBBlot ATGGGAAGCATCGATGCTG   RPKSBBlot GACATCAAGGTTTCGAGCGATAA   44  3.4 Results  3.4.1 Analysis of ACOS5 co-expression genes  Previously we reported that ACOS5 encodes a fatty acyl-CoA synthetase required for sporopollenin biosynthesis in Arabidopsis (de Azevedo Souza et al., 2009). To define other potential enzymes in the sporopollenin biosynthetic pathway, I used data mining tools to identify coexpressed genes in public global gene expression data sets. Using the Correlated Gene Search tool (http://prime.psc.riken.jp), I queried 237 microarray experiments in the Tissue and Development data set, using a cutoff Pearson coexpression coefficient (r 2 ) of 0.80. This analysis identified 35 coexpressed genes, most of unknown function. Among these coexpressed genes, several have been shown to encode enzymes involved in sporopollenin biosynthesis, such as MS2 (At3g11980), CYP703A2 (At1g01280), and DRL1 (At4g35420) (Aarts et al., 1997; Morant et al., 2007; Tang et al., 2009). Among the coexpressed genes, I focused on those that encode enzymes that could utilize the potential fatty acyl-CoA product(s) generated by the ACOS5 as substrate(s), and therefore might be important in sporopollenin biosynthesis. Two of the most promising potential candidates were genes annotated as encoding plant-specific type III PKSs, LAP6/PKSA (At1g02050) and LAP5/PKSB (At4g34850), which were previously reported to generate triketide and tetraketide α-pyrone compounds using fatty acyl-CoAs (up to 20 carbon chain length) as starter substrates (Mizuuchi et al., 2008) and were strongly coexpressed with ACOS5 (r 2  for LAP6/PKSA of 0.94; r 2  for LAP5/PKSB of 0.99). To facilitate their description and represent their enzymatic function for sporopollenin biosynthesis in the following paragraphs, genes and proteins corresponding to At1g02050 and At4g34850 are referred to as PKSA and PKSB, respectively, consistent with the established nomenclature of Mizuuchi et al., (2008).  3.4.2 PKSA and PKSB-like genes are conserved in land plant lineage  To investigate a potential conserved function for PKSA and PKSB genes in pollen wall development, I performed in silico searches of the full genome sequences of Arabidopsis, poplar (Populus spp), rice (Oryza sativa) and Physcomitrella patens using 45  PKSA and PKSB as queries to retrieve potential PKSA- and PKSB-related PKS genes in these plants (Table 3.2). I also retrieved the PKS-related Nicotiana sylvestris CHSLK, Silene latifolia Chs, and Pinus radiata CHS1genes, previously shown to have high expression in male flowers or anthers (Atanassov et al., 1998; Walden et al., 1999; Ageez et al., 2005) and generated an un-rooted maximum likelihood tree of aligned CHS and PKS-related protein sequences. This analysis, shown in Figure 3-2, indicated that PKSA and PKSB are located in two distinct PKS subclades that are clearly distinct from the more distantly related clade containing the bona fide Arabidopsis and Physcomitrella CHS genes and other putative CHS genes from poplar and rice. Each subclade including either PKSA or PKSB contains homologs from the fully sequenced poplar and rice genomes, as well as the rice or Silene homologs known to be expressed in male organs. According to this analysis, the Pinus CHS1 gene is a PKSA/B homolog basal to the angiosperm PKSA and PKSB clades, and the Physcomitrella PKS (CHS10) and CHS genes are basal to the tracheophyte PKSA/B and CHS clades, respectively (Figure 3.2). These data indicate that PKSA/B clade PKS genes arose early in land plant evolution and may have common roles in male organ or spore development in land plant lineages.  Table 3.2 Putative PKSA and PKSB orthologs and expression in other species. Table was reprinted with permission of American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).  Species Gene name Accession or gene model Expression Arabidopsis thaliana PKSA At1g02050 Tapetum 1   PKSB At4g34850 Tapetum 1   CHSL2 2  At4g00040 Flower and leaf 3   Oryza sativa CHSL1 Os10g34360 Immature panicle 4   CHSL2 Os07g22850 Immature panicle 4  Physcomitrella patens CHS10 5  e_gw1.304.37.1, Protein ID149790 Sporophyte 6   46  Table 3.2 Putative PKSA and PKSB orthologs and expression in other species. (cont.) Table was reprinted with permission of American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).  Species Gene name Accession or gene model Expression Pinus radiata CHS1 AAB80804 Male cone 7  Nicotiana sylvestris NSCHSLK CAA74847 Anther 8  Silene latifolia SlChs AB182106 Male flower 9  Populus trichocarpa CHSL4 2  LG_II:10548880-10550149 N/A Populus trichocarpa CHSL5 2  scaffold_40:395399-396653 N/A Populus trichocarpa CHSL6 2  LG_IV:15418736-15420441 N/A Populus trichocarpa CHSL7 2  LG_IX:2399625-2400948 N/A 1  This study 2  Tsai et al., New Phytologist 2006 3 http://bar.utoronto.ca/ 4  http://mpss.udel.edu/rice/ 5  Jiang et al., Phytochemistry 2006 6  http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?LID=23755&PAGE=1 7  Walden AR et al., Plant physiol 1999 8  Atanassov I et al., Plant Mol Biol 1998 9  Ageez A et al., Genes Genet Syst 2005 N/A, no information available    47    Figure 3.2 Phylogenetic analysis of CHS and CHS-like (CHSL) protein sequences from land plants.  Sequences retrieved from the complete genome sequences of Arabidopsis (At), poplar (Poptr), rice (Os), and Physcomitrella (Pp), as well as selected sequences from Silene (St), pine (Pt) and Nicotiana sylvestris (Ns) were included in the maximum-likelihood (ML) tree built using 1000 bootstrap replicates in PhyML 2.4.4. Bootstrap values are indicated on branches (out of 100). The Arabidopsis PKSA and PKSB proteins are highlighted (ovals). The proteins encoded by genes known to be expressed in tapetum cells during anther development are indicated by a flash. Protein sequences used in this analysis are given in Appendix A., and the alignment is available in Appendix B. Bar = 0.1 amino acid substitutions (Kim et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).  3.4.3 Tapetum-specific expression of PKSA and PKSB proteins  To test possible functions of the Arabidopsis PKSA and PKSB proteins in male organ development, first I used quantitative reverse transcription PCR to analyze the expression of PKSA and PKSB in different Arabidopsis organs. Expression profiles are shown in Figure 3.3. Both genes were preferentially expressed in flowers, and PKSB transcripts were detected exclusively in this organ.  48   Figure 3.3 Developmental expression profiles of PKSA and PKSB.  Quantitative reverse transcription-PCR analysis of relative PKSA and PKSB expression levels in various Arabidopsis organs. Expression was calculated using the ΔΔCT method and is represented relative to the organ with the highest level of expression (flowers), set at 1.0. Actin2 was used as a reference gene. Bars represent standard deviations from the means of triplicate determinations. 7Day, 7-day old seedlings; FW, flower; ML, mature leaf; MR, mature root; MS, mature stem; YL, young leaf; YS, young stem (Kim et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   To investigate the spatio-temporal patterns of PKSA and PKSB expression in anthers, in situ hybridization experiment was performed. Because PKSA and PKSB share 62.9% nucleotide identity and could potentially cross-hybridize, the specificity of the PKSA- and PKSB-derived riboprobes used for in situ hybridization analysis was demonstrated by DNA gel blotting, showing that both probes hybridized specifically with the target templates, with no detectable cross-hybridization (Figure 3.4). To elucidate the specific expression patterns of PKSA and PKSB, these RNA probes were hybridized to sections of developing wild-type flowers (Figure 3.5) focusing on anther stages 6-11 as 49  defined by Sanders et al., (1999), during which free microspores are generated and sporopollenin-containing exine is deposited. Both PKSA and PKSB were strongly and transiently expressed in the tapetum cell layer of developing anthers. Whereas the hybridization signal was largely specific to tapetal cells, low levels of signal appeared to be present in stage 7 tetrads, so that a function in microspores cannot be excluded. Interestingly the temporal patterns of expression in the developing tapetum were slightly different. PKSA expression was first detected at stage 6, and by stage 7, strong hybridization was detected in the tapetum. By stage 8, PKSA hybridization to tapetum cells had weakened, and at stage 11 it had disappeared. By contrast, PKSB expression was initiated at stage 7 and maximal hybridization was seen in the tapetum at stage 8.       Figure 3.4 DNA gel blot showing specificity of PKSA or PKSB RNA probes used for in situ hybridization.  PKSA and PKSB digoxigenin labeled antisense probe were hybridized against a blot of PCR amplified full-length PKSA and PKSB coding sequences (above). The Gel Red stained gel showing prior to DNA gel blot transfer is shown below (Kim et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).    50    Figure 3.5 Transient tapetum-specific expression of PKSA and PKSB.  PKSA and PKSB mRNAs were localized by in situ hybridization to sections taken from developing anthers of wild-type (Col-0) flowers using gene-specific antisense probes for PKSA and PKSB and control sense probes. Stages of anther development are according to Sanders et al. (1999). Dark precipitates indicate hybridization of the probe. MC, meiotic cell; T, tapetum; Tds, tetrads; Msp, microspores; PG, pollen grain. Scale bars = 70 m (Kim et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).  3.4.4 Identification and phenotypic analysis of PKSA and PKSB loss-of-function alleles  To test the roles of PKSA and PKSB in pollen development and male fertility, both T-DNA insertion lines pksa-1 for PKSA and pksb-3 for PKSB were obtained from public collections (Alonso et al., 2003). The locations of each T-DNA insertion in the PKSA and PKSB genes were verified by sequencing analysis (Figure 3.6A). PKSA and PKSB expression in the insertion lines was assayed by RT-PCR, using template cDNAs derived from both wild type and mutant flowers (Figure 3.6B), and no PKSA or PKSB expression was detected. This analysis suggested that each of the two alleles is a loss-of- 51  function allele of PKSA or PKSB. Homozygous lines for either pksa-1 or pksb-3 are fertile and there were no obvious morphological differences between each homozygous and wild-type.     Figure 3.6 Molecular characterization of pksa, pksb and pksa pksb insertion alleles and effects on gene expression. (A) Position of T-DNA insertions in the different mutant lines is shown. The cartoons for 52  gene model were drawn base on TAIR (The Arabidopsis Information Researce) database search (http://www.arabidopsis.org). Grey boxes denote exons, with lighter gray indicating 5’ and 3’ untranslated regions. Thin horizontal lines denote introns. The location of T-DNA and absence of mRNA in pksa-1 and pksb-3 were verified by me and those in pksa-2, pksb-1 and pksb-2 were verified by our collaborator, Dr. Michel Legrand’s lab. (B) RT-PCR analysis of gene expression in flower buds of wild-type (wt, Col-0) and single and double mutants. No amplicon was detectable in mutant samples. TUBULIN and ACTIN are shown as positive controls (Kim et al., 2010). Image was adapted and reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).  3.4.5 PKSA and PKSB have partially redundant function in male fertility  Since the Arabidopsis PKSA and PKSB genes encode PKSs with similar in vitro activities (Mizuuchi et al., 2008; Dobritsa et al., 2010), biochemical redundancy between PKSA and PKSB was a strong possibility. To test this, I generated a homozygous double mutant, pksa-1 pksb-3, identified within F2 populations derived from crossing the corresponding homozygous pksa and pksb lines. Initial phenotypic examination of pksa-1 pksb-3 mutant plants (Figure 3.7) revealed anthers devoid of visible pollen, male sterility, and siliques devoid of seeds. Whereas no visible pollen was ever observed in plants homozygous for the pksa-1 pksb-3 alleles, pksa-1 pksb-3 flowers were female-fertile when pollinated with wild-type pollen. There were no other obvious morphological differences between the pksa-1 pksb-3 mutant and wild-type plants grown to maturity (Figure 3.7).  53   Figure 3.7 Phenotypic characterization of plants segregating for pksa and pksb alleles.  Plants homozygous for pksa-1 and pksb-3 alleles were crossed, and an F1 individual self- pollinated to generate a population segregating for pksa-1 and pksb-3 alleles. Plants were subjected to PCR-aided genotyping and grown to maturity. PKSA alleles are symbolized by A (WT) and a (pksa-1), and PKSB alleles are symbolized by B (WT) and b (pksb-3). Phenotypes of mature aabb, aaBb, and AABB (WT) plants are shown. Double mutant plants (aabb) had no pollen in anthers (black arrow) and undeveloped siliques (arrowheads), resulting in a complete absence of seeds, whereas Col-0 anthers had abundant pollen at this stage (white arrows). However, there are no other obvious morphological differences except that they flowered for a longer time (Kim et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).  Within the pksa-1 pksb-3 F2 population, I identified plants homozygous for pksa- 1 and heterozygous for pksb-3. Interestingly, these plants displayed a partially sterile phenotype, with smaller siliques containing fewer seeds or empty siliques. Therefore, I quantified seed set in siliques taken at random from plants with different PKSA and PKSB allelic combinations (Table 3.3; n = 15 siliques for each genotype). pksa-1 and pksb-3 single mutants and plants heterozygous for pksa-1 and homozygous for pksb-3 show slightly reduced numbers of seeds relative to wild-type control plants, whereas plants homozygous for pksa-1 and heterozygous for pksb-3 showed clear reduction in fertility, with most siliques having 10 or fewer seeds. 54   Table 3.3 Quantification of seed set in plants with different PKSA and PKSB allelic combinations.   Number of siliques containing the following numbers of seeds Genotype a  >71 b  70-61 60-51 50-41 40-31 30-21 20-11 10-1 0 AABB 6.0  9.0  0 0 0 0 0 0 0 AAbb 4.3  8.3  2.3 0 0 0 0 0 0 Aabb 3.7  10.3  1.0  0 0 0 0 0 0 AaBb 5.3  9.7  0 0 0 0 0 0 0 aaBB 1.0  10.0  4.0 0 0 0 0 0 0 aaBb  0 0 0 0 0.7  0.7  2.7  10.0  1.0 aabb  0 0 0 0 0 0 0 0 15.0 a  At1g02050 (PKSA) alleles are symbolized by A (WT) and a (pksa-1), and At4g34850 (PKSB) alleles are symbolized by B (WT) and b (pksb-3). b  Values represent the average number of siliques on one branch from the indicated genotype that contains seeds numbering within the given range. Genotype AABB (wild type) contained at least 61 seeds in each silique. On the other hand, genotype aabb (double mutant pksa-1 pksb-3) had no seeds in any siliques. Genotype aaBb showed significantly reduced fertility with most siliques having 10 or fewer seeds (Kim et al., 2010). Table was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   3.4.6 Anther and microspore development in the pksa-1 pksb-3 double mutant  To determine the point at which pollen development was impaired in the completely male sterile pksa-1 pksb-3 double mutant, I examined developing anthers in the double mutant background relative to wild-type by light microscopy (Figure 3.8), using the stages of anther development defined by Sanders et al. (1999). Microspore and anther development in pksa-1 pksb-3 plants appeared normal through stage 8, when individual microspores could be seen, indicating that the callose wall had degenerated, and releasing microspores from tetrads in a normal manner. However, by stage 9 to 11, aberrant microspore development in pksa-1 pksb-3 anthers relative to wild type was observed. Free microspores appeared to have thin walls and aberrant structures, and locules had accumulated debris of defective pollen grains (Figure 3.8). By stage 12, 55  mature pollen grains were observed in locules of wild-type plants, while most pksa-1 pksb-3 anthers were devoid of pollen. In a smaller number of pksa-1 pksb-3 mutant anthers in stages 9-12 (lower pksa-1 pksb-3 panels in Figure 3.8) some pollen grains appeared to be still in the tetrad stage or were fused with each other, and the tapetum layers were highly enlarged and vacuolated, and failed to undergo programmed cell death.     Figure 3.8 Phenotypic characterization of anther and microspore development in wild-type (Col-0) and pksa-1 pksb-3 flowers.  Anther cross sections (1 µm) were taken from developing flowers of wild type plants and pksa pksb mutant plants and stained with toluidine blue. Numbers indicate anther developmental stages according to Sanders et al. (1999). The two panels at the bottom illustrate anther phenotypes at stages 9-12 occasionally found in pksa pksb mutants.E, epidermis; En, endothecium; MC, meiotic cell; ML, middle layer; MSp, microspores; PG, pollen grains; Sm, septum; T, tapetum; Td; tetrad. Scale bars = 40 μm (Kim et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).    56  I used TEM to examine pksa-1 pksb-3 microspore development at greater resolution. In agreement with light microscopy observations, at stages 5 to 7, microspore and tapetum development were normal in the mutant, and free microspores were observed at stage 8 (Figure 3.8 and Figure 3.9). However, at stage 9 pksa-1 pksb-3 microspores had thin cell walls apparently devoid of an exine and by stage 12, locules were mostly devoid of pollen grains, although occasional defective pollen grains were observed (Figure 3.9). I next used TEM to examine pksa-1 pksb-3 mutant anthers and microspores at stages 9 and 11 at greater detail, relative to wild type. Figure 3.10 shows that at stage 9, wild-type anthers contained uninucleate microspores with a thick, reticulate exine, intact tapetum and an electron-dense cuticle on the outer anther epidermis, which exhibited hair-like protrusions (Figure 3.10A, D, G, J and M). By contrast, aberrant microspore development was observed at the same stage in pksa-1 pksb-3 anthers (Figure 3.10B, E and K). While uninucleate microspores, an intact tapetum and a normal anther epidermis with an intact cuticle were present (Figure 3.10E, H and N), microspores were devoid of a recognizable exine (Figure 3.10E). At higher magnification, a defective, thin fibrillar matrix, presumably defective exine, was apparent on mutant microspores (Figure 3.10K). At stage 11 most pksa-1 pksb-3 mutant anthers contained only a few degenerating pollen grains (Figure 3.8 and Figure 3.9). However, in a subset of pksa-1 pksb-3 mutant individuals, enlarged pollen grains were present at this stage (Figure 3.10C) that had an abnormal exine structure without a thick and reticulated wall (Figure 3.10F and 3.10L). Under higher magnification, it was also apparent that the locules of these anthers were filled with misshapen structures and an electron-dense network, possibly unpolymerized sporopollenin precursors (Figure 3.10I and 3.10L). In these individuals, the tapetum and anther outer wall epidermis and cuticle appeared to be normal (Figure 3.10I and 3.10O). 57    Figure 3.9 Anther development in the double mutant pksa-1 pksb-3.  C, callose wall; De, debris of defective pollen grains; Ed, electron-dense material; Lo, 58  locule; MMC, microspore mother cell; MSp, microspore; N, nucleus; P, plastid filled with plastoglobuli; PG, pollen grain; T, tepetal cell; Td, tetrad; V, vacuole. Scale bar = 2μm (Kim et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   59    Figure 3.10 Transmission electron micrographs of wild-type (Col-0) and pksa-1 pksb- 3 anthers and pollen.  (A), (D), (G), (J) and (M) Microspore structure, tapetum structure, exine formation, and 60  outer wall of anther epidermis at anther stage 9 in Col-0 wild-type plants. (B), (E), (H), (K) and (N) Microspore structure, tapetum structure, exine formation, and outer wall of anther epidermis at anther stage 9 in pksa-1 pksb-3 plants. (C), (F), (I), (L) and (O) Pollen grain structure, tapetum structure, exine formation, and outer wall of anther epidermis at anther stage 11 in pksa-1 pksb-3 plants.  Ba, bacula; Cu, cuticle; Cw, cell wall; Dex, defective exine structure; Ed, electron-dense material; Ex, exine; Lo, locule; MSp, microspore; Ne, nexine; P, plastid filled with plastoglobuli; PG, pollen grain; PM, plasma membrane; T, tapetal cell; Te, tectum; V, vacuole containing electron-dense material. Scale bars = 10 μm in (A) to (C), 2 μm in (D) to (F), 500 nm in (G) to (I) and (M) to (O) and 100 nm in (J) to (L) (Kim et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   3.5 Discussion  In my work, I documented defects in exine and pollen formation leading to complete loss of fertility in the pksa pksb double mutant. My detailed phenotypic analysis of the double mutant revealed new features of its loss-of-function phenotype, providing insights into functions of the wild-type enzymes. In the majority of anthers observed, defective microspore development was first observed at stage 9 (Figure 3.7), consistent with the timing of transient PKSA and PKSB expression (Figure 3.4) in the tapetum, and the timing of exine formation (Blackmore et al., 2007). High-resolution TEM images of stage 9 wild type and double mutant anthers (Figure 3.9) showed that mutant microspores completely lacked exine, which was replaced by an amorphous material similar to other mutants defective in sporopollenin biosynthesis (acos5, abcg26, drl1/tkpr1; de Azevedo Souza et al., 2009; Quilichini et al., 2010; Grienenberger et al., 2010). No abnormalities in tapetum cells were observed, and anther epidermal wall cuticle deposition was similar to that in wild type plants. Thus, the pksa pksb defect appears to be highly specific to exine formation and sporopollenin biosynthesis, consistent with PKSA and PKSB tapetum-specific expression patterns. Thus, unlike the fatty acid hydroxylase CYP704B1, which is involved in generating both sporopollenin and cutin precursors in developing rice anthers (Li et al., 2010), PKSA and PKSB appear to be specific in generating sporopollenin constituents. In some of the pksa pksb mutant anthers, additional more complex microspore 61  and locule phenotypes were observed at stage 9 and later stages. The presence of aberrant microspores showing signs of developmental arrest and cell fusion suggests that lack of PKSA/PKSB-derived sporopollenin constituents affects cell surface properties of developing microspores at the tetrad and subsequent stages. The densely staining material found in the locules of such pksa pksb mutant anthers (Figures 3.7 and 3.9) was never observed in wild-type anthers and could represent high levels of unpolymerized fatty acid derived precursors and/or material that normally co-polymerizes with such sporopollenin constituents to form the exine. Abnormal accumulation of such potentially lipophilic material could also result in the abnormal microspore cellular structure and apparent cell fusions observed in these anthers, and the complex phenotype of the double mutant could explain the extensive changes in the anther metabolome observed in lap5/pksa lap6/pksb mutants (Dobritsa et al., 2010). Taken together, my results indicate an essential function for PKSA- and PKSB-derived products in sporopollenin biosynthesis and microspore development. The phylogenetic analysis (Figure 3.2) I performed showed that the plant PKS clade containing PKSA and PKSB is clearly distinct from the clade containing the bona fide Arabidopsis and Physcomitrella CHALCONE SYNTHASE (CHS) genes and other putative CHS genes from poplar and rice. This relationship between the true CHS genes and the PKS CHS-like (CHSL) genes, also observed by others (Mizuuchi et al., 2008; Wu et al., 2008; Dobritsa et al., 2010), and is similar to the relationship between ACOS5 and true 4CL enzymes (Souza Cde et al., 2008; de Azevedo Souza et al., 2009). The CHSL clade containing PKSA and PKSB has two distinct sub-clades of angiosperm PKS genes that are related to either Arabidopsis PKSA or PKSB, with at least one PKSA and one PKSB homolog found in each of the fully sequenced poplar and rice genomes. In addition, the Nicotiana sylvestris PKSA homolog CHSlk (Atanassov et al., 1998) and Silene latifolia PKSB homolog CHSL (Ageez et al., 2005) are known to be expressed in male reproductive organs, and the wheat and triticale homologs of the Arabidopsis PKSs also have anther and tapetum-preferred expression patterns (Wu et al., 2008). The CHSL sub-clade containing Arabidopsis PKSA and PKSB contains both pine and Physcomitrella members, both of which occupy positions at or near the base of the clade (Figure 3.2). The Pinus radiata ChS1 gene is specifically expressed in male cones 62  and is likely tapetum-expressed (Walden et al., 1999). I surveyed the expression pattern of the Physcomitrella PKS (CHS10) gene (Jiang et al., 2006; Koduri et al., 2010), an apparent PKSA and PKSB homolog (Figure 3.2), by assessing transcript abundance in a Physcomitrella patens cDNA database (http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?LID=23755&PAGE=1). This analysis showed that PpCHS10 cDNAs are found exclusively in a library derived from RNA extracted from the sporophyte. Together, these data suggest a conserved function in sporopollenin monomer biosynthesis for PKSA and PKSB and their apparent orthologs in land plants, and indicate that this function arose early in land plant evolution prior to the divergence of bryophytes and tracheophytes. The exine in pollen walls may have evolved a more elaborate structure in seed plants, based on specialized functions of the duplicated PKSA and PKSB genes found in common within the angiosperm lineage. Type III polyketide synthases (PKSs) produce secondary metabolites that play a variety of roles in plants. The studies performed in the lab of our collaborator, Dr. Michel Legrand and published in Kim et al. (2010), together with the recent report of Mizuuchi et al. (2008) shows that both PKSA and PKSB produce triketide and tetraketide α- pyrones by condensation with long chain fatty acyl-CoAs (up to 20 carbon chain lengths) and malonyl-CoA. The two PKSs have unusually broad substrate specificities as compared to typical plant type III PKSs (Mizuuchi et al., 2008). In contrast to their results and those of Mizuuchi et al., (2008), Dobritsa et al. (2010) failed to observe activity of recombinant LAP5/PKSA or LAP6/PKSB against fatty acyl substrates greater than C12 in length. The reason for this discrepancy is not clear, but activity against C16 to C18 fatty acyl-CoA substrates was consistently observed in multiple assays using their recombinant enzyme preparations (Kim et al., 2010). Moreover, the results from another collaborator, Dr. Dae-Yeon Suh, also show that, in vitro, PKSA preferentially catalyzes condensation of hydroxy fatty acyl-CoAs, which may be sequentially generated by CYP703A2 (Morant et al., 2007) and/or CYP704B1 (Dobritsa et al., 2009) with ACOS5 (de Azevedo Souza et al., 2009) to produce corresponding hydroxy tri- and tetraketide α- pyrones (Kim et al., 2010). Since ACOS5 also accepts a broad range of fatty acid substrates (de Azevedo Souza et al., 2009), the exact nature of its in vivo products that could be used as potential 63  in vivo PKSA and PKSB substrates remains unclear. However, ACOS5 shows highest activity against medium-chain hydroxylated fatty acids (de Azevedo Souza et al., 2009), and could thus generate medium-chain hydroxy fatty acyl-CoAs, for which PKSA has a strong substrate preference. Thus, an attractive hypothesis is that the hydroxylated acyl chains generated by ACOS5 and a suite of cytochrome P450 hydroxylases (Morant et al., 2007; de Azevedo Souza et al., 2009; Dobritsa et al., 2009; Li et al., 2010) are incorporated into multi-hydroxy tri- and tetraketide α-pyrones products in vivo. This model is supported by data from Dr. Michel Legrand’s group showing the preferential subcellular localization of PKSA and PKSB to the ER (Kim et al., 2010). Since the P450 hydroxylases are likely ER-localized, they may form metabolons with the ER-associated PKSs to form alkyl -pyrones. Both PKSA and PKSB recombinant enzymes catalyze the decarboxylative condensations of fatty acyl-CoAs with malonyl-CoA in vitro to generate tri- and tetraketide α-pyrones (Mizuuchi et al., 2008). Based on SEM data provided by our collaborator Dr. Michel Legrand (Kim et al., 2010), single pksa and pksb mutants, display subtle changes in exine patterning and deposition (data not shown) but are fertile. By contrast, the pksa pksb double mutant produced very small amounts of pollen and was completely male sterile (Figures 3.7 and 3.9), consistent with the observations of Dobritsa et al. (2010). Whereas these data suggest that they have partially redundant functions in exine formation, I present several lines of evidence suggesting that PKSA and PKSB could fulfill different in vivo functions. First, exine patterning defects in the pksa and pksb mutants were slightly different, with pksb mutants showing more pronounced defects including ectopic globular exine protrusions (Kim et al., 2010). Secondly, results from quantification of seed set in siliques of plants with different PKSA and PKSB allelic combinations (Table 3.1) showed that partial addition of PKSA activity to the pksb pksb background in PKSA pksa pksb pksb plants partially restored fertility relative to fully sterile pksa pksa pksb pksb plants, whereas addition of PKSB activity to pksa pksa pksb pksb plants (pksa pksa PKSB pksb plants) did not have this effect (Table 3.1). One interpretation of these data is that PKSA plays a more critical role in exine formation than does PKSB. Recent microarray analyses comparing gene expression in Arabidopsis wild-type 64  anthers relative to that in sporocyteless/nozzle or excess microsporocytes1/extra- sporogenous cells mutants suggest that SPL and/or EMS1 positively regulate transcription of ACOS5, PKSA and CHSL2 (At4g00040), all of which showing highly decreased expression levels in the spl/nzz and ems1/exs mutants (Wijeratne et al., 2007). By contrast, expression of PKSB was unaffected in the mutant backgrounds (Wijeratne et al., 2007). My results show that the timing of maximal tapetum-localized PKSA and PKSB mRNA accumulation differs over the course of anther development (Figure 3.4), further supporting distinct regulatory control and potential specialized functions of the two genes. It is noteworthy that another Arabidopsis PKS gene, CHSL2 (At4g00040) is 79% similar to PKSA. However, when expressed in bacteria, the cognate recombinant protein displayed no activity with the various fatty acyl-CoAs and malonyl-CoA used as substrates (Dr. Michel Legrand, personal communication). These results, together with expression data from public databases showing that CHSL2 is expressed at later stages of flower bud development, indicate that CHSL2 performs an unknown enzymatic function distinct from that of PKSA. Recently, Dobritsa et al. (2010) suggested that LAP5/PKSB and LAP6/PKSA could play roles both in the synthesis of alkylpyrones and in synthesis of phenolic constituents of sporopollenin in exine (Dobritsa et al., 2010). Metabolic profiling of developing anthers indicated that several flavonoids, including chalcone, naringenin, dihydrokaempferol and isorhamnetin 3-sophoroside, were significantly reduced in single mutants and undetectable in the double mutant. However, such flavonoids are not likely to be direct products of LAP5/PKSB or/and LAP6/PKSA. Whereas LAP5/PKSB and LAP6/PKSA are closely related to CHS, the recombinant enzymes do not exhibit CHS activity (Dobritsa et al., 2010). Furthermore, whereas CHS activity and flavonoid biosynthesis appear to be crucial to pollen development in some plants (Mo et al., 1992; van der Meer et al., 1992; Fischer et al., 1997; Hofig et al., 2006; Schijlen et al., 2007), complete disruption of CHS expression in Arabidopsis, leading to the absence of foliar anthocyanins and flower flavonoids, has no impact on male or female fertility (Burbulis et al., 1996), suggesting that CHS-generated flavonoids are not required for normal Arabidopsis pollen development. 65  One possible reason for reduced flavonoid levels in pksa, pksb, and pksa pksb mutants is that the defective exine walls of pollen grains in these mutants affect subsequent deposition of pollen coat tryphine that contains phenolics, flavonoids, fatty acid derivatives, and proteins (Piffanelli et al., 1998; Scott et al., 2004; Grienenberger et al., 2009). Thus, reduction or absence of flavonoids could be the indirect consequence of reduced deposition of flavonoid-containing tryphine. Consistent with this, pollen coat deposition is affected in the pksa and pksb mutants, and is more severely deficient in the pksb mutant (data not shown). The more severe tryphine defect in lap5/pksb observed in TEM images is consistent with the much greater reduction of flavonoid accumulation lap5/pksb anthers relative to lap6/pksa anthers (Dobritsa et al., 2010). PKSA and PKSB are strongly co-expressed in tapetum cells with ACOS5 (de Azevedo Souza et al., 2009), ACOS5 preferentially generates hydroxy fatty acyl-CoAs but has no activity towards hydroxycinnamic acids (de Azevedo Souza et al., 2009), and PKSA preferentially accepts hydroxy fatty acyl-CoAs to generate tri- and tetraketide α- pyrones (Kim et al., 2010). These observations suggest that the most plausible in vivo substrates for PKSA and PKSB are hydroxy fatty acyl-CoAs rather than phenolics such as hydroxycinnamoyl-CoAs, and that alkyl pyrones are natural products generated by PKSA and PKSB that are required for sporopollenin biosynthesis. The biosynthesis of the tri- and tetraketide α-pyrones in plants has not been well studied and their presence in Arabidopsis has not been reported. Thus, while in vitro biochemical assays indicate that the in vivo functions of PKSA and PKSB are to catalyze condensation of malonyl-CoA with hydroxy fatty acyl-CoAs generated by ACOS5 to generate alkyl pyrones, this hypothesis requires further testing. For example, reduction of keto functions after elongation of the chain by PKSA/PKSB, would prevent the formation of the α-pyrone ring, and alkyl phloroglucinols could be formed as sporopollenin natural products. The tri- and tetraketide α-pyrones generated in vitro by PKSA and PKSB also contain a ketone group on the α-pyrone rings and an additional ketone on the alkyl carbon chain, in the case of the tetraketide. These carbonyl groups could be the targets for further reduction to generate even more highly hydroxylated polyketides. One candidate enzyme for such activity is the reductase encoded by the Arabidopsis DIHYDROFLAVNONOL 4- REDUCTASE LIKE1 (DRL1)/TETRAKETIDE α-PYRONE REDUCTASE (TKPR1) 66  (At4g35420) gene, which is tightly co-expressed with ACOS5, PKSA, and PKSB and is required for male fertility and exine formation (Tang et al., 2009). The remarkable conservation of Arabidopsis PKSA and PKSB, ACOS5 (de Azevedo Souza et al., 2009) and CYP703A2 (Morant et al., 2007) genes in land plants suggests that the encoded enzymes are part of an ancient sporopollenin biosynthetic pathway. The in vitro biochemical functions of PKSA and PKSB that we explored in detail, together with similar data on ACOS5, and CYP703A2, the coordinated co- expression of these genes in the tapetum during free microspore stages of anther development, and the ER localization of PKSA and PKSB support the hypothesis that this pathway catalyzes sequential modification of fatty acid starter molecules to generate integral sporopollenin components of the pollen exine. Based on these new data, I propose a reaction sequence localized to the ER leading from hydroxylation of medium to long chain fatty acids (catalyzed by CYP703A2), to fatty acyl-CoA formation (catalyzed by ACOS5), and condensation of fatty acyl-CoAs with malonyl-CoA (catalyzed by PSKA and PSKB) to generate triketide and tetraketide α-pyrone sporopollenin precursors. Work reported in Chapter 4 and recently published (Grienenberger et al., 2010) extends this work and shows that reductases encoded by tapetum-expressed DRL/TKPR genes are also part of this pathway, and accept the tetraketide -pyrone products generated by PKSA and PKSB in vitro to form reduced derivatives that appear to be sporopollenin precursors. 67  Chapter 4. Analysis of TETRAKETIDE -PYRONE REDUCTASE (TKPR) function in Arabidopsis thaliana reveals a novel and conserved biochemical pathway in sporopollenin monomer biosynthesis  4.1 Summary  In this chapter, I show that two Arabidopsis genes encoding oxidoreductases, TKPR1 and TKPR2, are co-expressed with ACOS5 and are specifically and transiently expressed in tapetal cells during microspore development. The null mutant tkpr 1-1 displayed severe pollen exine layer defects, was male sterile and was shorter in stature than wild-type (Col-0) plants and had smaller leaves. Phylogenetic studies indicated that the two reductases belong to a large reductase/dehydrogenase gene family and cluster in two distinct clades with putative orthologs from several angiosperm lineages and the moss Physcomitrella patens. Recombinant proteins produced in bacteria reduced the carbonyl function of tetraketide α-pyrone compounds synthesized by PKSA/B rather than the CoA esters to generate aldehyde or alcohol. Thus the proteins were therefore named TETRAKETIDE α-PYRONE REDUCTASE1/2 (TKPR1/2) (previously called DRL1 and CCRL6, respectively). TKPR activities, together with those of ACOS5 and PKSA/B, identify a conserved biosynthetic pathway leading to hydroxylated α-pyrone compounds that were previously unknown to be sporopollenin precursors.     68  4.2 Introduction  4.2.1 DIHYDROFLAVONOL 4-REDUCTASE (DFR) and DIHYDROFLAVONOL 4-REDUCTASE-LIKE1 (DRL1)  Flavonoids are comprised of a relatively diverse family of aromatic molecules generated by the sequential decarboxylative addition of three acetate units from malonyl- CoA to a p-coumaryl-CoA starter molecule derived from the general phenylpropanoid pathway. These flavonoids compounds are normally classified to six major subgroups such as the chalcones, flavones, flavonols, flavandiols (leucoanthocyanidins), anthocyanins, and proanthocyanidins (condensed tannins) (Winkel-Shirley, 2001). Dyhydroflavonol 4-reductase (DFR) is the first committed enzyme of anthocyanin biosynthesis in the flavonoid pathway (Shimada et al., 2004). DFR acts on dihydroflavonols, generating leucoanthocyanidins by reduction of a ketone to a hydroxyl group (Figure 4.1). These leucoanthocyanidins are converted into colored anthocyanidins via an oxidation step catalyzed by anthocyanidin synthase (ANS), a 2-oxoglutarate iron- dependent oxygenase. Subsequent reduction of anthocyanidins by anthocyanindin reductase (ANR) produces condensed tannins or proanthocyanidins (Xie et al., 2003). DFR genes have been cloned from a variety of plants and DFR is considered to regulate carbon flux into anthocyanin biosynthesis (Bernhardt et al., 1998; Tanaka et al., 1998; Itoh et al., 2002; Shimada et al., 2004). 69    Figure 4.1 Overview of the flavonoid biosynthesis pathway. Enzyme names are abbreviated as follows: chalcone synthase (CHS), chalcone isomerise (CHI), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), and anthocyanidin synthase (ANS). Image was reprinted with permission of Che Caswell Colpitts (Copyright ©  2009 C.C. Colpitts).   The completed Arabidopsis thaliana genome has revealed that in addition to DFR, Arabidopsis has a family of four additional related genes (Yuan et al., 2007). True DFR (At5g42800) was first identified by its role in synthesis of brown pigments in the seed coat, a phenotype collectively termed transparent testa (tt) (Shirley et al., 1995). Other DFR-like genes in Arabidopsis have been verified to have different biochemical and physiological functions. BANYULS (BAN, At1g61720) encodes anthocyanidin reductase (ANR) mentioned above (Winkel-Shirley, 2001; Xie et al., 2003). In addition, 70  studies on another DFR-like gene, BEN1 (At2g45400) suggest that BEN1 could be a brassinosteroid reductase that catalyzes the conversion of typhasterol (TY), castasterone (CS) and brassinolide (BL) to biologically inactive 6-OHTY, 6-OHCS and 6-OHBL, respectively (Yuan et al., 2007). Thus, it appears that this DFR-like enzyme can act on an classes of molecules entirely different from DFR, but one that shares structural similarity in carbon-ring structure to flavonoids. In a recent study of the DFR-like gene DRL1 (At4g35420) published while my research was in progress, this gene was shown to be essential for pollen wall development (Tang et al., 2009), suggesting that this DFR-like enzyme also acts on an different class of molecules than DFR. The likely substrate diversity of DFR and DFR-like enzymes also has been highlighted by the phylogenetic analysis and amino acid alignment of DFRs and DFR-like proteins in various plant species. These studies showed that proteins related to DFR contain not only a putative NADPH-binding domain but also a variable putative substrate specificity domain between well-conserved regions (Johnson et al., 2001; Shimada et al., 2004). The data were interpreted to indicate that DFR-like enzymes with minor amino acid difference in the presumed substrate-binding region could have different substrate preferences (Johnson et al., 2001). In Chapter 3 and in Kim et al. (2010), we demonstrated that two Arabidopsis polyketide synthases, POLYKETIDE SYNTHASE A/B (PKSA/B), play critical roles in sporopollenin biosynthesis, acting downstream of ACOS5. pksa pksb double mutants are completely male sterile and lack an exine. In vitro, both proteins accept fatty acyl-CoA esters synthesized by ACOS5 and condense them with malonyl-CoA to yield triketide and tetraketide α-pyrones as reaction products (Kim et al., 2010). Here, I show by in situ hybridization of mRNAs of two Arabidopsis oxidoreductases, one encoded by the DRL1 gene previously described by Tang et al. (2009) and the other annotated as CINNAMOYL COA REDUCTASELIKE6 (CCRL6) (Hamberger, 2007), are coexpressed with ACOS5, PKSA, and PKSB in anther tapetum cells. Our collaborator showed that the recombinant enzymes produced in bacteria accept the tetraketide α-pyrones produced by PKSA and PKSB as substrates to reduce the carbonyl function on the tetraketide alkyl chain to a secondary alcohol function (Grienenberger et al., 2010). Phylogenetic studies showed that the oxidoreductases belong to a gene family conserved from moss to flowering plants. 71  Since similar gene conservation holds true for PKSA, PKSB, and ACOS5, it appears that the whole biosynthetic pathway leading from medium or long-chain fatty acids to sporopollenin units is highly conserved and may have been a key determinant in the evolution of land plants.  4.3 Materials and methods  4.3.1 Plant material and growth conditions  Arabidopsis thaliana Columbia (Col-0) seeds were sterilized and after a cold treatment (2 days at 4°C in the dark) and germinated at 20°C under 70 µmol m -2  s -1  fluorescent lighting. Twelve days later, the plants were transferred to a growth chamber with a light/dark cycle of 16 hr/8 hr. T-DNA insertion mutants were obtained from SAIL (Alonso et al., 2003) via The Arabidopsis Information Resource. In progeny, homozygous insertion lines SALK_837_D01 for tkpr-1 was identified by PCR using gene-specific and T-DNA–specific primers (Table 4.1).  4.3.2 Identification and characterization of TKPR1 insertion mutant  The T-DNA insertion line tkpr1-1 (SAIL_837_D01) was identified using the Salk Institute T-DNA Express Arabidopsis gene-mapping tool (Alonso et al., 2003). Homozygous plants were identified in PCR reactions on genomic DNA with the primers 5RP and 5LP in combination with LB1 which is left border primer of T-DNA insertion. Primers are listed in Table 4.1. Crosses of wild-type pollen to homozygous tkpr1 mutant plants were performed to obtain F2 generation plants. The patterns of TKPR1 T-DNA insertion allele segregation in the F2 generations were tested by chi-square statistical analysis of observed phenotypes and genotypes using Graph-Pad software (http://graphpad.com/quickcalcs/chisquared1.cfm), with expected values based on Mendelian segregation, observed values on the F2 population, and two degrees of freedom (genotypes) or one degree of freedom (phenotypes).  72  4.3.3 Complementation of tkpr1 mutant  A 3593bp DRL1 genomic fragment was amplified using the Plantinum Taq DNA polymerase High Fidelity (Invitrogen) with the gene-specific primers (Table 4.1) and cloned into pCR8/GW/TOPO (Invitrogen). After verification by sequencing, the fragment was subcloned into pGWB1, Gateway binary vector (Nakagawa et al., 2007). The transformants were selected using 25 mg/L gentamycin, 25mg/L rifampicin and 50 mg/L kanamycin. Verified transformant was introduced into acs5 and dfrl1 heterozygous plants using the floral dip method (Clough and Bent, 1998). Mature plants were harvested for seeds, and seeds (T1) were sown in ½  MS (Murashige and Skoog) salts (Sigma Aldrich), supplemented with 1% sucrose and 0.6% agar medium containing 25 mg/L hygromycin.  4.3.4 Phylogenetic studies  The Arabidopsis TKPR1 (At4g35420) gene was used in BLAST searches to identify potential homologs in the genomes of Arabidopsis (TAIR, http//www.arabidopsis.org), poplar (Joint Genomics Institute, Populus trichocarpa v.1.1; http://genome.jgi-psf.org/Poptr1/Poptr1.home.html) rice (The Institute for Genome Research; http://www.tigr.org/tdb/e2k1/osa1/), Physcomitrella patens (Joint Genomics Institute, Physcomitrella patens v.1.1 http://genome.jgi- psf.org//Phypa1_1/Phypa1_1.home.html), and Chlamydomonas reinhardtii (Joint Genomics Institute Chlamydomonas reinhardtii v. 3.0; http://genome.jgi- psf.org/Chlre3/Chlre3.home.html) All sequences obtained are given in Appendix C. Protein sequences were aligned using MUSCLE 3.6 using the default parameters (sequencing clustering; UPGMA, objective score; classic sum-of-pairs score) (Edgar, 2004), and the multiple protein sequence alignments were manually optimized. Aligned sequences are available in Appendix D. To reconstruct phylogenetic trees, maximum likelihood analyses with 1000 bootstrap replicates were performed using PhyML v2.4.4 and default settings (Guindon and Gascuel, 2003) with the JTT model of amino acid substitution.  73  4.3.5 Microscopy  Tissue fixation, embedding, and sectioning of Arabidopsis wild type (Col-0) and tkpr1-1 mutant inflorescences were performed as described in section 2.3.4.  4.3.6 RT-PCR  RNA quality was assessed by visual inspection of rRNA on a 1.2% formaldehyde-agarose (FA) gel and quantified spectrophotometrically, and 2.5 μg RNA/ 20 µL reaction was used to generate first strand cDNA using Superscript II Reverse Transcriptase (Invitrogen) following the manufacturer’s protocol. For RT-PCR, gene- specific and intron-spanning primers (Table 4.1) were used in PCR reactions to amplify corresponding cDNA sequences under the following PCR conditions: 95°C for 3 min, followed by 35 cycles of (94°C for 30 s, 56°C for 30 s, 72°C 1 min) followed by 72°C for 10 min, using Taq polymerase in a 50 µL total reaction. Actin2 was used as control. For quantitative RT-PCR analysis of TKPR1, TKPR2 and At1g25460 expression, 10 ng of cDNA was incubated with 10 µL iQ SYBR Green Supermix (Bio-Rad) and 5 pmol of each forward and reverse primer (Table 4.1) in a total volume of 20 µL. After an initial denaturation step at 95°C for 3 min, 40 cycles at 95°C for 15 s, 60°C for 15 s, and 72°C for 30 s were followed by a fluorescence reading. A melting curve was generated ranging from 95°C to 60°C. Threshold cycles (CT) were adjusted manually, and the CT values for a housekeeping control Actin2 amplified in parallel on each plate were subtracted from CT values obtained for each gene of interest, thus generating normalized CT values (∆CT). The relative starting quantities of each gene were determined by setting as a base value the gene with the highest CT value within a tissue panel or treatment series, and relative quantities were calculated using the ∆∆CT method as described in (Hietala et al., 2003). ∆∆CT was calculated using immature flower buds as the highest expressing tissue.    74  4.3.7 In situ hybridization and validation of RNA probes  Tissue fixation, embedding, hybridization, and signal detection were performed as described in section 3.3.5. For sense and antisense TKPR1 and TKPR2 probe synthesis, 981 bp and 966 bp DNA template corresponding to the TKPR1 and TKPR2 coding region, respectively, were PCR amplified from flower cDNA using gene-specific forward and reverse primers (Table 4.1). To validate specificity of RNA antisense probes, I performed DNA gel blotting. PCR-amplified cDNA clones of TKPR1 and TKPR2 (Table 4.1) were blotted to positively charged nylon membranes, Hybond-XL (GE Healthcare Life Sciences), using 10x SSC as the transfer buffer. Transfer of cDNA to the nylon membrane was monitored via ethidium bromide. The probe hybridization, and signal detection were performed as described in section 3.3.5.  4.3.8 Production of TKPR1 recombinant proteins and activity assay in vitro  cDNAs of TKPR1 were amplified and ligated to the pET-28a expression vector containing His-tag (Novagen). After confirmation of the sequences, each plasmid was transformed into BL21 (DE3). The cells harboring the plasmid were cultured in 4 mL of LB medium containing 50 ug/mL of kanamycin at 37C overnight. The culture was diluted 1:100 in LB medium containing 50 ug/ml of kanamycin and cultured to an A600 of 0.5 at 37C. Then, the each protein was induced by adding IPTG to a final concentration of 1mM. The culture was further incubated at 25C for 20 hr to allow for overproduction to occur. The E.coli cells were harvested by centrifugation at 5000 x g for 10 min. The cell pellets were washed once with PBS buffer (140 mM NaCl, 3 mM KCl, 10 mM Na2HPO4, and 2mM KH2PO4, pH of 7.4) and centrifuged at 5000 x g for 10min. The cell pellets were stored at -80C to be purified subsequently. Cell pellets were suspended in 20 mM potassium phosphate buffer, pH 7.4, containing 300 mM NaCl, 0.1% Triton X-100, 5 mM imidazole, β-mercaptoethanol,10% glycerol, 1 mM PMSF and 1 mg/mL lysozyme and incubated for 30 min at 4C. Cells were disrupted by sonication and centrifuged at 10,000 g for 30 min. The supernatant was gently mixed up with 50% Ni-NTA agarose (Qiagen) for 1 hr at 4C. The lysate-Ni-NTA 75  mixture is loaded into an Econo-Pac column (Bio-Rad). After washing with 20 mM potassium phosphate buffer, pH 7.4, containing 300 mM NaCl and 40 mM imidazole, the recombinant proteins were eluted with 20 mM potassium phosphate buffer, pH 7.4, containing 30 mM NaCl and 300 mM imidazole. To concentrate and reconstitute proteins into enzyme assay buffer (100 mM Na2HPO4/KH2PO4, pH 6.25 for CCR buffer condition) or 100 mM Tris-HCl, pH 7.6, 10 mM MgCl2, 2.5 mM DTT for ACOS5 buffer condition) for comparison between CCR1 and TKRP1, Ultra-15 filter (Amicon) was used, following manufacturer’s instructions. Protein concentration was estimated by SDS-PAGE and determined more accurately using Nanodrop spectrophotometer. The enzyme purity was assessed by SDS-PAGE. Enzymatic activity against synthetic alkyl phloroglucinol was tested by incubating 100 µM substrate in a reaction mixture containing, 1 mM NADPH and 10 µg enzyme in 500 µl assay buffer (100mM Na2HPO4/KH2PO4, pH 6.25) for 1 hr at 30C. To extract potential reaction products, 1 mL chloroform (CHCl3) was directly added to the reaction mixtures vials, vigorously vortexed, before using for GC-MS aided product identification.  4.3.9 Identification of products by GC-MS  For GC-MS  analyses, extraction from reaction mixture, derivatization of organic compounds and running condition of samples in GC-MS are described by Wang et al., (2010). (Wang et al., 2010)  4.3.10 Accession numbers  Sequence data from this article can be found in the Arabidopsis Genome Initiative or GenBank/EMBL databases under the following accession numbers: At4g35420 (TKPR1), At1g68540 (TKPR2), At1g02050 (PKSA), At4g34850 (PKSB), At1g62940 (ACOS5) and At3g18780 (ACTIN2).   76  4.3.11 Sequences of primers  Table 4.1 Primers used in this study.  Qantitative RT-PCR Gene Primer name Sequence (5' → 3') AT4g35420 qRT DFRL2F CAGAGATCCAGGAAATGAGAAGAAAC  qRT DFRL2R AAGCACCGGAGAAGCAGTATGGAA Actin2 Actin2-RT-FW CCAGAAGGATGCATATGTTGGTGA  Actin2-RT-RW GAGGAGCCTCGGTAAGAAGA   Genotyping Gene Primer name Sequence (5' → 3') AT4g35420 5RP AAAGAATTCCATTGCGGTATCTCCGCA  5LP GAAGAAACTTGCGCACCTATG  LB1 GCCTTTTCAGAAATGGATAAATAGCCTTGCTTCC   Complementation construct Gene Primer name Sequence (5' → 3') AT4g35420 DFRL1F GCAATCCAAAGGGAATCGAAA  DFRL1R CGATTCTGTGTTTACGAATGCTG   In situ hybridization Gene Primer name Sequence (5' → 3') AT4g35420 DFRL RTPCR1F GATCCAGGAAATGAGAAGAAAC  T7 DFRL 2R CATAATACGACTCACTATAGGGTTTCTCAAACCTCTT GGGG  T7 DFRL 1F CATAATACGACTCACTATAGGGATCCAGGAAATGAG AAGAAAC  DFRL RTPCR2R GTTTCTCAAACCTCTTGGGG AT1g68540 T7 CCRL6-Sense CAT AAT ACG ACT CAC TAT AGG ATG TCT GAG TAT TTG GTA ACT GG  R CCRL6-Sense TTA GAG CAG ACC CTT CTT CTG AAA AC  F CCRL6-Anti ATG TCT GAG TAT TTG GTA ACT GG  T7 CCRL6-Anti CAT AAT ACG ACT CAC TAT AGG TTA GAG CAG ACC CTT CTT CTG AAA AC   4.4 Results  4.4.1 Genes involved in pollen cell wall formation are tightly co-regulated  Pollen wall formation requires exquisite and coordinated spatio-temporal regulation of numerous biosynthetic genes by specific transcriptional regulators (Alves- 77  Ferreira et al., 2007; Yang et al., 2007a). In particular, many genes involved in exine biosynthesis in Arabidopsis have been shown to be repressed by the MALE STERILITY1 (MS1) transcription factor in wild type plants, and to be over-expressed in ms1 mutant (Ito et al., 2007; Yang et al., 2007a). Examination of Arabidopsis microarray data showed that, during development of wild type and ms1 anthers, several uncharacterized genes are co-regulated with genes involved in exine formation. These genes may therefore encode unknown players of sporopollenin biosynthesis (http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi;) (Toufighi et al., 2005). Among the genes co-expressed during pollen development, two were annotated as CHALCONE SYNTHASE-LIKE and identified in Chapter 3 and Kim et al., (2010) as encoding PKSA and PKSB. PKSA and PKSB catalyze the condensation of fatty acyl-CoA esters produced by ACOS5 with malonyl-CoA to yield tri- and tetraketide - pyrone compounds as reaction products (Kim et al., 2010). Several other tightly co- regulated genes were annotated as oxido-reductases/dehydrogenases that all have unknown physiological substrates (http://www.arabidopsis.org/). Among them, the proteins encoded by At4g35420 (DRL1; Tang et al., 2009) and At1g68540 (CCRL6; Hamberger et al., 2007) contain putative NAD(P)H-binding domains. Both proteins display sequence similarity with two well-characterized plant oxidoreductases: DFR, an enzyme of anthocyanin synthesis (52% and 43% similarity, respectively) (Shirley et al., 1992), and cinnamoyl-CoA reductase (CCR) that is involved in lignin biosynthesis (53% similarity for both At4g35420 and At1g68540 encoded proteins) (Lacombe et al., 1997). These plant enzymes belong to a superfamily whose members are also encountered in microbial and mammalian kingdoms and share a conserved N-terminal sequence that is likely involved in the interactions with NAD(P)H (Baker and Blasco, 1992; Lacombe et al., 1997). DRL1 has been shown to be required for male fertility (Tang et al., 2009), but neither the DRL1 expression pattern nor its exact role in pollen wall formation have been described in detail.    78  4.4.2 At4g35420 and At1g68540 expression profiles during flower development  I explored publicly available microarray databases, such as Genevestigator (https://www.genevestigator.com/gv/index.jsp) (Hruz et al., 2008) and the Arabidopsis eFP browser (http://bbc.botany.utoronto.ca/efp/cgi-bin/efpWeb.cgi) (Winter et al., 2007), to determine the tissue expression patterns of At4g35420 (DRL1) and At1g68540 (CCRL6). The results of this search indicated that both were preferentially expressed in young flower buds, in accordance with their high coregulation scores, similar to the expression patterns reported for PKSA, PKSB, and ACOS5 (de Azevedo Souza et al., 2009; Kim et al., 2010). To facilitate their designation in the following paragraphs, genes corresponding to At4g35420 (DRL1) and At1g68540 (CCRL6) were named TETRAKETIDE a-PYRONE REDUCTASE1 (TKPR1) and TKPR2, respectively, in anticipation of the enzymatic activities described later for the two corresponding proteins. Measurements of relative mRNA abundance by quantitative RT-PCR in RNA preparations from various organs confirmed the flower-specific expression of TKPR1 and TKPR2 in contrast with At1g25460, a close homolog (Figure 4.2) that displayed a strikingly different expression pattern.  79      Figure 4.2 Developmental expression profile of TKPR1, TKPR2 and At1g25460.  Quantitative RT-PCR analysis of relative TKPR1, TKPR2 and At1g25460 expression levels in various Arabidopsis organs. Expression was calculated using the ΔΔCT method and is represented relative to the organ with the highest level of expression (TKPR1 and TKPR2; flowers, At1g25460; 7day), set at 1.0. Actin 2 (At3g18780) was used reference as a reference gene. Bars represent standard deviations from the means of triplicate determinations. 7Day, 7-day old seedlings; Fw, flower; ML, mature leaf; MR, mature root; MS, mature stem; YL, young leaf; YS, young stem (Grienenberger et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   To determine the precise sites of TKPR1 and TKPR2 expression in flower tissues, in situ hybridization experiments were performed and showed the specific accumulation of transcripts in the anthers (Figure 4.3). In situ hybridization experiments at different 80  stages of anther development demonstrated the tapetum-specific expression of both TKPR genes. The two genes displayed similar but distinct temporal expression patterns. The highest hybridization signal for both was found at stage 7 of anther development (Figure 4.3); however, the TKPR1 expression pattern was broader over developmental time. The specificity of the TKPR1- and TKPR2-derived riboprobes used for in situ hybridization analysis was demonstrated by DNA gel blotting, showing that both probes hybridized specifically with the target templates, with no detectable cross-hybridization (Figure 4.4).    Figure 4.3 Transient tapetum-specific expression of TKPR1 and TKPR2.  TKPR1 and TKPR2 mRNA were localized by in situ hybridization to sections taken from developing anther locules of wild-type (Col-0) flowers. TKPR1 and TKPR2 localization were detected by using a gene-specific antisense probe and control sense probe. Stages of anther development are according to Sanders et al. (1999). Dark precipitates indicate hybridization of the probe. Stage 5 locules show hybridisation signal in the tapetum. Stage 7 shows highest hybridisation signal in both of TKPR1 and TKPR2 tapetum as well as tetrads. Tapetum signal weakens by stage 9 and disappears by stage 11. MMC, microspore mother cells; Tds, tetrads; T, tapetum; MSp, microspores; PG, pollen grain. Scale bars=70μm (Grienenberger et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).  81      Figure 4.4 Specificity of TKPR nucleotidic probes.  Specificity of probes used for in situ hybridization was evaluated by DNA gel blotting. Coding sequences of TKPR transcripts were amplified by PCR using gene-specific primers. Amplicons of 0.95 kb predicted size were visualized on Gel Red-stained 0.7% agarose gels (lower panels) before transfer onto nylon membranes. Blots were hybridized separately with digoxigenin-labelled riboprobes corresponding to coding sequences of TKPR1(A) or TKPR2 (B). An indication of size positions in kb is given on the left. Arrows indicate positions of amplicons on gel and blot. Data show the absence of cross- hybridization between the two transcripts (Grienenberger et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   4.4.3 Genetic and phenotypic analysis of tkpr1-1  T-DNA insertion alleles of tkpr1-1 in At4g35420/TKPR1 and tkpr2-1 in At1g68540/TKPR2 were obtained from public collections (Alonso et al., 2003) and homozygous populations were generated. Since only tkpr1-1 homozygous line showed a sterile phenotype with siliques devoid of seeds in initial phenotypic examination, further genetic and phenotypic analysis focused on tkpr1-1. There were no other obvious morphological differences between tkpr2-1 and wild-type (Col-0). The location of the T- DNA insertion in the fourth exon of TKPR1 gene was verified (Figure 4.5) and TKPR1 expression in tkpr1-1 mutant plants assayed by RT-PCR, using template cDNA derived from both wild type and mutant flowers. This analysis suggested that tkpr1-1 is a null allele of TKPR1 (Figure 4.5). I allowed F1 heterozygote plants derived from pollination 82  with wild-type pollen to self-pollinate and analyzed the resulting F2 population for co- segregation of the male sterile phenotype with tkpr1-1. The results showed that the mutant phenotype was inherited in a Mendelian fashion, with one quarter of the F2 progeny displaying complete male sterility (χ2 = 4.596; p>0.1; n=89), showing that the mutant phenotype is caused by a mutation at a single locus. In the F2 population generated from this cross, the male sterile phenotype co-segregated with tkpr1-1 (19/89 tkpr1-1 TKPR1 homozygotes male sterile, 39/89 tkpr1-1 heterozygotes and 31/89 wild type (Col-0), strongly suggesting that the male sterile phenotype, and complete block in pollen formation in the tkpr1-1 mutant line is caused by loss of function of the TKPR1 gene. Examination of tkpr1-1 mutant plants (Figure 4.6) revealed anthers devoid of visible pollen, and it was completely male sterile, with no seeds recovered from siliques derived from mutant plants. While no pollen was ever observed in plants homozygous for the tkpr1-1 allele, tkpr1-1 flowers were female fertile when pollinated with wild-type pollen. In addition to this male sterile phenotype, mature tkpr1-1 plants were consistently shorter than wild-type (Col-0) plants and had smaller leaves (Figure 4.6).     Figure 4.5 Molecular characterization of tkpr1 insertion alleles and effects on gene expression.  Location of the T-DNA insertion in the fourth exon of TKPR1 in SAIL_837_D01 is shown above. The cartoon for gene model was drawn base on TAIR (The Arabidopsis Information Researce) database search (http://www.arabidopsis.org). The other allele, 83  tkpr1-2 was identified and characterized by our collaborator, Dr. Michel Legrand’s lab. RT-PCR analysis of TKRP1 expression in wild-type and SAIL_837_D01 (tkpr1-1) flowers is shown below. Expression was evaluated using intron-spanning primers on either side of the T-DNA insertion (Grienenberger et al., 2010). Image was adapted and reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).     Figure 4.6 Phenotypic characterization of tkpr1 plant.  Vegetative phenotype of the tkpr1 mutant is shown. Mutant plants are smaller in size and have smaller rosette leaves than wild-type. Mature wild-type (Col-0) and tkpr1flowers are shown. Mutant anthers are devoid of pollen and no pollen grains were observed attached to the stigma. All tkpr1 siliques are undeveloped and no seeds were recovered from from siliques.   4.4.4 Complementation analysis  To test for the ability of the TKPR1 gene to complement the male sterile and morphological phenotypes in the tkpr1-1 background, I PCR-amplified an approximately 84  3.6-kb region from Col-0 genomic DNA containing 577bp of sequence upstream of the TKPR1 start codon, and the complete transcribed region (Figure 4.7), introduced the construct into a T-DNA vector, and transformed TKPR1-1 tkpr1-1 heterozygote plants by Agrobacterium mediated transformation. The genotypes of 14 transgenic lines harboring the TKPR1 transgene were characterized by PCR using primers to differentially detect the presence of the potentially complementing transgene and the T-DNA insertion in the TKPR1 gene of the 14 T1 plants investigated, three tkpr1-1/tkpr1-1 homozygote T1 lines were fully fertile with normal morphology, showing that the TKPR1 transgene had complemented the tkpr1-1 mutation. Taken together, these analysis show that a mutation in the TKPR1 gene causes the male sterile phenotype observed in the tkpr1-1 mutant.    Figure 4.7 Schematic representations of the construct for tkpr1 complementation test.  Gray shaded box shows TKPR1 transgene, containing 577bp of promoter sequence and 3'UTR/terminator.   4.4.5 Anther and microspore development in the tkpr1 mutant  To determine the point at which pollen development was impaired in the tkpr1 mutant, I examined developing anthers in the tkpr1-1 mutant background and compared their development to that seen in wild-type anthers (Figure 4.8). Anther, microspore, and pollen development proceeded normally through stage 8. However, development of microspores was arrested in stage 9. tkpr1-1 anthers and pollen grains were subsequently lost and presumably degraded while anthers devoid of visible pollen grains continued to develop. 85    Figure 4.8 Phenotypic characterization of anther and microspore development in wild-type (Col-0) and tkpr1 flowers.  Anther cross sections (1µm) were taken from developing flowers of the genotypes indicated. Numbers indicate anther developmental stages according to Sanders et al. (1999). E, epidermis; En, endothecium; MSp, microspores; Sm, septum; T, tapetum. Scale Bar=40um.   Since a primary defect in the tkpr1 mutant appeared to be formation of the pollen wall, which was arrested at stage 9 of anther development, tkpr1-1 anthers and microspores were examined in detail by TEM and compared to wild-type at stage 9 of development (Sanders et al., 1999). Figure 4.9 shows that in wild-type anthers, a thick reticulate exine with distinct baculae and tecta had formed around free, uninucleate microspores. In mutant flowers, however, the tapetum was highly vacuolated (Figure 4.9F) and microspores were profoundly affected with an exine structure that appeared very thin (Figure 4.9D) and completely disorganized without baculae and tecta (Figure 4.9H). In contrast to the cytoplasmicaly dense microspores in wild-type anthers (Figure 4.9C), tkpr1-1 microspores at this stage were disorganized, largely devoid of cytoplasm, and showed signs of rupture. Finally, tkpr1-1 locules contained a fibrillar, electron-dense network (Figure 4.9F) that was never observed in wild-type anthers and could represent 86  unpolymerized sporopollenin precursors. In contrast, cell walls of wild-type and mutant anthers were similar with visible superficial cuticle layer (Figures 4.9I and 4.9J). 87   88  Figure 4.9 Exine formation is impaired in tkpr1-1 anthers.  Wild type ([A], [C], [E], [G], and [I]) or tkpr1-1 ([B], [D], [F], [H], and [J]) plants at stage 9 of anther development (Sanders et al., 1999). Details are shown for anther locule ([A] and [B]), microspore ([C] and [D]), tapetum ([E] and [F]), exine ([G]and [H]), and anther wall ([I] and [J]). Ba, baculae; Cu, cuticle; Cw, cell wall; Dex, defective exine structure; Ed, electron-dense material; L, lipid droplets; Lo, locule; MSp, microspore; N, nucleus; Ne, nexine; P, plastid filled with plastoglobuli; PM, plasma membrane; T, tapetal cell; Te, tectum; V, vacuole containing electron-dense material. Bars = 10 µm in (A) and (B), 2 µm in (C) to (F), 500 nm in (I) and (J), and 100 nm in (G) and (H) (Grienenberger et al., 2010). Image was reprinted with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   4.4.6 Testing TKPR1 enzymatic function in vitro  Sequence analysis of TKPR1 (At4g35420) suggested that it encodes a protein possessing a consensus NADPH/NADH binding motif (Tang et al., 2009). Therefore, considering the fact that this putative oxido-reductase gene is tightly co-expressed with ACOS5 and the polyketide synthases PKSA and PKSB in tapetal cells during pollen development (de Azevedo Souza et al., 2009; Kim et al., 2010), it could act downstream of PKSA and/or PKSB, utilizing a tri- and tetraketide compounds or alkyl phloroglucinol products by condensation of fatty acyl-CoAs with malonyl-CoA (Mizuuchi et al., 2008). First, the coding region of TKPR1 was cloned in a vector that introduced a His- tag and was expressed in E. coli. TKPR1 recombinant protein was purified by affinity chromatography on Ni-NTA agarose (Figure 4.10). 89    Figure 4.10 Analysis of recombinant protein preparations at different steps of purification.  Bacterial protein extracts were prepared and purified as described in Methods section. Protein preparations were analyzed by electrophoresis on SDS-polyacrylamide gels and Coomassie Blue staining. Purification steps of TKPR1 are illustrated. Lane 1, soluble protein from induced bacteria that was further fractionated; lane 2, Flow through fraction; lane 3, washed fraction; lane 4, eluates, lane 5, concentrated eluates.   One of possible compounds generated from PKSA/B condensation, alkyl phloroglucinol, which contains an alkyl chain bearing a carbonyl function was chemically synthesized by Yan Cao in Dr. Jetter Reinhard’s lab and incubated with TKPR1 (Figure 4.11 and Figure 4.12). Assay mixtures were analyzed by GC-MS and the ketoalkyl phloroglucinol compounds gave rise to strong signals (characteristic mass (m/z) at 369 and 509) but no reduction products could be detected (Figure 4.12 and Figure 4.13), thus indicating that the alkyl phloroglucinol compound is not a substrate of TKPR.  90    Figure 4.11 Structure of a synthetic alkyl phloroglucinol tested as a TKPR1 substrate and predicted MS fragmentation patterns.  (A) Synthetic alkyl phloroglucinol kindly provided by Yan Cao (UBC). Chemical formula: C18H28O4; Exact Mass: 308.20; Molecular weight: 308.41; m/z 308.20 (100.0%), 309.20 (19.6%), 310.21 (1.9%). (B) Predicted fragmentation pattern of the alkyl phloroglucinol. After derivatization with TMS, total mass is 524. (C) Predicted fragmentation pattern of reduced hydroxyl alkyl phloroglucinol. After derivatization with TMS, total mass is 598.    Figure 4.12 GC analysis of reaction products generated by TKPR1 incubation with a synthetic alkyl phloroglucinol.  The synthetic alkyl phloroglucinol shown in Figure 4.11 was incubated in optimized reaction conditions (described in 4.3.9) without recombinant TKPR1 (upper panel) and with TKPR1 (lower panel), and the mixture analyzed by GC-FID. The alkyl phloroglucinol was synthesized together with the major unknown products such as A and B. Arrow heads indicate the synthetic alkyl phloroglucinol. 91    Figure 4.13 Mass spectra of a peak indicated by arrowhead in the GC chromatogram of Figure 4.12.  The m/z values of the GC peak observed in the mass spectrum shown are identical to the predicted values of the unreduced alkyl phloroglucinol substrate added (Figure 4.11 B).    4.4.7 Phylogenetic analysis of TKPR genes  TKPR1 and TKPR2 belong to a gene superfamily that includes members of mammalian, bacterial, and plant origins (Baker et al., 1990; Baker and Blasco, 1992; Lacombe et al., 1997). Plant family members whose functions are unknown have been referred to as DRL (Tang et al., 2009) and CCR-like (CCRL) (Hamberger, 2007) since the functions of DFR in anthocyanin synthesis and CCR in lignin biosynthesis had been characterized several years ago (Shirley et al., 1992; Lacombe et al., 1997). Alignment and phylogenetic analysis of DFR, CCR and related genes from several plant taxa including those from the fully sequenced genomes of Arabidopsis, poplar, rice, and the moss Physcomitrella patens (Figure 4.14) showed that known and putative DFR, CCR, and ANR genes fall into distinct clades in flowering plants, but do not contain Physcomitrella representatives. Furthermore, TKPR1 and TKPR2 define two new clades of plant reductases, formerly annotated as DRL and CCRL genes, that are distinct from the DFR, ANR, and CCR clades (Figure 4.14). These two new clades both include 92  homologs from all plant species, ranging from the moss Physcomitrella patens to various angiosperms. Strikingly, most of the species examined possess a single homolog in each clade. This indicates that these genes appeared early in evolution and were likely present in a common land plant ancestor (Figure 4.14; see the list of genes in Table 4.2), and may be enzymes ancestral to CCR and DFR. As previously reported, Arabidopsis ACOS5, PKSA, and PKSB genes show similar patterns of phylogenetic conservation (de Azevedo Souza et al., 2009; Kim et al., 2010), and, like ACOS5, PKSA, and PKSB homologs, a TKPR homolog is expressed in male organs of rice (Oryza sativa). These results suggest conservation of the biosynthetic pathway involving ACOS5, PKS, and TKPR activities that leads to sporopollenin precursors in land plants, and that this pathway was present early in land plants, including the last common ancestor of bryophytes and angiosperms.  93    Figure 4.14 Phylogenetic analysis of DFR and DFR related protein sequences in Arabidopsis, poplar, rice, and Physcomitrella.  An unrooted maximum-likelihood tree was constructed from aligned sequences using PhyML 2.4.4. Bootstrap values (1000 replicates) above 70% are shown on branches. Clades highlighted in orange contain Arabidopsis genes that are co-expressed in silico and relative to exine development. ANR, anthocyanin reductase; CCR, cinnamyl CoA reductase; CCRL, CCR-like; DFR, dihydroflavonol reductase; DFRL; DFR-like, TKPR, tetraketide α-pyrone reductase. The protein encoded by a rice gene annotated as OsDFR2 (GenBank Accession AF134807) and expressed in tapetum cells during anther development is indicated by a flash. Protein sequences used in this analysis are given in Appendix C., and the alignment is available in Appendix D. The scale represents 0.5 amino acid changes.    94  Table 4.2 Putative TKPR orthologs and expression in other species.  Species Gene name Accession or gene model Expression Arabidopsis thaliana AtTKPR1 At4g35420 Tapetum 1  Populus trichocarpa PoptrDFRL1 fgenesh4_pm.C_LG_VIII000606 N/A Oryza sativa OsDFR2 AF134807; Os09g32020 Tapetum 2  Immature panicle 3   No name Os08g40440 Immature panicle 3  Physcomitrella patens PpDFRL1 e_gw1.144.123.1 Ppa.26189 (PHYPADRAFT_86351) Sporophyte 4  Arabidopsis thaliana AtTKPR2 At1g68540 Tapetum, Tetrad 1   No name At1g25460 Young Seed, silique 5  Populus trichocarpa PoptrDFRL2 fgenesh4_pg.C_LG_VIII001076 N/A  PoptrDFRL4 estExt_fgenesh4_pg.C_LG_X1136 N/A Oryza sativa No name Os01g03670 Tetrad 6  Immature panicle 6  Physcomitrella patens PpDFRL2 estExt_Genewise1.C_1140128 Ppa.18009 (PHYPADRAFT_215362) Protonema 6  1  This study 2 Yau et al., Sexual Plant Reprod 2005 3 http://mpss.udel.edu/rice/ 4 http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?LID=23755&PAGE=1 5 http://bar.utoronto.ca/ 6 Huang et al., Plant physiol 2009 N/A, no information available   4.5 Discussion  In this chapter, I used reverse genetics and co-expression analysis to identify candidate oxidoreductase genes required for male fertility, exine formation and sporopollenin deposition during anther development. TKPR1 and TKPR2 were identified by their tight co-expression with ACOS5 and are closely related to the known enzymes DFR and CCR, but they have likely different functions in sporopollenin synthesis. Loss of function mutants in TKPR1 display apparently identical phenotypes of to acos5 with respect to pollen development, with arrest of pollen maturation after release from tetrads 95  and apparent lack of exine formation (de Azevedo Souza et al., 2009; Figure 4.8), whereas tkpr2 is fertile and produced pollen grains exhibiting only slightly modified exine patterns (data not shown). In situ hybridization data in my study reveals that the two genes share a highly similar transient, tapetum-localized expression over the course of anther development. However, TKPR1 expression is initiated at an earlier stage of anther development (Figure 4.3), suggesting that TKPR1-catalized sporopollenin monomer synthesis is essential at an early step of exine formation, possibly for initiating the reticulated exine pattern. As shown in phylogenetic analysis (Figure 4.14), TKPR1 lies within a clade of NADPH-dependent reductases similar to proteins encoding CINNAMYL-CoA REDUCTASE (CCR) and DIHYDROFLAVONOL 4-REDUCTASE (DFR), well known enzymes in lignin monomer and flavonoid metabolism. The close structural and phylogenetic relationship between plant CCR and DFR genes has been previously noted (Lacombe et al., 1997; Yau et al., 2005), and the close relationship of DFR to the Arabidopsis BANYLUS/ANTHOCYANIDIN REDUCTASE (BAN/ANR) gene, encoding a reductase involved in condensed tannin biosynthesis (Xie et al., 2003) and has also been noted (Devic et al., 1999). First TKPR1 function could be analagous to that of DFR, reducing a hypothetical ketone group generated from a condensing reaction catalyzed by a co-expressed PKSA/B (Kim et al., 2010) to a corresponding hydroxyl group. This reaction would be consistent with presence of oxygenated aliphatic moieties in sporopollenin, and the extensive ether and ester bonds in the polymer that would rely on polyhydroxylated sporopollenin monomers (Ahlers et al., 2000; Ahlers et al., 2003; Morant et al., 2007). Alternatively, based on the known substrates of CCR and DFR enzymes, TKPR1 could act in a manner analogous to CCR, by reducing a fatty-acyl CoA ester generated by ACOS5 to the aldehyde, or possibly on to the primary alcohol, in a manner analogous to CER4, and Arabidopsis primary alcohol forming fatty acyl-CoA reductase involved in cuticular wax biosynthesis (Rowland et al., 2006). Finally, TKPR1 could have a true DFR activity and use dihydroflavanols, such as taxifolin, as substrates to generate leucoanthocyanin products. In this chapter, I explored one possibility by which TKPR1 could participate in downstream of PKSA/B of the sporopollenin biosynthesis pathway. TKPR1 was tested 96  for activity against a synthetic alkyl phloroglucinol containing an alkyl chain bearing a ketone group, which was reported as one of the products generated by PKSA/B in vitro (Mizuuchi et al., 2008). No reduction products could be detected by GC-MS (Figure 4.12). This result indicates that TKPR1 may act on another substrate such as the tri- or/and tetraketide α-pyrones generated by PKSA and PKSB. Additionally to test the alternative possibilities that TKPR catalyzes the reduction of acyl-CoA esters to the aldehyde or alcohol, or reduction of taxifolin (dihydroquercetin) to leucoanthocyanidin, I carried out preliminary assays of recombinant TKPR against a set of cinnamoyl CoAs, fatty acyl CoAs, and taxifolin. I employed a spectrophotometric assay to monitor consumption of NADPH and used recombinant Arabidopsis CCR1 as a positive control for reduction of hydroxycinnamoyl-CoAs. While some TKPR reductase activity, judged by NADPH consumption, was observed for both cinnamoyl CoAs and fatty acyl CoAs, it was difficult to draw concrete conclusions about the biological relevance of these results since they could not be compared quantitatively to activity against potential optimal TKPR substrates (eg tetraketide -pyrones). It would be beneficial to repeat these assays to determine what products are made, test enzyme kinetic parameters against these substrates, and compare TKPR result to results from both the Arabidopsis DFR and CCR1 enzymes as positive controls. Recently biochemical data for two proteins, which were reported by our collaborator, showed that TKPR1 and TKPR2 catalyze the reduction of the ketone group on the alkyl chain of tetraketide -pyrones, generated in vitro by the sequential reactions of ACOS5 and PKSA/B, to secondary alcohols while leaving the lactone ring unaffected (Grienenberger et al., 2010). These data provide evidence that the in vivo functions of these enzymes are likely to be tetraketide -pyrone reductases and that TKPR activity creates a new alcohol function on putative alkyl -pyrone sporopollenin precursors, whose biosynthetic origin is thus distinct from those of the hydroxyl groups introduced in ω- and in-chain positions of fatty acids by CYP450 enzymes in generating such precursors (Morant et al., 2007; Dobritsa et al., 2009). However, the two reductases do not fulfill exactly the same functions in vivo. One evidence of different functions comes from the distinct subcellular localization of TKPR1 and TKPR2 analyzed by transient expression of GFP fusion proteins (Grienenberger et al., 2010). Most TKPR1 is localized 97  to the ER, similar to PKSA and PKSB (Kim et al., 2010), while TKPR2 is primarily cytosolic and not associated with ER. This ER-localization of TKPR1 suggests that it may form a metabolon composed of CYP703A2, PKS A/B and TKPR1 to yield polyhydroxylated α-pyrones in the ER. Cytosolic TKPR2 would act on different substrates in the cytoplasm, but likely one of similar structure containing a ketone group. Putative rice, poplar, and Physcomitrella TKPR1 orthologs are present in the TKPR1 clade, and the rice DFR2/Os09g32020 gene within this clade is transiently expressed in rice anther tapetum cells during microsporogenesis (Yau et al., 2005). While Yau et al., (2005) speculated that the rice DFR2/Os09g32020 gene may be required for flavonoid biosynthesis during pollen development, results in this study together with our collaborator’s data suggest instead that TKPR and its orthologs encode enzymes in a pathway for sporopollenin aliphatic monomer biosynthesis. Data in support of this hypothesis are: 1) the conservation of TKPR genes in land plants including Physcomitrella, 2) the tight co-expression of TKPR with MS2, CYP703A2, ACOS5 and PKSA/B, all required for sporopollenin biosynthesis, 3) the highly similar loss of function mutant phenotypes and transient tapetum localized expression patterns of the Arabidopsis ACOS5 and TKPR1 genes, and 4) the ability of ACOS5, PKSA/B, and TKPR1/2 to catalyze three sequential reactions leading from medium chain fatty acids to reduced alkyl -pyrones in vitro. Of the Arabidopsis genes known or inferred to be required for sporopollenin biosynthesis, CYP703A2, ACOS5, PKSA/B and TKPR1/2 are conserved in land plant lineages including Physcomitrella but are absent in Chlamydomonas (Morant et al., 2007; de Azevedo Souza et al., 2009; Kim et al., 2010). This provides strong support for an ancient origin of the biochemical pathway(s) defined by these genes, which probably arose early in land plant evolution and was likely shared by a common ancestor of bryophytes and angiosperms. Thus, acquisition of sporopollenin biosynthesis was likely a key land plant innovation essential for protection of haploid spores from desiccation, UV irradiation, and other stresses of the terrestrial environment and its evolution likely pre- dated vascular system development (Bowman et al., 2007). Further definition of the pathway defined by ACOS5, PKSA/B and TKPR1/2 at the biochemical level should not only reveal details regarding the nature of sporopollenin monomeric constituents and 98  sporopollenin structure, but also shed light on the evolution of the diversity of enzymes that generate the diversity of polyether and polyester polymers now found in plants.  99  Chapter 5. The introduction of sporopollenin biosynthesis enzymes CYP703A2, ACOS5, PKSA and TKPR1 into the yeast Saccharomyces cerevisiae in different combinations  5.1 Summary  Sporopollenin is a poorly characterized mixed aliphatic and aromatic polymer with ester and ether linkages found in the pollen exine layer. Recently, our studies including my work reported in Chapters 2, 3, and 4 have shown that polyhydroxylated α- pyrone polyketide compounds, generated by the sequential action of Arabidopsis thaliana ACOS5, PKSA/B and TKPR1/2 are potential and previously unknown sporopollenin precursors. The yeast Saccharomyces cerevisiae offers a useful system for expression of heterologous genes, including cytochrome P450 (CYP) genes, and using sets of dual expression vectors with different selectable makers it is possible to express various combinations of genes in a single stain. This system allows, for example the reconstruction of plant natural product biosynthetic pathways in yeast (Ro et al., 2004). In this Chapter, I used the yeast expression system to express different combinations of sporopollenin biosynthetic enzymes to test different models of potential sporopollenin biosynthetic pathways in vivo. Because hydroxy fatty acids and acyl-CoAs are the preferred substrates for ACOS5 and PKSA/B in vitro, CYP703A2 was first introduced alone to test the ability of CYP703A2 to generate hydroxy fatty acids. Subsequently, a CYP703A2/ACOS5 dual expresser was generated and PKSA and TKPR1 activities added alone or in combination with CYP703A2/ACOS5. Product identification was achieved by GC-FID and GC-MS. My results indicate that heterologous expression of PKSA can catalyze condensation of endogenous fatty acyl-CoAs with malonyl-CoA to generate α-pyrone triketides, while CYP703A2 and ACOS5 could not access endogenous substrates.   100  5.2 Introduction  Sporopollenin, a heterogeneous biopolymer found in the pollen exine layer and in spores of mosses, is composed of polyhydroxylated unbranched aliphatic and phenolic constituents as the main monomeric units (Scott et al., 2004). These units are covalently coupled by ether linkages in order to provide the characteristic high resistance to chemical degradation (Scott et al., 2004). In a previous study, an exine defective, partially male sterile mutant of Arabidopsis CYP703A2, a member of cytochrome P450 super gene family was reported (Morant et al., 2007). CYP703A2 hydroxylated medium-chain saturated fatty acids to the corresponding mono-hydroxyl fatty acids, with a preferential hydroxylation of lauric acid (C12:0) at the C-7 position in vitro and in vivo (Morant et al., 2007). A model for the role of CYP703A2 was proposed to explain its involvement of sporopollenin formation, suggesting that it is involved in generating hydroxy fatty acid components of mixed fatty acyl-phenolic sporopollenin polymer (Morant et al., 2007). Recently, we showed that an evolutionariy conserved metabolic pathway involving fatty acyl-CoA condensation and extension followed by reduction, catalyzed by POLYKETIDE SYNTHASE A and B (PKSA/B) and and TETRAKETIDE -PYRONE REDUCTASE (TKPR) enzymes respectively, leads to polyketide α-pyrone compounds that are essential sporopollenin precursors (Grienenberger et al., 2010; Kim et al., 2010). Based on these results, we proposed a model for sporopollenin precursor biosynthesis that includes different possibilities for the sequential actions of the enzymes involved in α- pyrone sporopollenin unit synthesis. After CoA ester formation by ACOS5, PKSs can catalyze acyl-CoA condensation with malonyl CoA and extension to generate tri- and tetraketide α-pyrones (Figure 5.1, route 1). CYP450 hydroxylases involved in sporopollenin biosynthesis have been shown to be active on free fatty acids (Morant et al., 2007; Dobritsa et al., 2009), thus implicating putative thioesterase and CoA ester regeneration steps upstream and downstream of the hydroxylation step as shown on the left side of the scheme (Figure 5.1, route A). We have shown that hydroxy fatty acyl- CoAs are the most efficient substrates for PKSA and PKSB, consistent with an ER localization (Kim et al., 2010), and can yield various hydroxy polyketides (route 2). These latter compounds might also arise from the hydroxylation of the alkyl α-pyrones by CYP450s (route B), but this possibility remains to be examined experimentally. Finally, 101  reduction of the carbonyl function of the hydroxy tetraketide α-pyrones by TKPRs gives rise to an additional hydroxyl function in the alkyl chain of the polyketide products, generating more highly hydroxylated polyketides that are proposed constituents of a sporopollenin polymer highly cross-linked by ester and ether bonds. The association of TKPR1 with ER, where hydroxylation by P450s takes place, may be important in this respect.   Figure 5.1 A putative scheme of sporopollenin biosynthesis (Grienenberger et al., 2010). Image was reprinted with permission of American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).  Fatty acid biosynthesis is an essential metabolic process. Unlike plants, which use the plastid as their fatty acid biosynthetic site, the yeast Saccharomyces cerevisiae synthesizes fatty acids predominantly in the cytoplasm. Fatty acid biosynthesis in yeast is carried out by a multifunctional type I protein composed of two polypeptide chains (α and β) (Lynen, 1980; Schweizer and Hofmann, 2004), whereas in plant plastids and bacteria, it is catalyzed by a type II fatty acid synthase (FAS), which is dissociable and typically consists of more than 8 separate proteins. The major fatty acids produced in yeast are 102  palmitoleic acid (C16:1), palmitic acid (C16:0), oleic acid (C18:1) and stearic acid (C18:0), which are required to generate lipids for biological membranes (Dittrich et al., 1998). In this study, the metabolic changes in yeast Saccharomyces cerevisiae containing CYP703A2, ACOS5, PKSA and TKPR1 in different combinations were examined by GC-MS.  5.3 Materials and methods  5.3.1 Construction of CYP703A2, ACOS5, PKSA and TKPR1 in pESC vector  Coding regions of CYP703A2, ACOS5, PKSA and TKPR1 were amplified by PCR using Phusion High Fidelity DNA polymerase (New England Biolabs). Each gene- specific primer was designed with an appropriate restriction enzyme site and a yeast consensus sequence for proper initiation of translation (Cigan and Donahue, 1987; Romanos et al., 1992). The sequence for primers is listed in Table 5-1. The PCR fragements were subcloned into pGEM-T vector for sequence verification as well as manipulation. After the digestion with a restriction enzyme, the products were subcloned into pESC vector containing one of four different auxotrophic selectable markers (HIS3, TRP1, LEU2, or URA3) for expression in yeast.  5.3.2 Yeast strains, culture and heterologous expression in yeast  Various strains of the yeast Saccharomyces cerevisiae were used. Untransformed YPH499 strain (MATa, ura3-52, lys2-801, ade2-101, trp1-Δ63, his3-Δ200 leu2- Δ1) and WAT11 (MATa; ade2–1; his3–11,-15; leu2–3,-112; ura3–1; canR; cyr+) were maintained in YPAD medium containing 0.08 g/L adenine hemisulfate salt, 10 g/L  yeast extract, 10 g/L Bactopeptone, and 20 g/L  dextrose. For solid medium, 15 g/L of agar was supplemented. In the WAT11 strain, the yeast reductase was replaced by the ATR1 reductase from Arabidopsis thaliana, controlled by the GAL10-CYC1 promoter (Pompon et al., 1996). Transformed strains with pESC were screened and maintained in each amino acid dropout minimal medium. For example dropout synthetic minimal medium 103  contained 6.7 g/L yeast nitrogen base without amino acids (BD science), 1.3 g/L His- dropout amino acid powder (Sigma), and 20 g/L dextrose (for synthetic dextrose [SD]- His dropout medium) or galatose (for synthetic galactose [SG]-His dropout medium). All the yeast expression vector stocks were independently transformed into yeast strains by the polyethylene glycol-LiAc method (Gietz et al., 1992). Briefly, a fresh yeast culture (OD600 = 0.25) was grown in complete YPAD medium for 5 hr. The cells were collected, washed twice with water and resuspended in 1.5 mL of a 0.1 M lithium acetate (LiAc) solution in TE buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA). For transformation, salmon sperm was added as DNA carrier (100 µg from a10 mg/mL solution in TE after 10 min boiling) to 1 ug of plasmid DNA. 100 µL of competent yeast cells and 250 µL of 50% polyethylene glycol 3500 in LiAc solution in TE buffer were added. The mixture was incubated for 1 hr at 42°C. After centrifugation, the transformed yeast cells were collected and then plated on SD minimum medium. Strains transformed with pESC were grown for 2 to 3 days at 30°C. For gene induction, transformed yeast strains were subcultured in 10 mL of SD minimum dropout  medium overnight. Cell densities were determined at OD600 and cell aliquots sufficient to obtain on OD600 of 0.4 in 50 mL of SG induction medium calculated. Culture pellets from these aliquiots were resuspended in 1 mL of SG induction medium and inoculated into 50 mL of SG medium. For exogenous fatty acid feeding experiment, 1 mM each fatty acid was added to SG induction medium with 150 µL 100% ethanol. Yeast cells were cultured at 28°C on a shaker at 200 rpm for 20 hr to 24 hr. The cell pellets were washed once with PBS buffer (140 mM NaCl, 3 mM KCl, 10 mM Na2HPO4, and 2 mM KH2PO4, pH of 7.4) and centrifuged at 1500 x g for 15 min. The cell pellets were stored at -80C for further studies. Time-dependent sampling was performed aseptically during 24 hr by taking out 1 mL aliquots from main culture. Samples were diluted 10x immediately in corresponding culture medium, and then subjected to duplicate absorbance determination in a spectrophotometer at 600 nm. Diluted cell-free medium was used to establish background readings and set zero absorbance levels. Values were averaged and corrected for dilution.  104  5.3.3 SDS-PAGE and immuno-blotting  Fresh or frozen yeast cell pellets were resuspended in 500 µL breaking buffer (50 mM sodium phosphate, pH 7.4, 1 mM EDTA, 5% glycerol and 1 mM PMSF) and centrifuged at 1500 g for 5 min at 4°C to pellet cells. After resuspending the cells in a volume of breaking buffer to obtain an OD600 of 50-100, an equal volume of 0.4-0.6 mm acid-washed glass beads (Sigma) were added and vortexed four times for 30 sec, followed by 30 sec on ice to lyse the cells. Prepared soluble total protein samples were separated on 10% polyacrylamide gels and either stained with Coomassie blue or transferred to PVDF membrane (GE Healthcare) for immunoblot analysis. The membranes were incubated in blocking buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 100 mM NaCl, 0.1% Tween-20) supplemented with 10% (w/v) non-fat dried milk powder. Alkaline Phosphatase (AP)-conjugated antibodies used, depending on target proteins, were anti-FLAG (Sigma) and anti-cMyc (Invitrogen), which were diluted at 1:1000 and 1:2000 in blocking solution, respectively. Immuno-detection was performed by adding 200 µL NBT/BCIT (Roche) in 20 mL staining buffer (100 mM Tris-HCl, pH9.5, 100 mM NaCl, 50 mM MgCl2).  5.3.4 Chemical analysis of yeast expression product  Total fatty acids in yeast cell extracts were transmethylated by adding 1 mL methanolic-HCl and incubating at 80°C for 1hr to 2hr. To obtain organic extracts, 1.5 mL hexane was added followed by vortexing. The organic phases were pooled and evaporated under nitrogen gas. For GC-MS  analyses, extraction from reaction mixture, derivatization of organic compounds and running condition of samples in GC-MS are described by Wang et al., (2010), except the following: the  oven temperature was programmed for 2 min at 50°C, followed  by a 40°C min –1  ramp to 120°C, held at 120°C  for 2 min, increased by 2°C min –1  to 225°C, and  held at 320°C for 10 min.   105  5.4 Results  5.4.1 CYP703A2 and/or ACOS5 expression in yeast  The cDNAs for CYP703A2 and ACOS5 were amplified, cloned into yeast vectors, and expressed to reconstruct the potential entry point of the sporopollenin monomer biosynthesis pathway in yeast cells. To generate CYP703A2, ACOS5, and CYP703A2/ACOS5 dual-expressing yeast strains, each cDNA was cloned into the pESC- His vector under the control of Gal1 promoter for ACOS5 and Gal10 promoter for CYP703A2, where they were expressed as fusions to the cMyc epitope tag (ACOS5) and FLAG epitope tag (CYP703A2). Functional expression of the two genes in yeast was verified by immunoblot analysis, using monoclonal anti-FLAG and anti-cMyc antibodies to detect epitope-tagged CYP703A2 and ACOS5, respectively (Figure 5.2). The CYP703A2 recombinant protein was not detected in the cytosolic fraction but rather in cell debris, indicating insoluble status embedded in microsomes, while ACOS5 was detected in both fractions of transformed yeast strains (Figure 5.2). Growth rates of yeast strains cultured in SG induction medium were monitored from initial OD 0.4 for 24 hr. Empty vector control strains increased up to OD600 of 5.32±0.09 while the cell growth of ACOS5 sole-, CYP703A2 sole- and CYP703A2/ACOS5 dual-expression strains was repressed, reaching ODs of 2.01±0.05, 2.00±0.08 and 2.00±0.02 at 24 h, respectively. 106    Figure 5.2 Immunoblot detection of CYP703A2 and ACOS5 proteins in transgenic yeast strains.  (A) Immunoblot analysis of proteins from cell debris (lane 1 and 2) and cytosolic fraction (lane 3 and 4) in the CYP703A2 expresser, reacted with a FLAG monoclonal antibody to detect CYP703A2. Lane 1 and 3, 16 hr culture; lane 2 and 4, 24 hr culture (B) Immunoblot analysis of proteins from cytosolic fraction in ACOS5 expresser reacted with a cMyc monoclonal antibody to detect ACOS5. Lane 1, 16 hr culture; lane 2, 24 hr culture (C) Immunoblot analysis of proteins from cytosolic fraction (lane 1, 2, 3 and 4) and cell debris (lane 5, 6, 7 and 8) in CYP703A2/ACOS5 dual expresser, reacted with a cMyc monoclonal antibody to detect ACOS5. Lane 1 and 5, 3 hr culture; lane 2 and 6, 9 hr culture; lane 3 and 7, 19 hr culture; lane 4 and 8, 24 hr culture (D) Immunoblot analysis of proteins from cytosolic fraction (lane 1, 2, 3 and 4) and cell debris (lane 5, 6, 7 and 8) in the CYP703A2/ACOS5 dual expresser, reacted with a FLAG monoclonal antibody to detect CYP703A2. Lane 1 and 5, 3 hr culture; lane 2 and 6, 9 hr culture; lane 3 and 7, 19 hr culture; lane 4 and 8, 24 hr culture   To assay the fatty acid (FA) metabolic profile in each strain, lipophilic  compounds were extracted with hexane and then derivatized. The FA 107  derivatives were identified by comparing their gas chromatography-mass spectrometry (GC-MS) characteristics with literature data. CYP703A2 preferentially catalyzes hydroxylation of lauric acid (C12) at the C-7 position in vitro (Morant et al., 2007). Because in yeast cells medium-chain fatty acids such as C12 FA are expected to be mostly intermediate products maintained as thioester conjugates to the acyl carrier protein (ACP) during fatty acid synthesis, Arabidopsis CYP703A2 may not be able to access endogenous medium-chain yeast FAs proposed to be the starting points for the sequential reactions of sporopollenin biosynthesis by Grienenberger et al., (2010). Thus, first I tested the ability of CYP703A2 to use C12 FA (lauric acid) fed exogenously to the growth media. Surprisingly, no new peaks were present in the chromatogram of the CYP703A2 expression strain compared with the empty vector strain under these conditions (Figure 5.3). The possibility that CYP703A2 might preferentially accept long- chain fatty acids in vivo was tested by feeding palmitic acid (C16:0) to the growth media. Whereas C16 FA was accepted as a substrate by CYP703A2 in yeast microsomes with 5 to 10% efficiency to generate hydoxy C16 FA derivatives (Morant et al., 2007), I could not identify hydroxyl C16 FAs. In parallel, the FA composition of ACOS5 and CYP703A2/ACOS5 dual-expressing strains was also assayed after feeding C12 FA. In both strains two new peaks; corresponding to myristic acid (C14:0) and tetradecenoate (C14:1) were observed in GC chromatograms (Figure 5.3). These C14 FA derivatives were never observed in the absence of exogenously supplied C12 FA.   108    109    Figure 5.3 GC analysis of fatty acid metabolites produced by vector control and transgenic yeast strains.  GC chromatograms of extracts from different yeast strains are shown. Fatty acid derivatives were converted into methyl esteresters or trimethylsilyl esters prior to GC analysis. 1, dodecanoic acid methyl ester (C12); 1-1, dodecanoic acid trimethylsilyl estertrimethylsilyl ester (C12); 2, 9-hexadecenoic acid methyl ester(C16:1); 2-1, 9- hexadecenoic acid trimethylsilyl estertrimethylsilyl ester (C16:1); 3, hexadecanoic acid methyl estermethyl ester (C16); 3-1, hexadecanoic acid trimethylsilyl ester (C16); 4, 9- octadecenoic acid methyl estermethyl ester (C18:1); 5, octadecanoic acid methyl estermethyl ester (C18); A, 11-tetradecenoic acid methyl ester (C14:1); B, tetradecanoic acid methyl ester (C14); C, tetradecanoic acid trimethylsilyl ester; *, 9-hexadecenoic acid (C16:1); **, dodecanoic acid (C12).  5.4.2 Triple and quadruple expression in yeast  The yeast strain transformed with pESC-HIS::CYP703A2/ACOS5 was co- transformed together with pESC-Ura::TKPR1, Ura::PKSA or Ura::PKSA/TKPR, to generate three different yeast strains: two triple-expressing strains expressing CYP703A2/ACOS5/TKPR1 and CYP703A2/ACOS5/PKSA, and one quadruple-expressing strains expressing all candidate genes, CYP703A2/ACOS5/PKSA/TKPR1. Immunoblot analysis failed to detect PKSA recombinant protein in either triple or quadruple expressers using the anti-cMyc antibody (Figure 5.4). However, FLAG-tagged TKPR1 was detected in the cytosolic fraction as well as in cell debris from both triple- and quadruple-transformed yeast strains (Figure 5.4). The OD600 of each strain increased from the initial value of 0.4 up to 5.60±0.09 for empty vector control, 5.71±0.10 for 110  CYP703A2/ACOS5/TKPR1 expresser, 4.32±0.21 for CYP703A2/ACOS5/PKSA expresser and 4.43±0.05 for CYP703A2/ACOS5/PKSA/TKPR1 expresser, respectively. These data suggest that accumulation of TKPR1 or/and PKSA can rescue the repressed growth rate due to the expression of CYP703A2 or/and ACOS5 in yeast cells. Moreover addition of the PKSA gene to both CYP703A2/ACOS5 and CYP703A2/ACOS5/TKPR1 expressers slightly reduced the growth rates. Therefore, it is likely that PKSA enzyme is present even though I could not detect the fusion tagged version using the anti-cMyc antibody.     Figure 5.4 Immunoblot detection of CYP703A2, ACOS5 and TKPR1 proteins in transgenic yeast strains.  (A) Immunoblot analysis of proteins from cell debris (lane 1 and 2) and cytosolic fraction (lane 3 and 4) in CYP703A2/ACOS5/TKPR1 triple expresser, reacted with a FLAG monoclonal antibody to detect CYP703A2 and TKPR1 (lane 1 and 2) as well as cMyc monoclonal antibody to detect ACOS5 (lane 3 and 4). (B) Immunoblot analysis of proteins from cell debris (lane 1 and 2) and cytosolic fraction 111  (lane 3 and 4) in CYP703A2/ACOS5/PKSA triple expresser, reacted with a FLAG monoclonal antibody to detect CYP703A2 (lane 1 and 2) as well as cMyc monoclonal antibody to detect ACOS5 and PKSA (lane 3 and 4). (C) Immunoblot analysis of proteins from cell debris (lane 1 and 2) and cytosolic fraction (lane 3, 4, 5 and 6) a in CYP703A2/ACOS5/PKSA/TKPR1 quadruple expresser, reacted with a FLAG monoclonal antibody to detect CYP703A2 and TKPR1 (lane 1, 2, 3 and 4) as well as cMyc monoclonal antibody to detect to detect ACOS5 and PKSA (lane 5 and 6). Lane 1, 3 and 5, 9 hr culture; lane 2, 4 and 6, 24 hr culture; black arrow head indicates TKPR1.   To explore the potential products generated by the sequential actions of the sporopollenin monomomer biosynthetic enzymes in triple or quadruple expressers in vivo, total lipophilic compounds ranging from medium FA derivatives to very long chain FA derivatives were profiled by GC-MS. Whereas triple expression of CYP703A2/ACOS5/TKPR1 did not result in metabolites changes compared with the empty vector strain, the CYP703A2/ACOS5/PKSA and CYP703A2/ACOS5/PKSA/TKPR1 expressers generated two unique peaks in GC chromatograms (Figure 5.5). Each peak had three fragments of the same characteristic masses (183, 198 and 211 m/z) while the two peaks had two different total masses (392 and 394 m/z). Since these novel peaks were present only in PKSA expressing strains, they are likely to be polyketide products, supporting the presence of active PKSA enzymes in the strains (Figure 5.6). Interestingly the total level of these novel peaks were much lower in the CYP703A2/ACOS5/PKSA/TKPR1 expresser than in the CYP703A2/ACOS5/PKSA expresser (Figure 5.5). These data indicate that the TKPR1 enzyme could act on the product generated by PKSA, leading to new compounds not detected in this metabolic profile. Alternatively, TKPR1 could metabolize endogenous PKSA substrates into unknown products, making them less available for PKSA activity. 112    Figure 5.5 GC analysis of fatty acid metabolites produced by vector control and transgenic yeast strains.  GC chromatograms of extracts from different yeast strains are shown. Fatty acid derivatives were converted into methyl esters or trimethylsilyl esters prior to GC analysis. 113  1-1, dodecanoic acid trimethylsilyl ester (C12); 2, 9-hexadecenoic acid methyl ester (C16:1); 2-1, 9-hexadecenoic acid trimethylsilyl ester (C16:1); 3, hexadecanoic acid methyl ester (C16); 3-1, hexadecanoic acid trimethylsilyl ester (C16); 4, 9-octadecenoic acid methyl ester (C18:1); 4-1, 9-octadecenoic acid trimethylsilyl ester (C18:1); 5, octadecanoic acid methyl ester (C18); 5-1, octadecanoic acid trimethylsilyl ester (C18); 6, 9-hexanedioic acid 2,3-bis ester; arrow heads indicate novel compounds generated by PKSA.      Figure 5.6 Mass spectra of two novel metabolites found in yeast strains expressing CYP703A2/ACOS5/PKSA or CYP703A2/ACOS5/PKSA/TKPR1.  Two mass spectra have three common characteristic peaks: 183, 198 and 211, together with different possible total molecular weight, 392 and 394, respectively. Upper spectrum was obtained at approximately 47.3 min of retention time and lower spectrum at approximately 48.3 min.   114  5.4.3 PKSA and/or TKPR1 expression in yeast  In vitro studies have shown that PKSA produces tri- and tetraketide α-pyrones by condensation of fatty acyl CoAs with malnoyl-CoAs (Mizuuchi et al., 2008; Dobritsa et al., 2010; Kim et al., 2010) and that TKPR1 reduces the keto function of tetraketide α- pyrone compounds synthesized by PKSA in vitro (Grienenberger et al., 2010). To determine the in vivo products generated by PKSA or/and TKPR1 using potential substrates present in wild-type yeast strains, PKSA, TKPR1, and PKSA/TKPR1 dual- expressing yeasts were generated. As with previous experiments 5.4.2, immunoblots failed to detect PKSA proteins in either PKSA or PKSA/TKPR1 expressers, whereas a high expression level of TKPR1 was found in soluble lysates as well as from cell debris from both TKPR1- and PKSA/TKPR-transformed yeast strains (Figure 5.7). The cell densities of each strain were measured at four time points during 24 hr culture. In most yeast strains, growth rates reached approximately 5 at OD600, except for PKSA/TKPR1 expresser showing 2.24±0.15. GC-MS analysis revealed that a total of six unidentified compounds were exclusively present in PKSA/TKPR1 dual-expressing yeasts (Figure 5.8). Figure 5.9 illustrates mass spectra containing not only the same characteristic mass (183, 198 and 211 m/z) reported in 5.4.2 but also different total mass (338, 366, 392, 394, 420 and 422 respectively). These new compounds could be potential in vivo compounds generated by PKSA or PKSA as well as TKPR even though they could not be identified by comparison to the library of mass spectra or theliterature.  115    Figure 5.7 Immunoblot detection of TKPR1 proteins in transgenic yeast strains.  (A) Immunoblot analysis of proteins from cytosolic fraction (lane 1, 2 and 3) and cell debris (lane 4, 5 and 6) and in PKSA/TKPR1 dual expresser, reacted with a FLAG monoclonal antibody to detect TKPR1. Lane 1 and 4, 12 hr culture; lane 2 and 4, 18 hr culture; lane 3 and 6, 24 hr culture (B) Immunoblot analysis of proteins from cytosolic fraction (lane 1 and 2) and cell debris (lane 3 and 4) and in TKPR1 expresser, reacted with a FLAG monoclonal antibody to detect TKPR1. Lane 1 and 3, 24 hr culture; lane 2 and 4, 9 hr culture   116     Figure 5.8 GC analysis of fatty acid metabolites produced by vector control and PKSA/TKPR1 expressing yeast strains.  Fatty acid derivatives were converted into methyl esters or trimethylsilyl esters prior to GC analysis. Total six new compounds (A to F) were detected in PKSA/TKPR1 expresser. 1-1, dodecanoic acid trimethylsilyl ester (C12); 2, 9-hexadecenoic acid methyl ester (C16:1); 2-1, 9-hexadecenoic acid trimethylsilyl ester (C16:1); 3, hexadecanoic acid methyl ester (C16); 3-1, hexadecanoic acid trimethylsilyl ester (C16); 4, 9-octadecenoic acid methyl ester (C18:1); 4-1, 9-octadecenoic acid trimethylsilyl ester (C18:1); 5, octadecanoic acid methyl ester (C18); 5-1, octadecanoic acid trimethylsilyl ester (C18); 6, 9-hexanedioic acid 2,3-bis ester.   117    118    Figure 5.9 Mass spectra of novel peaks from the GC chromatogram obtained from the yeast strain expressing PKSA/TKPR1.  Each mass spectrum has three common characteristic peaks at m/z 183, 198 and 211, together with different possible total molecular weights of 338, 366, 392, 394, 420 and 422, respectively. Spectra were obtained at 33.89 min (A), 41.21 min (B), 47.30 min (C), 48.35 min (D), 53.34 min (E) and 54.33 min (F) of retention time.  119    Figure 5.10 Predicted GC-MS fragmentation patterns and estimated molecular weights of α-pyrones containing various alkyl chain lengths.  (A) Based on characteristic m/z values from mass spectra in Figure 5.9, predicted fragments are drawn for triketide compound (A) and possible alkyl chains on the R position (B). Calculated molecular weights of alkyl α-pyrones are 338, 366, 394 and 422 from R-group alkyl chain lengths of C11, C13, C15 and C17, respectively. These values correspond to total molecular weight (m/z) present in Figure 5.9. Both 392 and 420 (m/z) would be unsaturated alkyl chains containing one double bond, of which start molecules are likely 9-hexadecenoic acid (C16:1) and 9-octadecenoic acid methyl ester (C18:1).   5.5 Discussion  Based on phenotypic, genotypic, in vitro biochemical data (Grienenberger et al., 2010; Kim et al., 2010), I postulated that CYP703A2, ACOS5, PKSA and TKPR1 work in the same biochemical pathway in vivo (Figure 5.1). However, as a reductase, it is 120  possible that in vivo TKPR1 acts directly on the CoA ester product of ACOS5 rather than on the polyketide product of PKSA as shown in Figure 5.1, which predicts that the in vivo fatty acid CoA ester of ACOS5 is the in vivo substrate of PKSA. I used a yeast system for expressing up to four heterologous genes to test different models of biosynthetic pathways involving these four enzymes. In vitro assays indicate that hydroxy fatty acids are the preferred substrates of ACOS5 and PKSA (de Azevedo Souza et al., 2009; Grienenberger et al., 2010). Thus, expression of CYP703A2 was tested first for its ability to generate hydroxy fatty acids in yeast. In spite of strong growth inhibition by CYP703A2 expression, no significant change in the fatty acid profile was detected by GC-FID and GC-MS in this yeast strain. Feeding of exogenous lauric acid (C12), which is the most highly preferred CYP703A2 substrate in vitro (Morant et al., 2007) did not result in hydroxy lauric acid accumulation in this strain. One possible explantion for these results is a lack of CYP703A2 activity due to misfolded protein or protein aggregates. In eukaryotes, properly folded cytochrome P450 enzymes are often localized to the ER membrane, anchored by a short hydrophobic sequence that exposes their enzymatically active domain into the cytoplasm, and misfolding or mislocalization could lead to loss of enzyme activity. Alternatively, endogenous or exogenously added C12 may not have been accessible to the enzyme in these strains if it does not exist in the acid form at significant concentrations. For example, fatty acids are not freely available in plants but are generally present as triacylglycerol or CoA ester forms (Morant et al., 2007). Even though a small amount of endogenous lauric acid derivative (dodecanoic acid trimethylsilyl ester) was detected in vector- control yeast cells by GC-MS (compound 1-1, Figure 5.5), it is not known if this derivative is derived from free lauric acid. To further test for CYP703A2 activity in this strain, CYP703A2-containing microsomes could be extracted and incubated with free lauric acid to determine if the hydroxy-lauric acid can be produced in vitro. While no significant change in the fatty acid profile was detected in the CYP703A2 expresser, ACOS5 expression altered the yeast fatty acid profile (Figure 5.3). In Saccharomyces cerevisiae, palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0) and oleic acid (C18:1) are the major fatty acyl constituents (Tuller et al., 1999), 121  while medium and short chain fatty acids, especially those less than C14, comprise less than 2% of total fatty acids (Tuller et al., 1999). Normally, only traces of endogenous medium chain fatty acids were detected in this study (Figure 5.3 and 5.5). However, it was striking that both the ACOS5 expresser and the CYP703A2/ACOS5 dual expresser accumulated tetradecanoic acid (C14) as well as 11-tetradecenoic acid (C14:1) upon feeding exogenous lauric acid (C12) (Figure 5.3). These data suggest that ACOS5 can generate accumulation of C14 fatty acyl-CoA esters from high levels of lauric cytoplasmic acid (C12). This is consistent with in vitro assays of ACOS5 activity that show a clear substrate preference for C10 to C14 fatty acids (de Azevedo Souza et al., 2009). This accumulation of C14 fatty acid derivatives was not observed in expresser without feeding lauric acid (data not shown). In the future, it would be beneficial to test whether accumulated C14 fatty acid derivatives are derived from exogenous lauric acid by feeding radio-labeled lauric acid to the growth media. Novel products were found in PKSA expressing strains, and GC-MS analysis indicated chemical structures consistent with triketide α-pyrone accumulation in these strains (Figure 5.10). This is consistent with previous studies suggesting that PKSA catalyzes the condensation of malonyl-CoA units with fatty acyl-CoAs of various chain lengths in vitro (Mizuuchi et al., 2008; Dobritsa et al., 2010; Kim et al., 2010). Based on the total masses of the putative α-pyrone polyketides that accumulated, it appears that PKSA accepts C12:0, C14:0, C16:0, C16:1, C18:0 and C18:1 fatty acids in vivo to generate triketide α-pyrones. Pentadecyl triketide α-pyrones, generated from condensation of C16:0 or C16:1 with malonyl-CoA were the major products in these yeast strains, suggesting that C16 and C16:1 are preferable substrates for PKSA in vivo. These results are consistent with our in vitro data (Kim et al., 2010) and the recent report (Mizuuchi et al., 2008), showing the production of triketide and tetraketide α-pyrones by condensation with long-chain fatty acyl-CoAs (up to C20 chain length) and malonyl-CoA. Interestingly while C12 and C14 fatty acid derivatives were not detected by GC, undecyl and tridecyl triketides α-pyrones generated by condensation reaction with C12 and C14, respectively, were present in the PKSA/TKPR1 expresser (Figure 5.8). This suggests that PKSA might have a higher affinity for medium chain fatty acyl-CoAs than acyl-CoA thioesterases catalyzing the hydrolysis of acyl-CoAs to the free acids and CoAs for 122  further reaction. The estimated molecular weights of triketides and tetraketides as well as the congruence of predicted and observed fragmentation patterns of triketide α-pyrones suggests that PKSA generated triketide α-pyrones, rather than tetraketide α-pyrones (the TKPR1 substrate in vitro; Grienenberger et al., 2010), accumulate in PKSA-expressing yeast strains. Moreover, no significant changes in the metabolite profiles were detected in strains expressing TKPR1, such as CYP703A2/ACOS5/TKPR1 and CYP703A2/ACOS5/PKSA/TKPR1expresser, even though TKPR1 was clearly present in both soluble and in cell debris fractions of these strains. The likely reason for the lack of TKPR1-specific products in these strains is that TKPR1 substrates were absent. We previously observed that the tri- to tetraketide α-pyrone ratio is inversely correlated with the level of activity of the PKSA enzyme preparation, suggesting that the triketide α- pyrone represents a derailment reaction product due to incomplete catalysis (Kim et al., 2010). Thus, heterologously expressed Arabidopsis PKSA apperars to perform only two round of condensation with malonyl-CoA in yeast cells, generating a trikedtide α-pyrones that do not provide substrates for TKPR1. While tetraketide alkyl-α-pyrones were not generated in yeast strains expressing PKSA, these results support an in vivo function of PKSA in generating alkyl-α-pyrones. In addition, my results suggest that TKPR1 does not reduce the acyl-CoA esters to aldehydes or alcohols in vivo, as postulated in Chapter 4.  123  Chapter 6. Conclusion and future directions   Formation of pollen and spore walls requires the deposition of sporopollenin to protect the gametophyte from desiccation, temperatures, UV light and mechanical damages. The biochemically and physically extremely resistant nature of sporopollenin has been an obstacle to precise determination of the constituents of exine. A few chemical analyses by nuclear magnetic resonance (NMR) have demonstrated that sporopollenin is composed of polyhydroxylated unbranched aliphatic and phenolic constituents as the main monomeric units. These units are covalently coupled by ester and ether linkages to provide the characteristic high resistance to chemical degradation. Our reverse genetic approach to elucidate the pathway of sporopollenin monomer biosynthesis provides evidence that medium to long-chain (i.e. C12 to C18) hydroxy fatty acids as well as tri- and tetraketide α-pyrones are likely important precursors of building blocks of sporopollenin. Moreover, the remarkable conservation of CYP703A2 (Morant et al., 2007), ACOS5 (de Azevedo Souza et al., 2009), PKSA/B and TKPR1/2 genes in land plants suggests that these enzymes are part of an ancient sporopollenin biosynthetic pathway. We showed that fatty acid modification such as hydroxylation (CYP703A2), CoA esterification (ACOS5), condensation with malonyl-CoA (PKSA and PKSB) and reduction of a carbonyl group (TKPR1 and TKPR2) are key steps for sporopollenin biosynthesis in the tapetum. However, confirmation that these sequential biochemical reactions also take place in vivo is still needed. We proposed different possibilities for the sequential actions of CYP703A2, ACOS5, PKSA/B and TKPR1/2, based on in vitro biochemical assays and subcellular localization (Grienenberger et al., 2010). In Chapter 5, yeast strains expressing various combinations of CYP703A2, ACOS5, PKSA and TKPR1 were generated to test the potential sequential pathway in vivo. Kinetic parameters provided by collaborators have indicated that hydroxy fatty acids and hydroxy fatty acyl- CoA are preferred substrates of ACOS5 (de Azevedo Souza et al., 2009) and PKSA (Kim et al., 2010), respectively. Thus, my hypothesis is that fatty acid hydroxylation is the first reaction in the sequence leading to sporopollenin monomer biosynthesis. Unfortunately, possibly due to the failure of CYP703A2 and ACOS5 to gain access to appropriate 124  endogenous substrates in yeast cells, these two putative sequential reactions could not be reproduced in vivo. In the future, it would be interesting to test the sequential pathway in yeast cells expressing PKS and TKPR fed with exogenous hydroxy fatty acyl CoAs such as 12-OH-C18-CoA and 16-OH-C16-CoA. If these compounds penetrate yeast cell plasma membrane and are able to be accessed by PKS and TKPR, I expect that the hydroxy fatty acyl CoAs would be used as substrates by these enzymes to generate hydroxy alkyl α-pyrones. Expression of PKSA in the yeast showed PKSA can catalyze condensation of a broad range of endogenous fatty acyl-CoAs in vivo (Chapter 5). In such cells with increased pool sizes of the preferred substrates (i.e. hydroxy fatty acyl CoAs), PKSA may be much less active in catalyzing condensation of endogenous fatty acyl- CoAs due to the competition with the exogenously fed substrates. This could confirm not only the importance of hydroxylation of fatty acids for the pathway but also the in vivo preference of PKSA for hydroxy fatty acyl CoAs. In addition, we could test an alternative pathway (route B, Figure 5.1), which postulates hydroxylation reactions occurring on polyketides rather than on fatty acids, by using the CYP703A2/PKSA dual-expresser and CYP703A2/PKSA/TKPR1 triple-expresser. While CYP703A2 has been shown to in- chain hydroxylate lauric acid (C12:0) (Morant et al., 2007), we cannot rule out the possibility that CYP703A2 hydroxylates alkyl α-pyrones in the last step of potential sequential reaction. If hydroxyl alkyl α-pyrones were present in metabolic profiles of CYP703A2/PKSA expressers, it would support the alternative pathway in which these novel alkyl α-pyrones are the true substrates to CYP703A2 in vivo. Recently, CYP704B1, which is also tightly coexpressed with ACOS5, was implicated in exine formation. Recombinant CYP704B1 catalyzes the ω-hydroxylation of C16 to C18 long-chain fatty acids, especially showing preference of unsaturated C18 fatty acids (Dobritsa et al., 2009). This indicates that CYP704B1 prefers longer carbon chain length fatty acids than CYP703A2 and can hydroxylate them at a different carbon position. Thus, two cytochrome P450s could provide different building blocks for sporopollenin synthesis. However, phenotypic analysis of the double mutant cyp703a2 cyp704b1 did not show either an additive or new phenotype (Dobritsa et al., 2009). This suggests that in planta the hydroxylation steps involving CYP704B1 and CYP703A2 take place in a common pathway and that their catalytic functions may generate a 125  common sporopollenin monomer. It would be interesting to obtain further information about the relationship of CYP704B1 to CYP703A2 by transferring CYP704B1 into a cyp703a2 mutant and vice versa. If cyp703a2 transgenic line harboring the CYP704B1 transgene is fully fertile with normal exine formation, it would support the interpretation that the two hydroxylation reactions are in the same pathway. Even if the composition of sporopollenin is not well known yet, it has been consistently reported that sporopollenin is produced largely from fatty acids and  phenylpropanoid precursors in various plant species (Piffanelli et al., 1998; Domínguez et al., 1999). In order to test the functional conservation of the set of co-expressed enzymes based on the results of the comparative genomics approach, it would be interesting to test the ability of ACOS5, PKSA/B and TKPR1/2 homologues from other plant species to complement the Arabidopsis mutations. As an initial attempt, the poplar PoptrACOS13 gene, which is preferentially expressed in the male flowers and is grouped in same clade with ACOS5 (Souza Cde et al., 2008), was chosen for heterologous complementation. The complementation construct was composed of a 2-kb promoter region of ACOS5, a 2.5-kb coding sequence of PoptrACOS13 and a 2.6-kb terminator region of ACOS5. This construct could be transformed into an ACOS5/acos5 heterozygous plant in the future. If the introduced PoptrACOS13 transgene complements the male sterile phenotype in the acos5 mutant background, transgenic plants will be fully fertile. This would suggest that the catalytic function of PoptrACOS13 in sporopollenin biosynthesis is conserved in Populus trichocarpa. In addition, a construct with the poplar PKSA/B or TKPR1/2 gene could be designed and tested in a similar way. While both CYP703A2 and ACOS5 orthologs could not be identified in the green alga Chlamydomonas reinhardtii, they are conserved in land plant lineages, including Physcomitrella (Morant et al., 2007; de Azevedo Souza et al., 2009). In mosses, a haploid spore is produced by the meiotic division of spore mother cells (archesporial cells) in the archesporium, the inner most tissue of the capsule in the sporophyte. The moss spore walls consist of three layers: the outermost perine, a separating layer, the exine and the inner intine. The major component of the exine layer of the spores is sporopollenin (Brown and Lemmon, 1984). Thus, acquiring the ability to generate the sporopollenin polymer to protect haploid spores was likely a key land plant innovation essential for 126  protection of haploid spores from various stresses of the terrestrial environment. The first draft genome of Physcomitrella patens was released by the JGI (Joint Genome Institute, http://genome.jgi-psf.org//Phypa1_1/Phypa1_1.home.html). By searching for genes by sequences similarity as well as by phylogenetic analysis, I confirmed the existence of candidate ACOS5, PKSA/B and TKPR1/2 homologues in Physcomitrella patens (de Azevedo Souza et al., 2009; Grienenberger et al., 2010; Kim et al., 2010). Moreover, recently the ppgs cDNA library (http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?ORG=Ppa&LID=23755), which is derived from green sporophytes containing archesporial cells and developing spores (Dr. Dae-Yeon Suh, personal communication) has been made available. Potential moss orthologs of Arabidopsis genes involved in sporopollenin biosynthesis, such as PpACOS6, PpCHS10 and PpDFRL1 genes were found exclusively in the ppgs library and were absent in other libraries from gametophytic  tissue (Che C. Colpitts et al., submitted). Thus, to test the functional conservation of the putative moss orthologs, I could use an approach similar to that described for PoptrACOS13 poplar genes. These Physcomitrella genes could be placed under the control of the respective Arabidopsis promoters and these candidate genes will be introduced into the Arabidopsis mutant lines to test heterologous complementation. Ability of the moss homologues to complement the Arabidopsis acos5, pksa pksb and tkpr1 mutations would support the idea that these genes encode enzymes that form part of an ancient biochemical pathway common to land plant, required for sporopollenin biosynthesis.      127  References   Aarts, M.G., Keijzer, C.J., Stiekema, W.J., and Pereira, A. (1995). 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Data was reprinted from (Kim et al., 2010) with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).   >PKSB MGSIDAAVLGSEKKSNPGKATILALGKAFPHQLVMQEYLVDGYFKTTKCDDPELKQKLTRLCKTTTVKTRYVVMSEEILK KYPELAIEGGSTVTQRLDICNDAVTEMAVEASRACIKNWGRSISDITHVVYVSSSEARLPGGDLYLAKGLGLSPDTHRVL LYFVGCSGGVAGLRVAKDIAENNPGSRVLLATSETTIIGFKPPSVDRPYDLVGVALFGDGAGAMIIGSDPDPICEKPLFE LHTAIQNFLPETEKTIDGRLTEQGINFKLSRELPQIIEDNVENFCKKLIGKAGLAHKNYNQMFWAVHPGGPAILNRIEKR LNLSPEKLSPSRRALMDYGNASSNSIVYVLEYMLEESKKVRNMNEEENEWGLILAFGPGVTFEGIIARNLDV*  >PpCHS10 MASRRVEAAFDGQAVELGATIPAANGNGTHQSIKVPGHRQVTPGKTTIMAIGRAVPANTTFNDGLADHYIQEFNLQDPVL QAKLRRLCETTTVKTRYLVVNKEILDEHPEFLVDGAATVSQRLAITGEAVTQLGHEAATAAIKEWGRPASEITHLVYVSS SEIRLPGGDLYLAQLLGLRSDVNRVMLYMLGCYGGASGIRVAKDLAENNPGSRVLLITSECTLIGYKSLSPDRPYDLVGA ALFGDGAAAMIMGKDPIPVLERAFFELDWAGQSFIPGTNKTIDGRLSEEGISFKLGRELPKLIESNIQGFCDPILKRAGG LKYNDIFWAVHPGGPAILNAVQKQLDLAPEKLQTARQVLRDYGNISSSTCIYVLDYMRHQSLKLKEANDNVNTEPEWGLL LAFGPGVTIEGALLRNLC*  >SlChsl mgfeniklngmgkkptpgkatvlslgkgfphtlvmqeflvdgyfrntncddpelkqkltrlcktttvktryvvmsdeilk kcpelamagqatvkqrldicndavtemaidaskacisdwgrpisdithlvyvsssearlpggdlylakglglspetnrvm lyfsgcsggvagfrvakdiaennpgsrvllatsettiigfkppnpdrpydlvgvalfgdgagamiigsdpnssenplfel htaiqhflpdtekiidgrlteegisftldralpqiiednieafcdklmssvgltskdyndmfwavhpggpailnrlekrl dlspdklsasrraltdygnassntivyvmeymieeglkrkngdkndndwglilafgpgl  >PrCHS1 msasngtngvvavksrrqhrpgkttamafgrafpdqlvmqeflvdgyfrntncqdpvlrqklerlcktttvktryvvmsd eilaqhpelavegsatvrqrleisnvavtdmavdacrdclkewgrpvseithlvyvssseirlpggdlylasrlglrsdv srvmlyflgcyggvtglrvakdlaennpgsrvllatsettilgfrppnperpydlvgaalfgdgaaamvlgtdprpeage qgfleldwavqqflpdthgtingrlteeginfklgrelpqiiedhiegfcrklmdkagvddynelfwgvhpggpailnrl ekklslgpeklyysrqaladygnassntivyvldamrqlkggekqspewglilafgpgitfegilarslv  >OsCHSL2 MVSTNAGGIASKQASSMAPNPGKATILALGHAFPQQLVMQDYVVDGFMRNTNCDDPELKEKLTRLCTVPDPNLIICSYKY IYSTIIELACKTTTVKTRYVVMSEEILKSYPELAQEGQPTMKQRLDISNKAVTQMATEASLACVRSWGGALSEITHLVYV SSSEARFPGGDLHLARALGLSPDVRRVMLAFTGCSGGVAGLRVAKGLAESCPGARVLLATSETTIVGFRPPSPDRPYDLV GVALFGDGAGAAVVGADPTPVERPLFELHSALQRFLPDTDKTIDGRLTEEGIKFQLGRELPHIIEANVEAFCQKLMQEHP QAADKLTYGDMFWAVHPGGPAILTKMEGRLGLDGGKLRASRSALRDFGNASSNTIVYVLENMVEETRQRREEAAEEEDCE WGLILAFGPGITFEGILARNLQARARARD*  >OsCHSL1 MADLGFGDARSGNGSRSQCSRGKAMLLALGKGLPEQVLPQEKVVETYLQDTICDDPATRAKLERLCKTTTVRTRYTVMSK ELLDEHPELRTEGTPTLTPRLDICNAAVLELGATAARAALGEWGRPAADITHLVYISSSELRLPGGDLFLATRLGLHPNT VRTSLLFLGCSGGAAALRTAKDIAENNPGSRVLVVAAETTVLGFRPPSPDRPYDLVGAALFGDGASAAIIGAGPIAAEES PFLELQFSTQEFLPGTDKVIDGKITEEGINFKLGRDLPEKIENRIEGFCRTLMDRVGIKEFNDVFWAVHPGGPAILNRLE VCLELQPEKLKISRKALMNYGNVSSNTVFYVLEYLRDELKKGMIREEWGLILAFGPGITFEGMLVRGIN*  >PKSA msnsrmngveklsskstrrvanagkatllalgkafpsqvvpqenlvegflrdtkcddafikeklehlcktttvktrytvl treilakypelttegsptikqrleianeavvemaleaslgcikewgrpvedithivyvssseirlpggdlylsaklglrn dvnrvmlyflgcyggvtglrvakdiaennpgsrvllttsettilgfrppnkarpydlvgaalfgdgaaaviigadprece apfmelhyavqqflpgtqnvidgrlteeginfklgrdlpqkieenieefckklmgkagdesmefndmfwavhpggpailn rletklklekeklessrralvdygnvssntilyvmeymrdelkkkgdaaqewglglafgpgitfegllirsl  143  >OsCHS1 MAAAVTVEEVRRAQRAEGPATVLAIGTATPANCVYQADYPDYYFRITKSEHMVELKEKFKRMCDKSQIRKRYMHLTEEIL QENPNMCAYMAPSLDARQDIVVVEVPKLGKAAAQKAIKEWGQPRSRITHLVFCTTSGVDMPGADYQLAKMLGLRPNVNRL MMYQQGCFAGGTVLRVAKDLAENNRGARVLAVCSEITAVTFRGPSESHLDSMVGQALFGDGAAAVIVGSDPDEAVERPLF QMVSASQTILPDSEGAIDGHLREVGLTFHLLKDVPGLISKNIERALGDAFTPLGISDWNSIFWVAHPGGPAILDQVEAKV GLDKERMRATRHVLSEYGNMSSACVLFILDEMRKRSAEDGHATTGEGMDWGVLFGFGPGLTVETVVLHSVPITAGAAA*  >NSCHSLK mgkafpaqlvpqdclvegyirdtncqdlaikeklerlcktttvktrytvmskeildkypelategtptikqrleianpav vemakqasqacikewgrsaeeithivyvssseirlpggdlylatelglrndigrvmlyflgcyggvtglrvakdiaennp gsrvllttsettilgfrppnkarpydlvgaalfgdgaaaviigtepimgkespfmelnfatqqflpgtnnvidgrlteeg infklgrdlpekiqdnieefckkiiakadlreakyndlfwavhpggpailnrlentlklqsekldcsrralmdygnvssn tifyvmeymreelknkknggeewglalafgpgitfegillrsl  >AtCHSL2 mlvsarvekqkrvayqgkatvlalgkalpsnvvsqenlveeylreikcdnlsikdklqhlcksttvktrytvmsretlhk ypelategsptikqrleiandavvqmayeaslvcikewgravedithlvyvsssefrlpggdlylsaqlglsnevqrvml yflgcygglsglrvakdiaennpgsrvllttsettvlgfrppnkarpynlvgaalfgdgaaaliigadptesespfmelh camqqflpqtqgvidgrlseegitfklgrdlpqkiednveefckklvakagsgalelndlfwavhpggpailsgletklk lkpeklecsrralmdygnvssntifyimdkvrdelekkgtegeewglglafgpgitfegflmrnl  >AtCHS MVMAGASSLDEIRQAQRADGPAGILAIGTANPENHVLQAEYPDYYFRITNSEHMTDLKEKFKRMCDKSTIRKRHMHLTEE FLKENPHMCAYMAPSLDTRQDIVVVEVPKLGKEAAVKAIKEWGQPKSKITHVVFCTTSGVDMPGADYQLTKLLGLRPSVK RLMMYQQGCFAGGTVLRIAKDLAENNRGARVLVVCSEITAVTFRGPSDTHLDSLVGQALFSDGAAALIVGSDPDTSVGEK PIFEMVSAAQTILPDSDGAIDGHLREVGLTFHLLKDVPGLISKNIVKSLDEAFKPLGISDWNSLFWIAHPGGPAILDQVE IKLGLKEEKMRATRHVLSEYGNMSSACVLFILDEMRRKSAKDGVATTGEGLEWGVLFGFGPGLTVETVVLHSVPL*  >PpCHS MASAGDVTRVALPRGQPRAEGPACVLGIGTAVPPAEFLQSEYPDFFFNITNCGEKEALKAKFKRICDKSGIRKRHMFLTE EVLKANPGICTYMEPSLNVRHDIVVVQVPKLAAEAAQKAIKEWGGRKSDITHIVFATTSGVNMPGADHALAKLLGLKPTV KRVMMYQTGCFGGASVLRVAKDLAENNKGARVLAVASEVTAVTYRAPSENHLDGLVGSALFGDGAGVYVVGSDPKPEVEK PLFEVHWAGETILPESDGAIDGHLTEAGLIFHLMKDVPGLISKNIEKFLNEARKPVGSPAWNEMFWAVHPGGPAILDQVE AKLKLTKDKMQGSRDILSEFGNMSSASVLFVLDQIRHRSVKMGASTLGEGSEFGFFIGFGPGLTLEVLVLRAAPNSA*  >OsCHS2 MVTSTVKLEEVRRMQRAEGMAAVLAIGTATPANCVYQTDYPDYYFRVTNSEHLTNLKERFQRMCESSQIRKRYTHLTEEI LQENPSMCVFTAPSLDARQDMVVAEVPKLGKAAAEEAIKEWGQPMSRITHLVFCTTNGVDMPGADYQVAKMLGLPTSVKR LMMYQQGCFAGGTVLRVAKDLAENNRGARVLVVCSEIMAMAFRGPSESHLDSLVGHALFGDGAAAVIVGSDPDEAADERP LFQIVSASQTILPGTEDAIVGHLREVGLTFHLPKDVPEFISDSVEGALTDAFMPLGVHDWNSIFWVVHPGGPAILDQVEE KVALHKARMRASRNVLSEYGNMASATVLFVLDEMRKLSADDGHATTGEGMDWGVLFGFGPGLTVETIVLHSVPITAAAPL IMQ*  >PoptrCHSL7 MGYEQIVQGGLTTKANPGKATILALGKAFPHQLVMQEFLVDGYFKNTNCDDLELKQKLTRLCKTTTVKTRYVVMSDEILK KYPELAIEGLPTVKQRLDICNDAVTRMAIDASRACIKKWGRPVSDITHLVYVSSSEARLPGGDLYLAGGLGLSPETQRVM LYFAGCSGGVAGLRVAKDIAENNPGSRVLLATSETTIIGFKPPSADRPYDLVGVALFGDGAGAMIVGTDPIPVTESPLFE LHTAIQNFLPNTEKTIDGRLTEEGISFKLSRELPQIIEDNIEGFCHKLIGNAGLTDKDYNKMFWAVHPGGPAILNRMEKR FDLLPDKLNASRRALMDYGNASSNTIVYVLEYMIEECRKMNGRL*  >PoptrCHSL6 MGSEQIGQGGLTSKASPGKATILALGKAFPHQLVMQEFLVDGYFKNTNCDDPELKQKLTRLCKTTTVKTRYVVMSDEILN KYPELAIEGIPTIKQRLDICNDAVTQMAIGASRACIKKWGRSVSDITHMVYVSSSEARLPGGDLYLAGGLGLSPETQRVM LYFSGCSGGVAGLRVAKDIAENNPGSRVLLATSETTIIGFKPPSVDRPYDLVGVALFGDGAGAMVIGTDPVPVTESPLFE LHTAIQNFLPNTEKTIDGRLTEEGISFKLARELPQIIEDNIEGFCHKLIGVAGLTDKDYNKMFWAVHPGGPAILNRMEKR LDLLPDKLNASRRALMDYGNASSNTIVYVLEYMIEESRKMKAGAANCDWGLILAFGPGITFEGILARNLTI*  >PoptrCHS1 MAPSIEEIRKAQRASGPATILAIGKATPANCVSQADYPDYYFRITNSEHMTELKEKFKRMCDKSMIKKRYMHLTEEILKE NSSMCEYMAPSLDARQDMVVVEVPKLGKEAAAKAIKEWGQPKSKITHLVFCTTSGVDMPGADYQLTKLLGLRSSVKRFMM YQQGCFAGGTVLRLAKDLAENNKGSRVLVVCSEITAVTFRGPSDTHLDSMVGQALFGDGAAAVIVGADPDTSIERPLFQI VSAAQTILPDSDGAIDGHLREVGLTFHLLKDVPGLISKNIEKSLVEAFAPIGINDWNSIFWIAHPGGPAILDQVEIKLDL KEEKLRATRNVLSDYGNMSSACVLFILDEMRNKSLEEGKSTTGEGLEWGVLFGFGPGLTVETVVLHSVPVEQTIYS* 144   >PoptrCHS2 MVTVDEIRKAQRAEGPATILAIGTSTPPNCVDQSTYPDYYFRITNSEHKVELKEKFKRMCEKSMIKKRYMHLTEEILKEN PSVCEYMAPSLDARQDMVVVEIPKLGKEAAAKAIKEWGQPKSKITHLVFCTTSGVDMPGADYQLTKLLGLRSSVKRFMMY QQGCFAGGTVLRLAKDLAENNKGARVLVVCSEITAVTFRGPSDTHLDSLVGQALFGDGAAAIIIGSDPVLGVEKPLFELV SAAQTILPDSEGAIDGHLREVGLTFHLLKDVPGLISKNVEKSLTEAFKPLGISDWNSLFWIAHPGGPAILDQVEAKLELK PEKLRATRQVLADYGNMSSACVLFILDEMRKKSAKDGLKSTGEGLEWGVLFGFGPGLTVETVVLHSLPATI*  >PoptrCHS3 MVTVDEVRKAQRAEGPAVILAIGTSTPPNCVDQSTYPDYYFRITNSEHKVELKEKFKRMCEKSMIKKRYMHLTEEILKEN PSVCEYMAPSLDARQDMVVVEVPKLGKEAAAKAIKEWGQPKSKITHLVFCTTSGVDMPGADYQLTKLLGLRSSVKRFMMY QQGCFAGGTVLRLAKDLAENNKGARVLVVCSEITAVTFRGPSDTHLDSLVGQALFGDGAAAIIIGSDPVLGVEKPLFELV SAAQTILPDSDGAIDGHLREVGLTFHLLKDVPGLISKNIEKSLTEAFKPLGISDWNSLFWIAHPGGPAILDQVEAKLELK PEKLRATRQVLADYGNMSSACVLFILDEMRKKSAKDGLKSTGEGLEWGVLFGFGPGLTVETVVLHSVASI*  >PoptrCHSL4 MSESDSNGASKHCTTPSRRAPTLGKATLLAIGKAFPSQLIPQECLVEGYIRDTKCDDASIKEKLERLCKTTTVKTRYTVM SREILDKYPELATEGTPTIRQRLEIANPAVVEMALKASMACINEWGGSVEDITHIVYVSSSEVRLPGGDLYLASQLGLRN DVGRVMLYFLGCYGGVTGLRVAKDIAENNPGSRVLLTTSETTILGFRPPSKARPYDLVGAALFGDGAAAVIIGANPVIGK ESPFMELNYSVQQFLPGTQNVIDGRLSEEGIHFKLGRDLPQKIEDNIEEFCNKLMSKAGLTDFNELFWAVHPGGPAILNR LESKLKLNEEKLECSRRALMDYGNVSSNTIVYVLEYMRDELKRGGGEWGLALAFGPGITFEGILLRSL*  >PoptrCHSL2 MALVDEIRKAQRARGPAMVLAIGTAVPVNCFYQADYPDYFFRVTKTENLTELKAKFERICQKSMINKRYMHLTEEMIKEN PEIGNFMTPSLNVRQDIVLAEVPKLGKEAALKAIQEWGHPMSKITHLVFCTTSGVHMPGADYQLANLLGLSSSIKRLMLY QQGCYGGGTALRVAKDLAENNAGARVLVVCSEITAITFHAPNEDQLGCLVGQALFGDGAGAAIIGSDPDTLVEKPIFQLV SAAQIMIPDSEHAIEGHVREMGLLIHLSEDVPKLISDNVEAALREVVTPIGGVLSDWNSLFWAVHAGGRAILDGVEAKLK LKKEKLGVTRHILREYGNVASACVLFVLDEMRERSVREGKATTGEGLEWGVVIGLGPGLTMETLVLHSVPVAITK*  >PoptrCHS4 MVTVDEVRKGQRAEGPATIMAIGTSNPPNCVDQSTYPDYYFRVTNSEHRAELKEKFKRMCEKSMIKKRYIYLTEDMLKEN PDMRAYMAPSLDARQDMVVVEVPKLGKEAATKAIKEWGQSKSKITHLVFCTTSGVDMPGADYQLTKLLGLRPSVKRLMMY QQGCFAGGTVLRLAKDLAENNKGARVLVVCSEITAIIFRGPNDTHLDSLIGQALFGDGAAAIIIGSDPVVGVEKPLFEIV SAAQTILPNSAGAIDGHLREAGLTFHLLKDVPGLISNNVEKSLTEAFKPLGISDWNSLFWIAHPGGPAILDQVEAKLGLK PEKLRATRHVLSEYGNMSSACVLFILDEMRKKSAEDGLQSTGEGLEWGVLFGFGPGLTVETVVLHSVATRV*  >PoptrCHS5 MVTVDEIRKTQRAEGPATIMAIGTSTPPNCVDQSAYPDYYFRITNSEHKAELKEKFKRMCEKSMIKKRYMYLTEEILKEN PSVCEYMAPSLDARQDMVVVEVPRLGKEAATKAIKEWGQPKSKITHLVFCTTSGVDMPGADYQLTKLLGLRSSVKRFMMY QQGCFAGGTVLRLAKDLAENNKGARVLVVCSEITAVTFRGPSDTHLDSLVGQALFGDGAAALIIGSDPVIGVEKPLFELV SAAQTILPDSDGAIDGHLREVGLTFHLLKDVPGLISKNVEKSLTEAFKPLGISDWNSLFWIAHPGGPAILDQVEAKLALK PEKLRATRHVLSEYGNMSSACVLFILDEMRKKSAEDGLQSTGEGLEWGVLFGFGPGLTVETVVLHSVAPTI*  >PoptrCHS6 MVTVDEIRKSQRAEGPATIMAIGTSTPPNCVDQSTYPDYYFRITNSEHKAELKEKFKRMCEKSMIKKRYMYLTEEILKEN PSVCEYMAPSLDARQDMVVVEVPKLGKEAATKAIKEWGQPKSKITHLVFCTTSGVDMPGADYQLTKLLGLRSSVKRFMMY QQGCFAGGTVLRLAKDLAENNKGARVLVVCSEITAVTFRGPSDTHLDSLVGQALFGDGAAALVIGSDPVIGVEKPLFELV SAAQTILPDSDGAIDGHLREVGLTFHLLKDVPGLISKNVEKSLTEAFKPLGISDWNSLFWIAHPGGPAILDQVEAKLALK PEKLRATRHVLSEYGNMSSACVLFILDEMRKKSAEDGLQSTGEGLEWGVLFGFGPGLTVETVVLHSVAPTI*  >PoptrCHSL3 MASDQTSQGAQAAQSPATILAIGTANPANFIYQADYPDYYFRVTRSEHMTDLKGKFKRLCEKSEVRKRHFHLTEEILNKN PTMCTYDGPSLDVRQDVLVTEVPKLGMEAALKAIEEWGRPKSNITHLIFSALAGIDMPGADYQLTRLLGLEPSIKRIMLY HQGCNIGAATLRIAKDFAENNAGARVLVVSSDLTVGTFRGPSNDNISCLVAQAITGEGAAALIIGADPDMSVERPLFQIL SASQTIIPDSNDGINGHLREVGLTVHFSRNVPELISRNIGKCLVEAFGPIGVSDWNSLFWIVQPSGAAILNLIEAEVGLA QEKLSATRHVLSEFGNMGGPTVLFILDEIRRRSLEKRKTTTGEGMEWGVLIGLGAGITVDTVVLHSVPIAEGR*  >PoptrCHSL1 MASILAIGTANPPNCFDQADYPDFYFRVTKSEHMTQLKDKFKRICEKSKIRKRYMYITEDTIKKNPSLSTYDAASLDARQ EILVTEVPKLGKEAALKAIEEWGQPKSKITHLIFCTSSGTHMPGADHELTKLLGLERSVKRFMMYQQGCFTAALALRLSK DLAENNPGARVLIVCSENMTVCFRAPSETHLDILVGSAIFSDGAAAIIVGADPDTATERPLFQLVSAEQCIVPDSDDGIV GHIREMGISYYLHKMVPKIVAEGAAQCLVETFNARYGIKDWNSLFYVVHPGGTGVLNKFEEHIGLTKDKLRASRHVLSEY GNMWGPSMFFVLDEMRRRSAKEGKATTGEGLDLGVLFGFGPGVTIETIVLRSFATD* 145   >PoptrCHSL5 MSKTIGNGASKHYATLTRRSPTPGKATILATGKAFPSQLVPQECLVEGYMRDTKCDDASIKEKLERLCKTTTVKTRYTVM SKEILEKYPELATEGSPTIKQRLEIANPAVVEMALKASIACINEWGGSVKDITHVVYVSSSEIRLPGGDLYLASQLGLRN DVGRVMLYFLGCYGGVTGLRVAKDIAENNPGSRILLTTSETTILGFRPPNKARPYDLVGAALFGDGAAAVIIGADPVIGK ESPFMELSYAVQQFLPGTQNVIDGRLSEEGINFKLGRDLPQKIEDNIEEFCRKLMSKAGLTEFNDLFWAVHPGGPAILNR LESNLKLNTEKLECSRRALINYGNVSSNTIVYVLEYMKEELKREGGEEWGLALAFGPGITFEGILLRSL*   Appendix B. Alignment of amino acid sequences used to generate the phylogenetic tree shown in Figure 3.2. Data was reprinted from (Kim et al., 2010) with permission of the American Society of Plant Biologists (Copyright ©  American Society of Plant Biologists).                ....|....| ....|....| ....|....| ....|....| ....|....|  ....|....|                  5          15         25         35         45 55 PpCHS10      MASRRVEAAF DGQAVELGAT IPAANGNGTH QSIKVPGHRQ VTPGKTTIMA IGRAVPANTT OsCHSL1      ---------- ---------- --MADLGFGD ARSGNGSRSQ CSRGKAMLLA LGKGLPEQVL PrCHS1       ---------- ---------- --MSASNGTN GVVAVKSRRQ HRPGKTTAMA FGRAFPDQLV AtCHSL2      ---------- ---------- -------MLV SARVEKQKRV AYQGKATVLA LGKALPSNVV PKSA         ---------- ---------- MSNSRMNGVE KLSSKSTRRV ANAGKATLLA LGKAFPSQVV NSCHSLK      ---------- ---------- ---------- ---------- ---------- MGKAFPAQLV PoptrCHSL4   ---------- ---------- MSESDSNGAS KHCTTPSRRA PTLGKATLLA IGKAFPSQLI PoptrCHSL5   ---------- ---------- MSKTIGNGAS KHYATLTRRS PTPGKATILA TGKAFPSQLV OsCHSL2      ---------- ---------- --MVSTNAGG IASKQASSMA PNPGKATILA LGHAFPQQLV SlChsl       ---------- ---------- ------MGFE NIKLNGMGKK PTPGKATVLS LGKGFPHTLV PKSB         ---------- ---------- ------MGSI DAAVLGSEKK SNPGKATILA LGKAFPHQLV PoptrCHSL7   ---------- ---------- ------MGYE QIVQGGLTTK ANPGKATILA LGKAFPHQLV PoptrCHSL6   ---------- ---------- ------MGSE QIGQGGLTSK ASPGKATILA LGKAFPHQLV PoptrCHSL1   ---------- ---------- ---------- ---------- ----MASILA IGTANPPNCF PpCHS        ---------- ---------- ---MASAGDV TRVALPRGQP RAEGPACVLG IGTAVPPAEF PoptrCHSL3   ---------- ---------- ---------M ASDQTSQGAQ AAQSPATILA IGTANPANFI PoptrCHSL2   ---------- ---------- ---------M ALVDEIRKAQ RARGPAMVLA IGTAVPVNCF OsCHS2       ---------- ---------- -----MVTST VKLEEVRRMQ RAEGMAAVLA IGTATPANCV OsCHS1       ---------- ---------- ------MAAA VTVEEVRRAQ RAEGPATVLA IGTATPANCV AtCHS        ---------- ---------- ----MVMAGA SSLDEIRQAQ RADGPAGILA IGTANPENHV PoptrCHS1    ---------- ---------- --------MA PSIEEIRKAQ RASGPATILA 146  IGKATPANCV PoptrCHS4    ---------- ---------- ---------M VTVDEVRKGQ RAEGPATIMA IGTSNPPNCV PoptrCHS5    ---------- ---------- ---------M VTVDEIRKTQ RAEGPATIMA IGTSTPPNCV PoptrCHS6    ---------- ---------- ---------M VTVDEIRKSQ RAEGPATIMA IGTSTPPNCV PoptrCHS2    ---------- ---------- ---------M VTVDEIRKAQ RAEGPATILA IGTSTPPNCV PoptrCHS3    ---------- ---------- ---------M VTVDEVRKAQ RAEGPAVILA IGTSTPPNCV                 ....|....| ....|....| ....|....| ....|....| ....|....|  ....|....|                  65         75         85         95        105 115 PpCHS10      FNDGLADHYI QEFNLQD-PV LQAKLRRL-- ---------- ---------- --CETTTVKT OsCHSL1      PQEKVVETYL QDTICDD-PA TRAKLERL-- ---------- ---------- --CKTTTVRT PrCHS1       MQEFLVDGYF RNTNCQD-PV LRQKLERL-- ---------- ---------- --CKTTTVKT AtCHSL2      SQENLVEEYL REIKCDN-LS IKDKLQHL-- ---------- ---------- --CKSTTVKT PKSA         PQENLVEGFL RDTKCDD-AF IKEKLEHL-- ---------- ---------- --CKTTTVKT NSCHSLK      PQDCLVEGYI RDTNCQD-LA IKEKLERL-- ---------- ---------- --CKTTTVKT PoptrCHSL4   PQECLVEGYI RDTKCDD-AS IKEKLERL-- ---------- ---------- --CKTTTVKT PoptrCHSL5   PQECLVEGYM RDTKCDD-AS IKEKLERL-- ---------- ---------- --CKTTTVKT OsCHSL2      MQDYVVDGFM RNTNCDD-PE LKEKLTRLCT VPDPNLIICS YKYIYSTIIE LACKTTTVKT SlChsl       MQEFLVDGYF RNTNCDD-PE LKQKLTRL-- ---------- ---------- --CKTTTVKT PKSB         MQEYLVDGYF KTTKCDD-PE LKQKLTRL-- ---------- ---------- --CKTTTVKT PoptrCHSL7   MQEFLVDGYF KNTNCDD-LE LKQKLTRL-- ---------- ---------- --CKTTTVKT PoptrCHSL6   MQEFLVDGYF KNTNCDD-PE LKQKLTRL-- ---------- ---------- --CKTTTVKT PoptrCHSL1   DQADYPDFYF RVTKSEHMTQ LKDKFKRI-- ---------- ---------- --CEKSKIRK PpCHS        LQSEYPDFFF NITNCGEKEA LKAKFKRI-- ---------- ---------- --CDKSGIRK PoptrCHSL3   YQADYPDYYF RVTRSEHMTD LKGKFKRL-- ---------- ---------- --CEKSEVRK PoptrCHSL2   YQADYPDYFF RVTKTENLTE LKAKFERI-- ---------- ---------- --CQKSMINK OsCHS2       YQTDYPDYYF RVTNSEHLTN LKERFQRM-- ---------- ---------- --CESSQIRK OsCHS1       YQADYPDYYF RITKSEHMVE LKEKFKRM-- ---------- ---------- --CDKSQIRK AtCHS        LQAEYPDYYF RITNSEHMTD LKEKFKRM-- ---------- ---------- --CDKSTIRK PoptrCHS1    SQADYPDYYF RITNSEHMTE LKEKFKRM-- ---------- ---------- --CDKSMIKK PoptrCHS4    DQSTYPDYYF RVTNSEHRAE LKEKFKRM-- ---------- ---------- --CEKSMIKK PoptrCHS5    DQSAYPDYYF RITNSEHKAE LKEKFKRM-- ---------- ---------- 147  --CEKSMIKK PoptrCHS6    DQSTYPDYYF RITNSEHKAE LKEKFKRM-- ---------- ---------- --CEKSMIKK PoptrCHS2    DQSTYPDYYF RITNSEHKVE LKEKFKRM-- ---------- ---------- --CEKSMIKK PoptrCHS3    DQSTYPDYYF RITNSEHKVE LKEKFKRM-- ---------- ---------- --CEKSMIKK                    ....|....| ....|....| ....|....| ....|....| ....|....|  ....|....|                 125        135        145        155        165 175 PpCHS10      RYLVVNKEIL DEHPEFLVDG AATVSQRLAI TGEAVTQLGH EAATAAIKEW GRPASEITHL OsCHSL1      RYTVMSKELL DEHPELRTEG TPTLTPRLDI CNAAVLELGA TAARAALGEW GRPAADITHL PrCHS1       RYVVMSDEIL AQHPELAVEG SATVRQRLEI SNVAVTDMAV DACRDCLKEW GRPVSEITHL AtCHSL2      RYTVMSRETL HKYPELATEG SPTIKQRLEI ANDAVVQMAY EASLVCIKEW GRAVEDITHL PKSA         RYTVLTREIL AKYPELTTEG SPTIKQRLEI ANEAVVEMAL EASLGCIKEW GRPVEDITHI NSCHSLK      RYTVMSKEIL DKYPELATEG TPTIKQRLEI ANPAVVEMAK QASQACIKEW GRSAEEITHI PoptrCHSL4   RYTVMSREIL DKYPELATEG TPTIRQRLEI ANPAVVEMAL KASMACINEW GGSVEDITHI PoptrCHSL5   RYTVMSKEIL EKYPELATEG SPTIKQRLEI ANPAVVEMAL KASIACINEW GGSVKDITHV OsCHSL2      RYVVMSEEIL KSYPELAQEG QPTMKQRLDI SNKAVTQMAT EASLACVRSW GGALSEITHL SlChsl       RYVVMSDEIL KKCPELAMAG QATVKQRLDI CNDAVTEMAI DASKACISDW GRPISDITHL PKSB         RYVVMSEEIL KKYPELAIEG GSTVTQRLDI CNDAVTEMAV EASRACIKNW GRSISDITHV PoptrCHSL7   RYVVMSDEIL KKYPELAIEG LPTVKQRLDI CNDAVTRMAI DASRACIKKW GRPVSDITHL PoptrCHSL6   RYVVMSDEIL NKYPELAIEG IPTIKQRLDI CNDAVTQMAI GASRACIKKW GRSVSDITHM PoptrCHSL1   RYMYITEDTI KKNPSLSTYD AASLDARQEI LVTEVPKLGK EAALKAIEEW GQPKSKITHL PpCHS        RHMFLTEEVL KANPGICTYM EPSLNVRHDI VVVQVPKLAA EAAQKAIKEW GGRKSDITHI PoptrCHSL3   RHFHLTEEIL NKNPTMCTYD GPSLDVRQDV LVTEVPKLGM EAALKAIEEW GRPKSNITHL PoptrCHSL2   RYMHLTEEMI KENPEIGNFM TPSLNVRQDI VLAEVPKLGK EAALKAIQEW GHPMSKITHL OsCHS2       RYTHLTEEIL QENPSMCVFT APSLDARQDM VVAEVPKLGK AAAEEAIKEW GQPMSRITHL OsCHS1       RYMHLTEEIL QENPNMCAYM APSLDARQDI VVVEVPKLGK AAAQKAIKEW GQPRSRITHL AtCHS        RHMHLTEEFL KENPHMCAYM APSLDTRQDI VVVEVPKLGK EAAVKAIKEW GQPKSKITHV PoptrCHS1    RYMHLTEEIL KENSSMCEYM APSLDARQDM VVVEVPKLGK EAAAKAIKEW GQPKSKITHL PoptrCHS4    RYIYLTEDML KENPDMRAYM APSLDARQDM VVVEVPKLGK EAATKAIKEW GQSKSKITHL PoptrCHS5    RYMYLTEEIL KENPSVCEYM APSLDARQDM VVVEVPRLGK EAATKAIKEW GQPKSKITHL 148  PoptrCHS6    RYMYLTEEIL KENPSVCEYM APSLDARQDM VVVEVPKLGK EAATKAIKEW GQPKSKITHL PoptrCHS2    RYMHLTEEIL KENPSVCEYM APSLDARQDM VVVEIPKLGK EAAAKAIKEW GQPKSKITHL PoptrCHS3    RYMHLTEEIL KENPSVCEYM APSLDARQDM VVVEVPKLGK EAAAKAIKEW GQPKSKITHL                   ....|....| ....|....| ....|....| ....|....| ....|....|  ....|....|                 185        195        205        215        225 235 PpCHS10      VYVSSSEIRL PGGDLYLAQL LGLRSDVNRV MLYMLGCYGG ASGIRVAKDL AENNPGSRVL OsCHSL1      VYISSSELRL PGGDLFLATR LGLHPNTVRT SLLFLGCSGG AAALRTAKDI AENNPGSRVL PrCHS1       VYVSSSEIRL PGGDLYLASR LGLRSDVSRV MLYFLGCYGG VTGLRVAKDL AENNPGSRVL AtCHSL2      VYVSSSEFRL PGGDLYLSAQ LGLSNEVQRV MLYFLGCYGG LSGLRVAKDI AENNPGSRVL PKSA         VYVSSSEIRL PGGDLYLSAK LGLRNDVNRV MLYFLGCYGG VTGLRVAKDI AENNPGSRVL NSCHSLK      VYVSSSEIRL PGGDLYLATE LGLRNDIGRV MLYFLGCYGG VTGLRVAKDI AENNPGSRVL PoptrCHSL4   VYVSSSEVRL PGGDLYLASQ LGLRNDVGRV MLYFLGCYGG VTGLRVAKDI AENNPGSRVL PoptrCHSL5   VYVSSSEIRL PGGDLYLASQ LGLRNDVGRV MLYFLGCYGG VTGLRVAKDI AENNPGSRIL OsCHSL2      VYVSSSEARF PGGDLHLARA LGLSPDVRRV MLAFTGCSGG VAGLRVAKGL AESCPGARVL SlChsl       VYVSSSEARL PGGDLYLAKG LGLSPETNRV MLYFSGCSGG VAGFRVAKDI AENNPGSRVL PKSB         VYVSSSEARL PGGDLYLAKG LGLSPDTHRV LLYFVGCSGG VAGLRVAKDI AENNPGSRVL PoptrCHSL7   VYVSSSEARL PGGDLYLAGG LGLSPETQRV MLYFAGCSGG VAGLRVAKDI AENNPGSRVL PoptrCHSL6   VYVSSSEARL PGGDLYLAGG LGLSPETQRV MLYFSGCSGG VAGLRVAKDI AENNPGSRVL PoptrCHSL1   IFCTSSGTHM PGADHELTKL LGLERSVKRF MMYQQGCFTA ALALRLSKDL AENNPGARVL PpCHS        VFATTSGVNM PGADHALAKL LGLKPTVKRV MMYQTGCFGG ASVLRVAKDL AENNKGARVL PoptrCHSL3   IFSALAGIDM PGADYQLTRL LGLEPSIKRI MLYHQGCNIG AATLRIAKDF AENNAGARVL PoptrCHSL2   VFCTTSGVHM PGADYQLANL LGLSSSIKRL MLYQQGCYGG GTALRVAKDL AENNAGARVL OsCHS2       VFCTTNGVDM PGADYQVAKM LGLPTSVKRL MMYQQGCFAG GTVLRVAKDL AENNRGARVL OsCHS1       VFCTTSGVDM PGADYQLAKM LGLRPNVNRL MMYQQGCFAG GTVLRVAKDL AENNRGARVL AtCHS        VFCTTSGVDM PGADYQLTKL LGLRPSVKRL MMYQQGCFAG GTVLRIAKDL AENNRGARVL PoptrCHS1    VFCTTSGVDM PGADYQLTKL LGLRSSVKRF MMYQQGCFAG GTVLRLAKDL AENNKGSRVL PoptrCHS4    VFCTTSGVDM PGADYQLTKL LGLRPSVKRL MMYQQGCFAG GTVLRLAKDL AENNKGARVL PoptrCHS5    VFCTTSGVDM PGADYQLTKL LGLRSSVKRF MMYQQGCFAG GTVLRLAKDL AENNKGARVL PoptrCHS6    VFCTTSGVDM PGADYQLTKL LGLRSSVKRF MMYQQGCFAG GTVLRLAKDL AENNKGARVL 149  PoptrCHS2    VFCTTSGVDM PGADYQLTKL LGLRSSVKRF MMYQQGCFAG GTVLRLAKDL AENNKGARVL PoptrCHS3    VFCTTSGVDM PGADYQLTKL LGLRSSVKRF MMYQQGCFAG GTVLRLAKDL AENNKGARVL                   ....|....| ....|....| ....|....| ....|....| ....|....|  ....|....|                 245        255        265        275        285 295 PpCHS10      LITSECTLIG YKSLSPDRPY DLVGAALFGD GAAAMIMGKD PIPVL-ERAF FELDWAGQSF OsCHSL1      VVAAETTVLG FRPPSPDRPY DLVGAALFGD GASAAIIGAG PIAAE-ESPF LELQFSTQEF PrCHS1       LATSETTILG FRPPNPERPY DLVGAALFGD GAAAMVLGTD PRPEAGEQGF LELDWAVQQF AtCHSL2      LTTSETTVLG FRPPNKARPY NLVGAALFGD GAAALIIGAD PTES--ESPF MELHCAMQQF PKSA         LTTSETTILG FRPPNKARPY DLVGAALFGD GAAAVIIGAD PREC--EAPF MELHYAVQQF NSCHSLK      LTTSETTILG FRPPNKARPY DLVGAALFGD GAAAVIIGTE PIMGK-ESPF MELNFATQQF PoptrCHSL4   LTTSETTILG FRPPSKARPY DLVGAALFGD GAAAVIIGAN PVIGK-ESPF MELNYSVQQF PoptrCHSL5   LTTSETTILG FRPPNKARPY DLVGAALFGD GAAAVIIGAD PVIGK-ESPF MELSYAVQQF OsCHSL2      LATSETTIVG FRPPSPDRPY DLVGVALFGD GAGAAVVGAD PTPV--ERPL FELHSALQRF SlChsl       LATSETTIIG FKPPNPDRPY DLVGVALFGD GAGAMIIGSD PNSS--ENPL FELHTAIQHF PKSB         LATSETTIIG FKPPSVDRPY DLVGVALFGD GAGAMIIGSD PDPIC-EKPL FELHTAIQNF PoptrCHSL7   LATSETTIIG FKPPSADRPY DLVGVALFGD GAGAMIVGTD PIPVT-ESPL FELHTAIQNF PoptrCHSL6   LATSETTIIG FKPPSVDRPY DLVGVALFGD GAGAMVIGTD PVPVT-ESPL FELHTAIQNF PoptrCHSL1   IVCSENMTVC FRAPSETHLD ILVGSAIFSD GAAAIIVGAD PDTAT-ERPL FQLVSAEQCI PpCHS        AVASEVTAVT YRAPSENHLD GLVGSALFGD GAGVYVVGSD PKPEV-EKPL FEVHWAGETI PoptrCHSL3   VVSSDLTVGT FRGPSNDNIS CLVAQAITGE GAAALIIGAD PDMSV-ERPL FQILSASQTI PoptrCHSL2   VVCSEITAIT FHAPNEDQLG CLVGQALFGD GAGAAIIGSD PDTLV-EKPI FQLVSAAQIM OsCHS2       VVCSEIMAMA FRGPSESHLD SLVGHALFGD GAAAVIVGSD PDEAADERPL FQIVSASQTI OsCHS1       AVCSEITAVT FRGPSESHLD SMVGQALFGD GAAAVIVGSD PDEAV-ERPL FQMVSASQTI AtCHS        VVCSEITAVT FRGPSDTHLD SLVGQALFSD GAAALIVGSD PDTSVGEKPI FEMVSAAQTI PoptrCHS1    VVCSEITAVT FRGPSDTHLD SMVGQALFGD GAAAVIVGAD PDTSI-ERPL FQIVSAAQTI PoptrCHS4    VVCSEITAII FRGPNDTHLD SLIGQALFGD GAAAIIIGSD PVVGV-EKPL FEIVSAAQTI PoptrCHS5    VVCSEITAVT FRGPSDTHLD SLVGQALFGD GAAALIIGSD PVIGV-EKPL FELVSAAQTI PoptrCHS6    VVCSEITAVT FRGPSDTHLD SLVGQALFGD GAAALVIGSD PVIGV-EKPL FELVSAAQTI PoptrCHS2    VVCSEITAVT FRGPSDTHLD SLVGQALFGD GAAAIIIGSD PVLGV-EKPL FELVSAAQTI 150  PoptrCHS3    VVCSEITAVT FRGPSDTHLD SLVGQALFGD GAAAIIIGSD PVLGV-EKPL FELVSAAQTI                   ....|....| ....|....| ....|....| ....|....| ....|....|  ....|....|                 305        315        325        335        345 355 PpCHS10      IPGTNKTIDG RLSEEGISFK LGRELPKLIE SNIQGFCDPI L-KRAG--GL K----YNDI- OsCHSL1      LPGTDKVIDG KITEEGINFK LGRDLPEKIE NRIEGFCRTL M-DRVG--IK E----FNDV- PrCHS1       LPDTHGTING RLTEEGINFK LGRELPQIIE DHIEGFCRKL M-DKAG--VD D----YNEL- AtCHSL2      LPQTQGVIDG RLSEEGITFK LGRDLPQKIE DNVEEFCKKL V-AKAG--SG ALE--LNDL- PKSA         LPGTQNVIDG RLTEEGINFK LGRDLPQKIE ENIEEFCKKL M-GKAG--DE SME--FNDM- NSCHSLK      LPGTNNVIDG RLTEEGINFK LGRDLPEKIQ DNIEEFCKKI I-AKAD--LR EAK--YNDL- PoptrCHSL4   LPGTQNVIDG RLSEEGIHFK LGRDLPQKIE DNIEEFCNKL M-SKAG--LT D----FNEL- PoptrCHSL5   LPGTQNVIDG RLSEEGINFK LGRDLPQKIE DNIEEFCRKL M-SKAG--LT E----FNDL- OsCHSL2      LPDTDKTIDG RLTEEGIKFQ LGRELPHIIE ANVEAFCQKL M-QEHP--QA ADKLTYGDM- SlChsl       LPDTEKIIDG RLTEEGISFT LDRALPQIIE DNIEAFCDKL M-SSVG--LT SKD--YNDM- PKSB         LPETEKTIDG RLTEQGINFK LSRELPQIIE DNVENFCKKL I-GKAG--LA HKN--YNQM- PoptrCHSL7   LPNTEKTIDG RLTEEGISFK LSRELPQIIE DNIEGFCHKL I-GNAG--LT DKD--YNKM- PoptrCHSL6   LPNTEKTIDG RLTEEGISFK LARELPQIIE DNIEGFCHKL I-GVAG--LT DKD--YNKM- PoptrCHSL1   VPDSDDGIVG HIREMGISYY LHKMVPKIVA EGAAQCLVET FNARYG--IK D----WNSL- PpCHS        LPESDGAIDG HLTEAGLIFH LMKDVPGLIS KNIEKFLNEA R-KPVG--SP A----WNEM- PoptrCHSL3   IPDSNDGING HLREVGLTVH FSRNVPELIS RNIGKCLVEA F-GPIG--VS D----WNSL- PoptrCHSL2   IPDSEHAIEG HVREMGLLIH LSEDVPKLIS DNVEAALREV V-TPIGGVLS D----WNSL- OsCHS2       LPGTEDAIVG HLREVGLTFH LPKDVPEFIS DSVEGALTDA F-MPLG--VH D----WNSI- OsCHS1       LPDSEGAIDG HLREVGLTFH LLKDVPGLIS KNIERALGDA F-TPLG--IS D----WNSI- AtCHS        LPDSDGAIDG HLREVGLTFH LLKDVPGLIS KNIVKSLDEA F-KPLG--IS D----WNSL- PoptrCHS1    LPDSDGAIDG HLREVGLTFH LLKDVPGLIS KNIEKSLVEA F-APIG--IN D----WNSI- PoptrCHS4    LPNSAGAIDG HLREAGLTFH LLKDVPGLIS NNVEKSLTEA F-KPLG--IS D----WNSL- PoptrCHS5    LPDSDGAIDG HLREVGLTFH LLKDVPGLIS KNVEKSLTEA F-KPLG--IS D----WNSL- PoptrCHS6    LPDSDGAIDG HLREVGLTFH LLKDVPGLIS KNVEKSLTEA F-KPLG--IS D----WNSL- PoptrCHS2    LPDSEGAIDG HLREVGLTFH LLKDVPGLIS KNVEKSLTEA F-KPLG--IS D----WNSL- PoptrCHS3    LPDSDGAIDG HLREVGLTFH LLKDVPGLIS KNIEKSLTEA F-KPLG--IS D----WNSL- 151                    ....|....| ....|....| ....|....| ....|....| ....|....|  ....|....|                 365        375        385        395        405 415 PpCHS10      FWAVHPGGPA ILNAVQKQLD LAPEKLQTAR QVLRDYGNIS SSTCIYVLDY MRHQSLKLKE OsCHSL1      FWAVHPGGPA ILNRLEVCLE LQPEKLKISR KALMNYGNVS SNTVFYVLEY LRDELKKGM- PrCHS1       FWGVHPGGPA ILNRLEKKLS LGPEKLYYSR QALADYGNAS SNTIVYVLDA MRQLKGGEK- AtCHSL2      FWAVHPGGPA ILSGLETKLK LKPEKLECSR RALMDYGNVS SNTIFYIMDK VRDELEKKG- PKSA         FWAVHPGGPA ILNRLETKLK LEKEKLESSR RALVDYGNVS SNTILYVMEY MRDELKKKG- NSCHSLK      FWAVHPGGPA ILNRLENTLK LQSEKLDCSR RALMDYGNVS SNTIFYVMEY MREELKNKK- PoptrCHSL4   FWAVHPGGPA ILNRLESKLK LNEEKLECSR RALMDYGNVS SNTIVYVLEY MRDELKRGG- PoptrCHSL5   FWAVHPGGPA ILNRLESNLK LNTEKLECSR RALINYGNVS SNTIVYVLEY MKEELKREG- OsCHSL2      FWAVHPGGPA ILTKMEGRLG LDGGKLRASR SALRDFGNAS SNTIVYVLEN MVEETRQRRE SlChsl       FWAVHPGGPA ILNRLEKRLD LSPDKLSASR RALTDYGNAS SNTIVYVMEY MIEEGLKRK- PKSB         FWAVHPGGPA ILNRIEKRLN LSPEKLSPSR RALMDYGNAS SNSIVYVLEY MLEESKKVR- PoptrCHSL7   FWAVHPGGPA ILNRMEKRFD LLPDKLNASR RALMDYGNAS SNTIVYVLEY MIEECRKMN- PoptrCHSL6   FWAVHPGGPA ILNRMEKRLD LLPDKLNASR RALMDYGNAS SNTIVYVLEY MIEESRKMK- PoptrCHSL1   FYVVHPGGTG VLNKFEEHIG LTKDKLRASR HVLSEYGNMW GPSMFFVLDE MRRRSAKEG- PpCHS        FWAVHPGGPA ILDQVEAKLK LTKDKMQGSR DILSEFGNMS SASVLFVLDQ IRHRSVKMG- PoptrCHSL3   FWIVQPSGAA ILNLIEAEVG LAQEKLSATR HVLSEFGNMG GPTVLFILDE IRRRSLEKR- PoptrCHSL2   FWAVHAGGRA ILDGVEAKLK LKKEKLGVTR HILREYGNVA SACVLFVLDE MRERSVREG- OsCHS2       FWVVHPGGPA ILDQVEEKVA LHKARMRASR NVLSEYGNMA SATVLFVLDE MRKLSADDG- OsCHS1       FWVAHPGGPA ILDQVEAKVG LDKERMRATR HVLSEYGNMS SACVLFILDE MRKRSAEDG- AtCHS        FWIAHPGGPA ILDQVEIKLG LKEEKMRATR HVLSEYGNMS SACVLFILDE MRRKSAKDG- PoptrCHS1    FWIAHPGGPA ILDQVEIKLD LKEEKLRATR NVLSDYGNMS SACVLFILDE MRNKSLEEG- PoptrCHS4    FWIAHPGGPA ILDQVEAKLG LKPEKLRATR HVLSEYGNMS SACVLFILDE MRKKSAEDG- PoptrCHS5    FWIAHPGGPA ILDQVEAKLA LKPEKLRATR HVLSEYGNMS SACVLFILDE MRKKSAEDG- PoptrCHS6    FWIAHPGGPA ILDQVEAKLA LKPEKLRATR HVLSEYGNMS SACVLFILDE MRKKSAEDG- PoptrCHS2    FWIAHPGGPA ILDQVEAKLE LKPEKLRATR QVLADYGNMS SACVLFILDE MRKKSAKDG- PoptrCHS3    FWIAHPGGPA ILDQVEAKLE LKPEKLRATR QVLADYGNMS SACVLFILDE MRKKSAKDG-   152                  ....|....| ....|....| ....|....| ....|....| ..                 425        435        445        455 PpCHS10      ANDNVNTEPE WGLLLAFGPG VTIEGALLRN LC-------- -- OsCHSL1      ------IREE WGLILAFGPG ITFEGMLVRG IN-------- -- PrCHS1       ------QSPE WGLILAFGPG ITFEGILARS LV-------- -- AtCHSL2      -----TEGEE WGLGLAFGPG ITFEGFLMRN L--------- -- PKSA         -----DAAQE WGLGLAFGPG ITFEGLLIRS L--------- -- NSCHSLK      -----NGGEE WGLALAFGPG ITFEGILLRS L--------- -- PoptrCHSL4   --------GE WGLALAFGPG ITFEGILLRS L--------- -- PoptrCHSL5   -------GEE WGLALAFGPG ITFEGILLRS L--------- -- OsCHSL2      -EAAEEEDCE WGLILAFGPG ITFEGILARN LQARARARD- -- SlChsl       -NGD-KNDND WGLILAFGPG L--------- ---------- -- PKSB         --NMNEEENE WGLILAFGPG VTFEGIIARN LDV------- -- PoptrCHSL7   ---------- -GRL------ ---------- ---------- -- PoptrCHSL6   ---AGAANCD WGLILAFGPG ITFEGILARN LTI------- -- PoptrCHSL1   -KATTGEGLD LGVLFGFGPG VTIETIVLRS FATD------ -- PpCHS        -ASTLGEGSE FGFFIGFGPG LTLEVLVLRA APNSA----- -- PoptrCHSL3   -KTTTGEGME WGVLIGLGAG ITVDTVVLHS VPIAEGR--- -- PoptrCHSL2   -KATTGEGLE WGVVIGLGPG LTMETLVLHS VPVAITK--- -- OsCHS2       -HATTGEGMD WGVLFGFGPG LTVETIVLHS VPITAAAPLI MQ OsCHS1       -HATTGEGMD WGVLFGFGPG LTVETVVLHS VPITAGAAA- -- AtCHS        -VATTGEGLE WGVLFGFGPG LTVETVVLHS VPL------- -- PoptrCHS1    -KSTTGEGLE WGVLFGFGPG LTVETVVLHS VPVEQTIYS- -- PoptrCHS4    -LQSTGEGLE WGVLFGFGPG LTVETVVLHS VATRV----- -- PoptrCHS5    -LQSTGEGLE WGVLFGFGPG LTVETVVLHS VAPTI----- -- PoptrCHS6    -LQSTGEGLE WGVLFGFGPG LTVETVVLHS VAPTI----- -- PoptrCHS2    -LKSTGEGLE WGVLFGFGPG LTVETVVLHS LPATI----- -- PoptrCHS3    -LKSTGEGLE WGVLFGFGPG LTVETVVLHS VASI------ --   Appendix C. Amino acid sequences used in construction of the phylogenetic tree shown in Figure 4.14.  >PoptrDFRL4 MKALVTGASGYLGGRLCHGLLKQGHSVRALVRRTSDISELPPPSSGGVFELAYGDITDYQSLLDAFSGCQ VIFHAAAIVEPWLPDPSKFFSVNVEGLNNVLQAAKETETIEKIIYTSSFFALGSTDGYVADESQVHCEKR FCTEYERSKMIADKIASQAAAEGVPIVMLYPGVIYGPGKLTTGNIVAQLLIERFAGRLPGYIGYGNDKFS FCHVDDLVDGHIAAMDKGRQGERYLLTGENASFKLVFDMAAIISETKKPRFSIPLCIIESYGWLLVLVSR LTGNLPLISPPTVHVLRHQWEYSCEKAKTELGYNPRGLEDGLKEVLPWLKSMGVIKY*  >PoptrDFRL5 MKKIVVTGASGFVGGVLCHTLLKQGHSVRALVRRTSDLSGLPSPSTGENFELAYGDVTDYRSLLDAIFGC DVIFHAAAAVEPWLPDPSKFFSVNVGGLKNVVQAAKETKMIEKIIYTSSMVALGSTDGYVADESQVHHEK YFSTEYERSKVAADKVASQAAAEGLPIVTLYPGVVYGPGKLTTGNALAKMLIDRFAGRLPGYIGRGNDRL SFCHVDDVVGGHIAAMDKGRLGERYLLTGENASFSRVLDIAAIITRTEKPRFSIPLWVIEAYGWLSILIF HFTGKLPLLCPPSVHVLRHQWEYSCEKARIELDYNPRSLKEGLDELLPWLKSLGAITY*   >At4g33360 MGPKMPNTETENMKILVTGSTGYLGARLCHVLLRRGHSVRALVRRTSDLSDLPPEVE LAYGDVTDYRSLTDACSGCDIVFHAAALVEPWLPDPSRFISVNVGGLKNVLEAVKET KTVQKIIYTSSFFALGSTDGSVANENQVHNERFFCTEYERSKAVADKMALNAASEGV PIILLYPGVIFGPGKLTSANMVARMLIERFNGRLPGYIGSGTDRYSFSHVDDVVEGH VAAMEKGRLGERYLLTGENASFKLVFDMAALITGTKKPNFSIPLWAINAYGWLSVLI SRVTGKLPLISPPTVTVLRHQWSYSCDKAKLELGYNPRSLKEGLEEMLPWLKSLGVI HY  >Os03g08624 153  MRIAVTGATGYLGSRLCGALADAGHAVRAFALRSAGGGGGGGDVEAGLLPASVELAYGDV ADVESLAAAFDRCDAVFHVAAAVEAWLPDPSIFITVNVGGLENVLKAARRTPTVKKIVYT SSFFAIGPTDGYVADETQMHQGKTFCTEYEKSKVLADQIALQAAAEGMPITIVYPGFMYG PGKLTAGNLVSRILIERFNGRLPGYVGHGHDRESFCHVDDVVAGHVAAMEKGREGERYLL TGENTSLVQIFDMASRITNTKAPRFHVPLWLLEIYGWISVLVSRITGKLPFISYPAVRVL RHQWAYSCEKAKKELGYSPRSLTEGLSETLLWLKDSEMIRF*  > PpDFRL4 MRRVMVTGATGYLGGRLCGMLVHAGLTVVALVRKTSQVQELPPEVELVEGDIRDGESVRRAIEGCDYVVHT AALVGSWLPDSSQFFKVNVEGFKNVIEAVKATPSVKKLIYTSSFFAVGPTDGYIGDETQFHSMKAFYSPYEES KAFADKLACEAAMEGVPIVSLYPGIIYGPGSMTKGNSLAEMMIERFNGRMPGYVGYKVKKFSFCHIDDVVVAY LAAIEIGRVGERYMLCGDNMSFHEVFDLAAGLTKTNPAKVTIPMWVLDVAGFLCVQWARFGAWTGISHQIPFI TTHSVNILKHQWAYSSEKAERELGYKSRPLEEGLLQLLTWLKATGRIKY*  >PoptrDFR1 MGTEAETVCVTGASGFIGSWLIMRLLEKGYAVRATVRDPDNMKKVTHLLELPKASTHLTLWKADLSVEGS YDEAIQGCTGVFHVATPMDFESKDPENEVIKPTINGVLDIMRACANSKTVRKIVFTSSAGTVDVEEKRKP VYDESCWSDLDFVQSIKMTGWMYFVSKTLAEQAAWKFAKENNLDFISIIPTLVVGPFIMQSMPPSLLTAL SLITGNEAHYGILKQGHYVHLDDLCMSHIFLYENPKAEGRYICNSDDANIHDLAKLLREKYPEYNVPAKF KDIDENLACVAFSSKKLTDLGFEFKYSLEDMFAGAVETCREKGLIPLSHRKQVVEECKENEVVPAS*  >PoptrDFR2 MGVEVETVCVTGASGFIGSWLVMRLLEKGYTVRATVRDPDNIRKVKHLLELPKADTYLTLWKADLSVEGS FDEAVQGCTGVFHVATPMDFESKDPENEVIKPTINGVLDIMKACAKAKTVRRIVFTSSAGTVDVEEHKKP VYDESCWSDLEFVQTVKMTGWMYFVSKTLAEQAAWKYAKENNLDFISVIPPLVVGPFIMHSMPPSLITAL SLITGNEAHYGIIKQGNYVHLDDLCRAHIVLFENPKAEGRYICSSHEATIHDLAKLLREKYPKYNVPAKF KDIDEDLASVVFSSKKLLDLGFEFKYSLEEMFAGAVETCREKGLIPLSHEK >AtDFR MVSQKETVCVTGASGFIGSWLVMRLLERGYFVRATVRDPGNLKKVQHLLDLPNAKTLLTL WKADLSEEGSYDDAINGCDGVFHVATPMDFESKDPENEVIKPTVNGMLGIMKACVKAKTV RRFVFTSSAGTVNVEEHQKNVYDENDWSDLEFIMSKKMTGWMYFVSKTLAEKAAWDFAEE KGLDFISIIPTLVVGPFITTSMPPSLITALSPITRNEAHYSIIRQGQYVHLDDLCNAHIF LYEQAAAKGRYICSSHDATILTISKFLRPKYPEYNVPSTFEGVDENLKSIEFSSKKLTDM GFNFKYSLEEMFIESIETCRQKGFLPVSLSYQSISEIKTKNENIDVKTGDGLTDGMKPCN KTETGITGERTDAPMLAQQMCA  >Os01g44260 MDFESEDPENEVVKPTVEGMLSIMRACRDAGTVKRIVFTSSAGTVNIEERQRPSYDH DDWSDIDFCRRVKMTGWMYFVSKSLAEKAAMEYAREHGLDLISVIPTLVVGPFISNG MPPSHVTALALLTGNEAHYSILKQVQFVHLDDLCDAEIFLFESPEARGRYVCSSHDA TIHGLATMLADMFPEYDVPRSFPGIDADHLQPVHFSSWKLLAHGFRFRYTLEDMFEA AVRTCREKGLLPPLPPPPTTAVAGGDGSAGVAGEKEPILGRGTGTAVGAETEALVK*  >PoptrDFRL6 TYCVTGANGYIGSWLVKLLLQRGYTVHATLRDLAKSLDLLSSWRGADRLRLFKADLREEGSFDEAVRGCD GVFHVAASMEFYVAGNEDNENYVQRNIIDPAIEGTLNLLTSCSKSNTVKRVVFTSSISTLTAKDGAGKWR QVVDETCQTPIDHVWNTKPPGWIYVLSKRLTEEAAFKYAKDNGIDLISVITTTVAGAFLTSSVPSSIRVL LSPITGDTKFFSILSAVNARMGSIALVHIDDICDAHIFLMEQTRAEGRYICSAHSCVLSQLINHLVEEYP CSNIQRLAEKQGSISPEISSKKLRDMGFKYKHSIKDIISETI  >At4g27250 MELQGEESKTATYCVTGASGYIGSWLVKSLLQRGYTVHATLRDLAKSEYFQSKWKEN ERLRLFRADLRDDGSFDDAVKGCDGVFHVAASMEFDISSDHVNLESYVQSKVIEPAL KGVRNVLSSCLKSKSVKRVVFTSSISTLTAKDENERMRSFVDETCKAHVDHVLKTQA SGWIYVLSKLVSEEEAFRYAKERGMDLVSVITTTVSGPFLTPFVPSSVQVLLSPITG DSKLFAILSAVNKRMGSIALVHIEDICRAHLFLMEQPKAKGQYICCVDNIDMHELML HHFSKDYLCKVQKVNEDEEERECMKPIISSKKLRELGFEYKYGIEEIVDQTIDASIK IKFPTLNHKLRQ  >Os04g53810 MSSEVERKTVCVTGGNGYVASLLVKMLLEKGYAVQTSVRDPNNPEKVSHFKDMEKLGPLK VFRANLEDEGSFDEAVAGCHYAFLVAAPVYDKSHKSDDLEKEIVQGGVEGTLNVMRSCAR AGTVKRVILTSSTAAVSSLRPLEGAGHVLDESSWSDIEYLRSMEKLSPTQAYSISKVLSE 154  KEATKFAEENGLSLVTLCPVVAVGASPAVRVDTSVPACLSLITGDEEMMNILKGIEKASG WSMPMVHIEDVCRAEIFVAEEESASGRYICGSLNTTVTEIAGFLAAKYPQYNVRCDCIEE HHPEKPTISLSSAKLIGEGFEFKYKNLDEMYDDLVAYGKALGLIPN*  >Os04g53800 MSAVERKTACVTGGSGYIASALIKMLLQKGYAVKTTVRNPDDMEKNSHFKELQALGPLKI FRADLEEEGSFDEAVAGCDYAFLVAAPMNLKSQNPEKELLEAGVQGTLNVLRSCVKAGTV KRVILTSSAAAVSGQPLQGDGNGSSHVLDESSWSDLDYLRSTNGISPAQAYAIAKVLSEK EASKLAEENGISLVAVCPVATVGASPAPVANESVANVLSLLSGNEEINTLRMIDQYSGGL KLVHVDDLCRAEIFLAEKASPSPSGRYICCALNTTMRQIARSLAAKYPHHNVDIDALGGG LPEKPTILLSSEKLTSEGFEFMYKTVDEMYDDAFVEYGMALGILHY*  >Os04g53850 MSAVERKTACVTGGNGYIASALIKMLLEKGYAVNTTVRNPDDMAKNSHLKDLQALGPLKV FRADMDEEGSFDDAIAGCDYAFLVAAPMNFNSENPEKDLVEAAVNGTLNAMRSCAKVGTV KRVIITSSDAAISRRPLQGDGYVLDEESWSDVDYLRTEKPPAWAYSVSKVLLEKAACKFA EENNMSLVTVFPVFTLGAAPAPVARTSVPGILSLLSGDETHLEVLKPLQWVTGSVSIVHV DDLCRAEIFLAEKESSSLSSAESSARYICCSFNTTVLALARFMAGRYPQYNVKTDRFDGM PEKPRVCCSSEKLIREGFEFKYTNMGDILDDLVEYGRALGILPH*  >Os04g53920 MSAVEMKTACVTGGNGYIASALIKMLLQKGYAVNTTVRNPGDDMKKTSHLKDLEALG PLEVFRADMDEEGSFDDAVAGCDYAFLVAAPVNFQSQNPEKELIEAGVQGTMNVMRS CVRAGTVKRVILTSSAPAVSGRPLQGDGHVLDEDSWSDVEYLTKEKPPAWAYSVSKV LMEKAACKLAEENNISLITVFPVFTLGAAPTPTAATSVSAMLSLLSSDETQLKTLKG LAATGPIPTVHVDDLCRAEVFVAEKESASGRYICSSLSTTVVAFARFVAGKHPRYNV KTDGFQGFPEKPRVCYSSEKLVREGFEFKWTDLDEVFDDLIEYGNVLGILPQ*  >PoptrANR1 MASQLTKKTACVIGGTGFVASLLVKLLLEKGYAVNTTVRDPDNQKKVAHLIALQNLGDLNIFGADLTDEE SFNAPIAGCELVFHVATPVNFASEDPENDMIKPAIQGVHNVLKACAKAKTVKRVILTSSAAALSINKLNG TGLIMDEKNWTDVEFLTSEKPPTWGYPASKTLAEKAAWKFAEENNIDLITVIPSLMTGPSLTLDIPSSVH LSMSLITGNEFLKNALKGMQMLSGSISITHVEDVCRAHIFLAEKESASGRYICCAVNTSVVELAEFLNKR YPQYQVPTDFGDFPSKAKLAITSEKLISEGFSFKYGIEEVYDQTVEYFKAKGLLN*  >PoptrANR2 MASQTKKNTACVIGGTGFVASLLIKLLLEKGYAVNTTVRDPDNQKKIAHLIALQNLGDLNIFGADLTNEE SFNAPIACCDLVFHVATPVNFASEDPENDMIKPAIQGVHNVLKACAKAKTVQRVILTSSAAAVSINKLNG TGLVMDEKNWTDVEFLTSEKPPTWGYPASKTLAEKAAWKFAEENNIDLITVIPSLMTGPSFTPHIPDSIN LAMSLITGNKFLINGLKGMQMLSGSISITHVEDVCRAHIFLAEKESASGRYICCGVNTSVVELAKFLNKR YPQYQVPTDCGDFPSEAKLIITSEKLSSEGFSFKYGIEEIYDQTVEYFKANGLLN*  > AtANR/BAN MDQTLTHTGSKKACVIGGTGNLASILIKHLLQSGYKVNTTVRDPENEKKIAHLRKLQ ELGDLKIFKADLTDEDSFESSFSGCEYIFHVATPINFKSEDPEKDMIKPAIQGVINV LKSCLKSKSVKRVIYTSSAAAVSINNLSGTGIVMNEENWTDVEFLTEEKPFNWGYPI SKVLAEKTAWEFAKENKINLVTVIPALIAGNSLLSDPPSSLSLSMSFITGKEMHVTG LKEMQKLSGSISFVHVDDLARAHLFLAEKETASGRYICCAYNTSVPEIADFLIQRYP KYNVLSEFEEGLSIPKLTLSSQKLINEGFRFEYGINEMYDQMIEYFESKGLIKAK  > PpDFRL1 MGHSTEKSKGTVCVTGATGFVASWLIKCLLQDGYRVRGAVRDPENYEKAAHLWAL SGAKERLQLVKGDLLVEGSYDAAVAGCEGVFHTAAALVRIKSDPKAEMLDPTILG TLNVLHSCAKSTTLKRVVLTSSTAAVRFRDDLEQPGAVTYLDEYSWSSIFFCTKY QIWYSLAKILSEQEAWKFAFLHSIDLVVVLPSFVIGPCLPYPLSKTAQDICDLLN GLCRNFGIHGRMGYVHVDDVARAHILVYETPSAQGRYICSAQEATPQELVQYLAD RYPHLQISTKFNDELPKMPYYKLNTTKLQRLGLNCKPLDVMFDDCISFLEEKGLL KRKPEKTPTSSSTPDEHSKDSVLQNV*  >AtTKPR1 MDQAKGKVCVTGASGFLASWLVKRLLLEGYEVIGTVRDPGNEKKLAHLWKLEGAKERLRL VKADLMEEGSFDNAIMGCQGVFHTASPVLKPTSNPEEEILRPAIEGTLNVLRSCRKNPSL KRVVLTSSSSTVRIRDDFDPKIPLDESIWTSVELCKRFQVWYALSKTLAEQAAWKFSEEN 155  GIDLVTVLPSFLVGPSLPPDLCSTASDVLGLLKGETEKFQWHGQMGYVHIDDVARTHIVV FEHEAAQGRYICSSNVISLEELVSFLSARYPSLPIPKRFEKLNRLHYDFDTSKIQSLGLK FKSLEEMFDDCIASLVEQGYLSTVLP  >PoptrDFRL1 MDQIKGRVCVTGASGYLASWLVKRLLLSGYHVTGTVRDPENEKKVAHLWRLEGAKERLRLVKADLMEEGS FDDAIMECRGVFHTASPAEILEPAIEGTLNVLRSCKRNPSLKRVILTSSSSTLRVRDDFDSNIPLEESSW SSVELCERLQIWYALSKTLAEKAAWEFCNGNGIDLITVLPSFVIGPSLSPDLCSTATDVLGLLTGESEKF HWHGRMGYVHIDDVALSHILVYEDETAGGRFLCSSIVLDNDELASFLSQRYPSLPIPKRFEQLKRPYYEF NTSRLERLGFKFKPIQEMFDDCIASLVEQGHLSSFSLAIN*  >Os08g40440 MENTTKGKVCVTGASGYVASWLVKRLLESGYHVLGTVRDPGNHKKVGHLWNLTGAKE RLELVRADLLEEGSFDDAVMACEGVFHTASPVITETDSSKAAVLDSAINGTLNVLRS CKKNPSLKRVVLTSSSSTVRLKDEADLPPNVLLDETSWSSMEFCESLQIWYAIAKTL AEKAAWEFAKENGIDLVAVLPTFVVGPNLSHELSPTTTDVLGLFQGETTKFTMYGRM GYVHIDDVASCHILLYETPRAAGSLPCVYGEQTYGFSTAKVRELGMKFRDVEEMFDD AVDSLRAHGYLLNSVP*  >Os09g32020 MLSRILHGYGGHGGRGFEQTYRCYSAAAFNKPQLEGGDKVIMPASALHRLASLHIDY PMLFELSHHGDAAAHRVTHCGVLEFVADEGTVIMPRWMMRGMRLDDGGLVVVRSASL PKGSYAKLQPHTGDFLDTANPKAVLEKTLRSFTCLTTGDTIMVAYNNKEFLIDIVET KPASAVCIIETDCEVDFAPPLDYKEPEKVQQKPSVPSSKAASEDQDQIKDEPEFRAF TGSGNRLDGKASKPLAAGISSNPAAASSAISDSNKKVNQETAASGVSNSTRQKKGKL VFGSNKSSSSSKEPEKAPPVKVDELAKKEEPKFQAFSGTSYSLKRNRDKVSHLWRLP SAKERLQLEEMLVPAINGTLNVLKSCKKNPFLKRVVLTSSSSTVRIRDESKHPEISL DETIWSSVALCEKLQLWYALAKISAEKAAWEFAKENNIDLVTVLPSFVIGPSLSHEL SVTASDILGLLQGDTDRFISYGRMGYVHIDDVASCHILVYEAPQATGRYLCNSVVLD NNELVALLAKQFPIFPIPRSLRNPYEKQSYELNTSKIQQLGFKFKGVQEMFGDCVES LKDQGHLLECPL*  >OryzaDFR2 MVISSKGKVCVTGASGFVASWLIKRLLEAGYHVIGTVRDPSNREKVSHLWRLPSAKE RLQLVRADLMEEGSFDDAVMACEGVFHTASPVLAKSDSNCKEEMLVPAINGTLNVLK SCKKNPFLKRVVLTSSSSTVRIMDESKHPEISLDETIWSSVALCEKLQLWYALAKIS AEKAAWEFAKENNIDLVTVLPSFVIGPSLSHELSVTASDILGLLQGDTDRFISYGRM GYVHIDDVASCHILVYEAPQATGRYLCNSVVLDNNELVALLAKQFPIFPIPRSLRNP YEKQSYELNTSKIQQLGFKFKGVQEMFGDCVESLKDQGHLLECPL  >PpDFRL2 MDLSKGAEVCVTGGTGYIASCLIQALLQRGYKVRTTARNPDDRAKTGFLWELPGA TERLEIVGAELLEEGTFDEAVHGVHTVFHTACPVVYDPNGDPEVSMLNPALKGNL NVLRACTKSHSIQRVVMTSSCSAIRYDHNRRPEDPPLSESVWSSPEYCRDHKMWY ALAKTLAEKEAFEFAAREGLNLVVICPSFVIGPSLTPIPTSTVFLILDLLRGRAQ EYPNKRIGFVHIDDVVTAHVLAMEVPEAHGRYICSSDVAHFGDIMSMLKTKYPKL QTPTRCSDMPPGDDIHHKMDTTKIKKLGLTEFKSIEQMFDDMLRSLHEKHLESL*  >Os01g03670 MPEYCVTGGTGFIASHLIRALLAASHTVRATVRDPEDEAKVGFLWELDGASERLQLV KADLMVEGSFDDAVRGVDGVFHAASPVVVVGNSSSNNGKPNDDDDEEEVQQRLVEPI VRGASNVLRSCARASPRPRRVVFTSSCSCVRYGAGAAAALNESHWSDAAYCAAHGLW YAYAKTLAEREAWRLAKERGLDMVAVNPSFVVGPILSQAPTSTALIVLALLRGELPR YPNTTVGFVHVDDAVLAHVVAMEDARASGRLICSCHVAHWSEIVGSLRERYPGYPIP AECGSHKGDDRAHKMDTAKIRALGFPPFLSVQQMFDDCIKSFQDKGLLPPHA*  >PoptrDFRL2 MPEYCVTGGTGFIAAYLVKSLLEKGHRVRTTVRDPGDVGKVGLLREFDGAKERLK IFKADLLEEGSFDEAIQGVDGVFHTASPVLLPHDDNIQAMLIDPCINGTLNVLNS CSKANTVKRVVLTSSCSSIRYRDDVQQVSPLNESHWSDPEYCKRYDLWYAYAKTI GEKEAWRSAKENGIDLVVVNPSFVVGPLLAPQPTSTLLLILAIVKGLRGEYPNMT IGFVHIDDVVAAHILAMEDKKASGRLVCSGSVAHWSEIIEMLRAKYPSYPYENKC SSQKGDCNPHSMDTTKIATLGFPPFKTLEEMFDDCIKSFQEKGFL* 156   >PoptrCCRL1 MPEYCVTGGTGFIAAYLVKSLLEKGHTVRITVRDPGNVRKVGFLQEFNGAKERLK IFKAELLEEGSFDEAIQGVDGVFHVAAPVLVPYSDRIQETLIDPCIKGTLNVLNS CLKASSVKRVVFTSSSSTVRYRDDTPQIFSLNESHWSDTEYCKRHNLWYAYAKTV AEKEAWRVSKENGIDLVSFIPSFVVGPLLAPEPNSTLLLIQSVVKGSRGEYPNMT VGFTHIDDVVAGNILAMENSEASGRLVCSGPVAHWSQIIKMLRAKYPSYPYENKC SSQEGDNIPHSMDTTKIAQLGLPPFKTHEQMFDDCIRSLQEKGFL*  >AtTKPR2 mseylvtggtgfiasyiiksllelghtvrttvrnprdeekvgflwefqgakqrlkil qadltvegsfdeavngvdgvfhtaspvlvpqdhniqetlvdpiikgttnvmsscaks katlkrivltsscssiryrfdateasplneshwsdpeyckrfnlwygyaktlgerea wriaeekgldlvvvnpsfvvgpllgpkptstllmilaiakglageypnftvgfvhid dvvaahvlameepkasgriicsssvahwseiielmrnkypnypfenkcsnkegdnsp hsmdtrkihelgfgsfkslpemfddciisfqkkgll  >At1g25460 MAEYLVTGGTSFIASHVIKSLLEFGHYVRTTVRDSEDEEKVGFLWDLKGAKERLKIF EADLTIEGSFDEAVNGVDGVFHIASRVSVRLDNNNLDKFDPNISGTMNVMNSCAKSR NTVKRIVLTSSSTAIRYRFDATQVSPLNESHWTDLEYCKHFKIWYAYKKTLGEKEAW RIAADKKLNLVVVIPSFCIGPILSPKPTSSPLIFLSIIKGTRGTYPNFRGGFVHIDD VVAAQILAMEEPKASGRILCSSSVAHWSEIIEMLRIKYPLYPFETKCGSEEGKDMPH SLDTTKIHELGFASFKSLTEMFDDCIKCFQDKGLL  >Os09g04050 MPTDETAAAAPATTALSGHGCTVCVTGAGGFIASWLVKRLLEKGYTVRGTVRNPMDPKND HLRALDGAGERLVLLRADLLDPDSLVAAFTGCEGVFHAASPVTDDPEKMIEPAIRGTRYV ITAAADTGIKRVVFTSSIGTVYMNPYRDPNKPVDDTCWSDLEYCKRTENWYCYAKTVAEQ GAWEVARRRGVDLVVVNPVLVLGPLLQATVNASTEHVMKYLTGSAKTYVNAAQAYVHVRD VAEAHVRVYDCGGARGRYICAESTLHRGDLCRALAKLFPEYPVPSRCKDEAAPPVKGYLF SNQRLRDLGMDFVPVRQCLYETVRSLQDKGLLPVLPPTADDHHHPSS*  >Os02g08420 MAAAVVCVTGAGGFIGSWIVKLLLARGYAVRGTSRRADDPKNAHLWALDGAAERLTMVSV DLLDRGSLRAAFAGCHGVIHTASPMHDDPEEIIEPVITGTLNVVEVAADAGVRRVVLSST IGTMYMDPRRDPDSPLDDSFWSDLDYCKNTKNWYCYAKTIAERKAWEVARGRGVDMAVVI PVVVLGELLQPGMNTSTKHILKYLTGEAKTYVNESHAYVHVVDAAEAHVRVLEAPGAGGR RYICAERTLHRGELCRILAGLFPEYPIPTRCRDEINPPKKGYKFTNQPLKDLGIKFTPVH EYLYEAVKSLEDKGFIKKTSNTKELHRQSSPPQNSPASMLMSKL*  >Os08g34280 MTVIDGAVAADAGGAAAAVVQPGNGQTVCVTGAAGYIASWLVKLLLEKGYTVKGTVRNPD DPKNAHLKALDGAGERLVLCKADLLDYDAICRAVAGCHGVFHTASPVTDDPEQMVEPAVR GTEYVINAAAEAGTVRRVVFTSSIGAVTMDPNRGPDVVVDESCWSDLDYCKETRNWYCYG KAVAEQAAWEAARRRGVELVVVNPVLVIGPLLQPTVNASVAHILKYLDGSASKFANAVQA YVDVRDVAAAHLLVFESPSAAGRFLCAESVLHREGVVRILAKLFPEYPVPTRCSDEKNPR KQPYKMSNQKLRDLGLEFRPASQSLYETVKCLQEKGHLPVLAAEKTEEEAGEVQGGIAIR A*  >Os09g25150 MTVVVVADDAAAAAAAAQQQEELPPGHGQTVCVTGAAGYIASWLVKLLLERGYTVKGTVR NPDDPKNAHLKALDGADERLVLCKADLLDYDSIRAAVDGCHGVFHTASPVTDDPEQMVEP AVRGTEYVIKAAAEAGTVRRVVFTSSIGAVTMDPNRGPDVVVDESCWSDLEFCKKTKNWY CYGKAVAEQEACKAAEERGVDLVVVSPVLVVGPLLQPTVNASAVHILKYLDGSAKKYANA VQAYVDVRDVAAAHVRVFEAPEASGRHLCAERVLHREDVVHILGKLFPEYPVPTR*  >PoptrCCR2 MPVDASSLSGQGQTICVTGAGGFIASWMVKLLLDKGYTVRGTARNPADPKNSHLRGLEGAEERLTLCKAD LLDYESLKEAIQGCDGVFHTASPVTDDPEEMVEPAVNGTKNVIIAAAEAKVRRVVFTSSIGAVYMDPNKG PDVVIDESCWSDLEFCKNTKNWYCYGKAVAEQAAWDMAKEKGVDLVVVNPVLVLGPLLQPTVNASITHIL KYLTGSAKTYANSVQAYVHVRDVALAHILVFETPSASGRYLCSESVLHRGEVVEILAKFFPEYPIPTKCS DEKNPRKQPYKFSNQKLRDLGFEFTPVKQCLYETVKSLQEKGHLPIPKQAAEESLKIQ* 157   >AtCCR1 MPVDVASPAGKTVCVTGAGGYIASWIVKILLERGYTVKGTVRNPDDPKNTHLRELEGGKERLILCKADLQ DYEALKAAIDGCDGVFHTASPVTDDPEQMVEPAVNGAKFVINAAAEAKVKRVVITSSIGAVYMDPNRDPE AVVDESCWSDLDFCKNTKNWYCYGKMVAEQAAWETAKEKGVDLVVLNPVLVLGPPLQPTINASLYHVLKY LTGSAKTYANLTQAYVDVRDVALAHVLVYEAPSASGRYLLAESARHRGEVVEILAKLFPEYPLPTKCKDE KNPRAKPYKFTNQKIKDLGLEFTSTKQSLYDTVKSLQEKGHLAPPPPPPSASQESVENGIKIGS  >AtCCR2 MLVDGKLVCVTGAGGYIASWIVKLLLERGYTVRGTVRNPTDPKNNHLRELQGAKERLTLHSADLLDYEAL CATIDGCDGVFHTASPMTDDPETMLEPAVNGAKFVIDAAAKAKVKRVVFTSSIGAVYMNPNRDTQAIVDE NCWSDLDFCKNTKNWYCYGKMLAEQSAWETAKAKGVDLVVLNPVLVLGPPLQSAINASLVHILKYLTGSA KTYANLTQVYVDVRDVALGHVLVYEAPSASGRYILAETALHRGEVVEILAKFFPEYPLPTKCSDEKNPRA KPYKFTTQKIKDLGLEFKPIKQSLYESVKSLQEKGHLPLPQDSNQNEVIIES  > PpDFRL3 MANGQVVCVTGANGFIASWLVKSLLERGYTVRGTVRNPEKSKHLLNLPGANERLELIEADLLAPEAFDSAVH GCHGVFHTASPFHFNITDPDSQLIEPAVKGTLNVLESCAKAGTKKIVLTSSVAAVAYSPKRAGASVVDETFFS DPEFCQKEQRWYVLSKTLAESAAWEFVKEHNLNMVAINPTMVIGPLLQSSMNTSNELLLGFLNGTAKSFPNQ AVGWVSVKDVAMAHILAYEKPEAEGRYIINERLIHYGEMVSLLMNRYPQYPIVAKDADDSTRLPSYNLSNEKIK KLGLTFQPLEEALDETVACFKELKLLD*  >PoptrCCRL4 MSSLVSYRAVATGTERMSRGGDGKVVCVTGGSGYIASWLVKLLLQRGYTVKTTVR DPNDPKKTEHLLALEGAKERLHLFKANLLEEGAFDPIVDGCEGVFHTASPVSFSP TDDPQVDLIDPALKGTLNVLRSCAKVHSIRRVVLTSSAAACIYSGKPLNHDVVID ETWYSDPAICKELKAWYALSKTLAEEAAWNFAKENATDLVTVHPSFVIGPLLQPT LNLSVEMILDLVNGAETYPNGYYRCIDVRDVANAHIQAFEIPSASGRYVLTAYVT TFSEVLKIIRENYPTLRLPEKSTESMFKPYQVSKEKAKTLGINFTPLDLSLVDTI ESLKEKGFLKI*  >PoptrCCRL3 MSGEGKVVSVTGASGYIASWLVKLLLERGYTVKASVRDPNDAKKTEHLLALDGAK ERLQLFKADLLDEGSFDPVVEGCECVFHTASPFYFTVNDPQAELVDPALKGTVNV LRSCTKIPSIKRVVITSSMAAVVFNGKSLAPDVVVDETWFSDSDFCEKSKLWYHL SKTLAEEAAWKFTKENGIDMVTLNPGLVIGPLLQPTLNQSAESVLDLINGAKSYP NTTYRWVDVRDVANAHIYALENPSANGRYCLVGTVIHSSEAVKILSKLYPDLTIP KQCADDKPPMPKYQVSKERAASLGVKYTPLEASLKDTIESLKEKNFVSF*  >Os01g34480 MSSESEAAPGTGKLVCVTGASGYIASWLVRLLLARGYTVRATIRDTSDPKKTLHLRA LDGANERLHLFEANLLEEGSFDAAVNGCDCVFHTASPFYHNVKDPKAELLDPAVKGT LNVLGSCKKASIRRVIVTSSMAAVAYNGKPRTPDVVVDETWFSVPEICEKHQQWYVL SKTLAEEAAWKFSKDNGFEIVTVNPAMVIGPLLQPSLNTSAEAILKLINGSSSTYPN FSFGWINVKDVALAHILAYEVPSANGRYCMVERVAHYSELVQIIREMYPNIPLPDKC ADDKPSVPIYQVSKEKIKSLGLELTPLHTSIKETIESLKEKGFVTFDSSNL*  >PoptrCCRL1 MSTGAGKIVCVTGASGYIASWIVKLLLSRGYTVKASVRDPNDPKKTQHLRALRGA QERLELVKANLLEEGSFDSIVEGCEGVFHTASPFYHDVKDPQAELLDPAVKGTLN VLGSCARHPSIKRVVLTSSMAAVAYNRKPRTPDVVVDETWFSDPELCRESKLWYV LSKTLAEDAAWKFAKEKGMDMVAINPSMVIGPLLQPTLNTSAAAILSLIKGAQTF SNASFGWINVKDVANAHIQAFELSSASGRYCLVERVAHHSEVVKILRELYPDLQL PEKCADDKPYVPIYQVSKEKAKSLGIEFIPLEASIKETVESLKEKGFVSF*  >PoptrCCRL2 MSSGAGKIVCVTGASGYIASWLVKLLLSRGYTVKASVRDPNDPKKTEHLRALNGA QERLQLFKANLLEEGSFDSIVEGCEGVFHTASPFYHDVKDPQVELLDPAVKGTLN VLGSCAKHPSIRRVVLTSSVAAVAYNGKPRTPDVVVDETWFSDPNLCRESKVWYV LSKTLAEDAAWKFAKEKDMDMVAINPAMVIGPLLQPTLNTSAAAILSLIKGAQTF PNASFGWINVKDVANAHIQAFELSSASGRYCLVERVAHYSEVVKILHELYPDLQL PEKCADDKPYVPIYQVSKEKAKSLGVEFIPLEASVKETVESLKEKGFVSF*  158  >AtCCRL14 mansgegkvvcvtgasgyiaswlvkfllsrgytvkasvrdpsdpkktqhlvslegak erlhlfkadlleqgsfdsaidgchgvfhtaspffndakdpqaelidpavkgtlnvln scakassvkrvvvtssmaavgyngkprtpdvtvdetwfsdpelceaskmwyvlsktl aedaawklakekgldivtinpamvigpllqptlntsaaailnlingaktfpnlsfgw vnvkdvanahiqafevpsangryclvervvhhseivnilrelypnlplpercvdenp yvptyqvskdktrslgidyiplkvsiketveslkekgfaqf   Appendix D. Alignment of amino acid sequences used to generate the phylogenetic tree shown in Figure 4.14.               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                  5          15         25         35         45         55 PpDFRL4      ---------- ---------- ---------- ---------- ---------- ---------- Os03g08624   ---------- ---------- ---------- ---------- ---------- ---------- At4g33360    ---------- ---------- ---------- ---------- ---------- ---------M PoptrDFRL5   ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFRL4   ---------- ---------- ---------- ---------- ---------- ---------- Os02g08420   ---------- ---------- ---------- ---------- ---------- ---------- Os09g04050   ---------- ---------- ---------- ---------- ---------- -MPTDETAAA Os08g34280   ---------- ---------- ---------- ---------- ------MTVI DGAVAADAGG Os09g25150   ---------- ---------- ---------- ---------- ---MTVVVVA DDAAAAAAAA PoptrCCR2    ---------- ---------- ---------- ---------- ---------- ---------M AtCCR1       ---------- ---------- ---------- ---------- ---------- ---------- AtCCR2       ---------- ---------- ---------- ---------- ---------- ---------- PpDFRL3      ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCRL4   ---------- ---------- ---------- ---------- --------MS SLVSYRAVAT PoptrCCRL3   ---------- ---------- ---------- ---------- ---------- ---------- Os01g34480   ---------- ---------- ---------- ---------- ---------- ---------M AtCCRL14     ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCRL1   ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCRL2   ---------- ---------- ---------- ---------- ---------- ---------- PpDFRL1      ---------- ---------- ---------- ---------- ---------- ---------- AtTKPR1      ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFRL1   ---------- ---------- ---------- ---------- ---------- ---------- Os08g40440   ---------- ---------- ---------- ---------- ---------- ---------- Os09g32020   MLSRILHGYG GHGGRGFEQT YRCYSAAAFN KPQLEGGDKV IMPASALHRL ASLHIDYPML OryzaDFR2    ---------- ---------- ---------- ---------- ---------- ---------- PpDFRL2      ---------- ---------- ---------- ---------- ---------- ---------- Os01g03670   ---------- ---------- ---------- ---------- ---------- ---------- At1g25460    ---------- ---------- ---------- ---------- ---------- ---------- AtTKPR2      ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFRL2   ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCRL1   ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFRL6   ---------- ---------- ---------- ---------- ---------- ---------- At4g27250    ---------- ---------- ---------- ---------- ---------- ---------- Os01g44260   ---------- ---------- ---------- ---------- ---------- ---------- AtDFR        ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFR1    ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFR2    ---------- ---------- ---------- ---------- ---------- ---------- AtANR/BAN    ---------- ---------- ---------- ---------- ---------- ---------- PoptrANR1    ---------- ---------- ---------- ---------- ---------- ---------- PoptrANR2    ---------- ---------- ---------- ---------- ---------- ---------- Os04g53810   ---------- ---------- ---------- ---------- ---------- ---------- Os04g53800   ---------- ---------- ---------- ---------- ---------- ---------- Os04g53850   ---------- ---------- ---------- ---------- ---------- ---------- Os04g53920   ---------- ---------- ---------- ---------- ---------- ----------               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                  65         75         85         95        105        115 159  PpDFRL4      ---------- MRRVMVTGAT GYLGG----- ---RLCGML- VHAGLTV--- ---------- Os03g08624   ---------- -MRIAVTGAT GYLGS----- ---RLCGAL- ADAGHAV--- ---------- At4g33360    GPKMPNTETE NMKILVTGST GYLGA----- ---RLCHVL- LRRGHSV--- ---------- PoptrDFRL5   ---------- MKKIVVTGAS GFVGG----- ---VLCHTL- LKQGHSV--- ---------- PoptrDFRL4   ---------- -MKALVTGAS GYLGG----- ---RLCHGL- LKQGHSV--- ---------- Os02g08420   --------MA AAVVCVTGAG GFIGS----- ---WIVKLL- LARGYAV--- ---------- Os09g04050   APATTALSGH GCTVCVTGAG GFIAS----- ---WLVKRL- LEKGYTV--- ---------- Os08g34280   AAAAVVQPGN GQTVCVTGAA GYIAS----- ---WLVKLL- LEKGYTV--- ---------- Os09g25150   QQQEELPPGH GQTVCVTGAA GYIAS----- ---WLVKLL- LERGYTV--- ---------- PoptrCCR2    PVDASSLSGQ GQTICVTGAG GFIAS----- ---WMVKLL- LDKGYTV--- ---------- AtCCR1       -MPVDVASPA GKTVCVTGAG GYIAS----- ---WIVKIL- LERGYTV--- ---------- AtCCR2       ------MLVD GKLVCVTGAG GYIAS----- ---WIVKLL- LERGYTV--- ---------- PpDFRL3      -------MAN GQVVCVTGAN GFIAS----- ---WLVKSL- LERGYTV--- ---------- PoptrCCRL4   GTERMSRGGD GKVVCVTGGS GYIAS----- ---WLVKLL- LQRGYTV--- ---------- PoptrCCRL3   ------MSGE GKVVSVTGAS GYIAS----- ---WLVKLL- LERGYTV--- ---------- Os01g34480   SSESEAAPGT GKLVCVTGAS GYIAS----- ---WLVRLL- LARGYTV--- ---------- AtCCRL14     ----MANSGE GKVVCVTGAS GYIAS----- ---WLVKFL- LSRGYTV--- ---------- PoptrCCRL1   -----MSTGA GKIVCVTGAS GYIAS----- ---WIVKLL- LSRGYTV--- ---------- PoptrCCRL2   -----MSSGA GKIVCVTGAS GYIAS----- ---WLVKLL- LSRGYTV--- ---------- PpDFRL1      --MGHSTEKS KGTVCVTGAT GFVAS----- ---WLIKCL- LQDGYRV--- ---------- AtTKPR1      ------MDQA KGKVCVTGAS GFLAS----- ---WLVKRL- LLEGYEV--- ---------- PoptrDFRL1   ------MDQI KGRVCVTGAS GYLAS----- ---WLVKRL- LLSGYHV--- ---------- Os08g40440   -----MENTT KGKVCVTGAS GYVAS----- ---WLVKRL- LESGYHV--- ---------- Os09g32020   FELSHHGDAA AHRVTHCGVL EFVADEGTVI MPRWMMRGMR LDDGGLVVVR SASLPKGSYA OryzaDFR2    -----MVISS KGKVCVTGAS GFVAS----- ---WLIKRL- LEAGYHV--- ---------- PpDFRL2      -----MDLSK GAEVCVTGGT GYIAS----- ---CLIQAL- LQRGYKV--- ---------- Os01g03670   ---------- MPEYCVTGGT GFIAS----- ---HLIRAL- LAASHTV--- ---------- At1g25460    ---------- MAEYLVTGGT SFIAS----- ---HVIKSL- LEFGHYV--- ---------- AtTKPR2      ---------- MSEYLVTGGT GFIAS----- ---YIIKSL- LELGHTV--- ---------- PoptrDFRL2   ---------- MPEYCVTGGT GFIAA----- ---YLVKSL- LEKGHRV--- ---------- PoptrCCRL1   ---------- MPEYCVTGGT GFIAA----- ---YLVKSL- LEKGHTV--- ---------- PoptrDFRL6   ---------- --TYCVTGAN GYIGS----- ---WLVKLL- LQRGYTV--- ---------- At4g27250    -MELQGEESK TATYCVTGAS GYIGS----- ---WLVKSL- LQRGYTV--- ---------- Os01g44260   ---------- ---------- ---------- ---------- ---------- ---------- AtDFR        ------MVSQ KETVCVTGAS GFIGS----- ---WLVMRL- LERGYFV--- ---------- PoptrDFR1    ------MGTE AETVCVTGAS GFIGS----- ---WLIMRL- LEKGYAV--- ---------- PoptrDFR2    ------MGVE VETVCVTGAS GFIGS----- ---WLVMRL- LEKGYTV--- ---------- AtANR/BAN    -MDQTLTHTG SKKACVIGGT GNLAS----- ---ILIKHL- LQSGYKV--- ---------- PoptrANR1    ----MASQLT KKTACVIGGT GFVAS----- ---LLVKLL- LEKGYAV--- ---------- PoptrANR2    ----MASQTK KNTACVIGGT GFVAS----- ---LLIKLL- LEKGYAV--- ---------- Os04g53810   ----MSSEVE RKTVCVTGGN GYVAS----- ---LLVKML- LEKGYAV--- ---------- Os04g53800   -----MSAVE RKTACVTGGS GYIAS----- ---ALIKML- LQKGYAV--- ---------- Os04g53850   -----MSAVE RKTACVTGGN GYIAS----- ---ALIKML- LEKGYAV--- ---------- Os04g53920   -----MSAVE MKTACVTGGN GYIAS----- ---ALIKML- LQKGYAV--- ----------               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                 125        135        145        155        165        175 PpDFRL4      ---------- ---------- ---------- ---------- ---------- ---------- Os03g08624   ---------- ---------- ---------- ---------- ---------- ---------- At4g33360    ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFRL5   ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFRL4   ---------- ---------- ---------- ---------- ---------- ---------- Os02g08420   ---------- ---------- ---------- ---------- ---------- ---------- Os09g04050   ---------- ---------- ---------- ---------- ---------- ---------- Os08g34280   ---------- ---------- ---------- ---------- ---------- ---------- Os09g25150   ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCR2    ---------- ---------- ---------- ---------- ---------- ---------- AtCCR1       ---------- ---------- ---------- ---------- ---------- ---------- AtCCR2       ---------- ---------- ---------- ---------- ---------- ---------- PpDFRL3      ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCRL4   ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCRL3   ---------- ---------- ---------- ---------- ---------- ---------- Os01g34480   ---------- ---------- ---------- ---------- ---------- ---------- 160  AtCCRL14     ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCRL1   ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCRL2   ---------- ---------- ---------- ---------- ---------- ---------- PpDFRL1      ---------- ---------- ---------- ---------- ---------- ---------- AtTKPR1      ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFRL1   ---------- ---------- ---------- ---------- ---------- ---------- Os08g40440   ---------- ---------- ---------- ---------- ---------- ---------- Os09g32020   KLQPHTGDFL DTANPKAVLE KTLRSFTCLT TGDTIMVAYN NKEFLIDIVE TKPASAVCII OryzaDFR2    ---------- ---------- ---------- ---------- ---------- ---------- PpDFRL2      ---------- ---------- ---------- ---------- ---------- ---------- Os01g03670   ---------- ---------- ---------- ---------- ---------- ---------- At1g25460    ---------- ---------- ---------- ---------- ---------- ---------- AtTKPR2      ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFRL2   ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCRL1   ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFRL6   ---------- ---------- ---------- ---------- ---------- ---------- At4g27250    ---------- ---------- ---------- ---------- ---------- ---------- Os01g44260   ---------- ---------- ---------- ---------- ---------- ---------- AtDFR        ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFR1    ---------- ---------- ---------- ---------- ---------- ---------- PoptrDFR2    ---------- ---------- ---------- ---------- ---------- ---------- AtANR/BAN    ---------- ---------- ---------- ---------- ---------- ---------- PoptrANR1    ---------- ---------- ---------- ---------- ---------- ---------- PoptrANR2    ---------- ---------- ---------- ---------- ---------- ---------- Os04g53810   ---------- ---------- ---------- ---------- ---------- ---------- Os04g53800   ---------- ---------- ---------- ---------- ---------- ---------- Os04g53850   ---------- ---------- ---------- ---------- ---------- ---------- Os04g53920   ---------- ---------- ---------- ---------- ---------- ----------               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                 185        195        205        215        225        235 PpDFRL4      ---------- ---------- ---------V ALVRKT---- ------SQVQ ELPPEVELVE Os03g08624   ---------- ---------- ---------R AFALRS-AGG GGGGGDVEAG LLPASVELAY At4g33360    ---------- ---------- ---------R ALVRRT---- ------SDLS DLPPEVELAY PoptrDFRL5   ---------- ---------- ---------R ALVRRT-SDL SG----LPSP STGENFELAY PoptrDFRL4   ---------- ---------- ---------R ALVRRT-SDI SE----LPPP SSGGVFELAY Os02g08420   ---------- ---------- ---------R GTSRRA-DDP KN-AHLWALD GAAERLTMVS Os09g04050   ---------- ---------- ---------R GTVRNP-MDP KN-DHLRALD GAGERLVLLR Os08g34280   ---------- ---------- ---------K GTVRNP-DDP KN-AHLKALD GAGERLVLCK Os09g25150   ---------- ---------- ---------K GTVRNP-DDP KN-AHLKALD GADERLVLCK PoptrCCR2    ---------- ---------- ---------R GTARNP-ADP KN-SHLRGLE GAEERLTLCK AtCCR1       ---------- ---------- ---------K GTVRNP-DDP KN-THLRELE GGKERLILCK AtCCR2       ---------- ---------- ---------R GTVRNP-TDP KN-NHLRELQ GAKERLTLHS PpDFRL3      ---------- ---------- ---------R GTVRNP---- EKSKHLLNLP GANERLELIE PoptrCCRL4   ---------- ---------- ---------K TTVRDP-NDP KKTEHLLALE GAKERLHLFK PoptrCCRL3   ---------- ---------- ---------K ASVRDP-NDA KKTEHLLALD GAKERLQLFK Os01g34480   ---------- ---------- ---------R ATIRDT-SDP KKTLHLRALD GANERLHLFE AtCCRL14     ---------- ---------- ---------K ASVRDP-SDP KKTQHLVSLE GAKERLHLFK PoptrCCRL1   ---------- ---------- ---------K ASVRDP-NDP KKTQHLRALR GAQERLELVK PoptrCCRL2   ---------- ---------- ---------K ASVRDP-NDP KKTEHLRALN GAQERLQLFK PpDFRL1      ---------- ---------- ---------R GAVRDP-ENY EKAAHLWALS GAKERLQLVK AtTKPR1      ---------- ---------- ---------I GTVRDP-GNE KKLAHLWKLE GAKERLRLVK PoptrDFRL1   ---------- ---------- ---------T GTVRDP-ENE KKVAHLWRLE GAKERLRLVK Os08g40440   ---------- ---------- ---------L GTVRDP-GNH KKVGHLWNLT GAKERLELVR Os09g32020   ETDCEVDFAP PLDYKEPEKV QQKPSVPSSK AASEDQ-DQI KDEPEFRAFT GSGNRLDGKA OryzaDFR2    ---------- ---------- ---------I GTVRDP-SNR EKVSHLWRLP SAKERLQLVR PpDFRL2      ---------- ---------- ---------R TTARNP-DDR AKTGFLWELP GATERLEIVG Os01g03670   ---------- ---------- ---------R ATVRDP-EDE AKVGFLWELD GASERLQLVK At1g25460    ---------- ---------- ---------R TTVRDS-EDE EKVGFLWDLK GAKERLKIFE AtTKPR2      ---------- ---------- ---------R TTVRNP-RDE EKVGFLWEFQ GAKQRLKILQ PoptrDFRL2   ---------- ---------- ---------R TTVRDP-GDV GKVGLLREFD GAKERLKIFK PoptrCCRL1   ---------- ---------- ---------R ITVRDP-GNV RKVGFLQEFN GAKERLKIFK PoptrDFRL6   ---------- ---------- ---------H ATLRDL---A KSLDLLSSWR GA-DRLRLFK 161  At4g27250    ---------- ---------- ---------H ATLRDL-AKS EYFQSKWKEN ---ERLRLFR Os01g44260   ---------- ---------- ---------- ---------- ---------- ---------- AtDFR        ---------- ---------- ---------R ATVRDP-GNL KKVQHLLDLP NAKTLLTLWK PoptrDFR1    ---------- ---------- ---------R ATVRDP-DNM KKVTHLLELP KASTHLTLWK PoptrDFR2    ---------- ---------- ---------R ATVRDP-DNI RKVKHLLELP KADTYLTLWK AtANR/BAN    ---------- ---------- ---------N TTVRDP-ENE KKIAHLRKLQ ELGD-LKIFK PoptrANR1    ---------- ---------- ---------N TTVRDP-DNQ KKVAHLIALQ NLGD-LNIFG PoptrANR2    ---------- ---------- ---------N TTVRDP-DNQ KKIAHLIALQ NLGD-LNIFG Os04g53810   ---------- ---------- ---------Q TSVRDP-NNP EKVSHFKDME KLGP-LKVFR Os04g53800   ---------- ---------- ---------K TTVRNP-DDM EKNSHFKELQ ALGP-LKIFR Os04g53850   ---------- ---------- ---------N TTVRNP-DDM AKNSHLKDLQ ALGP-LKVFR Os04g53920   ---------- ---------- ---------N TTVRNPGDDM KKTSHLKDLE ALGP-LEVFR               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                 245        255        265        275        285        295 PpDFRL4      GDIRDGESVR RAIEGCDYVV HT-------- ---------- ---------- ---------- Os03g08624   GDVADVESLA AAFDRCDAVF HV-------- ---------- ---------- ---------- At4g33360    GDVTDYRSLT DACSGCDIVF HA-------- ---------- ---------- ---------- PoptrDFRL5   GDVTDYRSLL DAIFGCDVIF HA-------- ---------- ---------- ---------- PoptrDFRL4   GDITDYQSLL DAFSGCQVIF HA-------- ---------- ---------- ---------- Os02g08420   VDLLDRGSLR AAFAGCHGVI HT-------- ---------- ---------- ---------- Os09g04050   ADLLDPDSLV AAFTGCEGVF HA-------- ---------- ---------- ---------- Os08g34280   ADLLDYDAIC RAVAGCHGVF HT-------- ---------- ---------- ---------- Os09g25150   ADLLDYDSIR AAVDGCHGVF HT-------- ---------- ---------- ---------- PoptrCCR2    ADLLDYESLK EAIQGCDGVF HT-------- ---------- ---------- ---------- AtCCR1       ADLQDYEALK AAIDGCDGVF HT-------- ---------- ---------- ---------- AtCCR2       ADLLDYEALC ATIDGCDGVF HT-------- ---------- ---------- ---------- PpDFRL3      ADLLAPEAFD SAVHGCHGVF HT-------- ---------- ---------- ---------- PoptrCCRL4   ANLLEEGAFD PIVDGCEGVF HT-------- ---------- ---------- ---------- PoptrCCRL3   ADLLDEGSFD PVVEGCECVF HT-------- ---------- ---------- ---------- Os01g34480   ANLLEEGSFD AAVNGCDCVF HT-------- ---------- ---------- ---------- AtCCRL14     ADLLEQGSFD SAIDGCHGVF HT-------- ---------- ---------- ---------- PoptrCCRL1   ANLLEEGSFD SIVEGCEGVF HT-------- ---------- ---------- ---------- PoptrCCRL2   ANLLEEGSFD SIVEGCEGVF HT-------- ---------- ---------- ---------- PpDFRL1      GDLLVEGSYD AAVAGCEGVF HT-------- ---------- ---------- ---------- AtTKPR1      ADLMEEGSFD NAIMGCQGVF HT-------- ---------- ---------- ---------- PoptrDFRL1   ADLMEEGSFD DAIMECRGVF HT-------- ---------- ---------- ---------- Os08g40440   ADLLEEGSFD DAVMACEGVF HT-------- ---------- ---------- ---------- Os09g32020   SKPLAAGISS NPAAASSAIS DSNKKVNQET AASGVSNSTR QKKGKLVFGS NKSSSSSKEP OryzaDFR2    ADLMEEGSFD DAVMACEGVF HT-------- ---------- ---------- ---------- PpDFRL2      AELLEEGTFD EAVHGVHTVF HT-------- ---------- ---------- ---------- Os01g03670   ADLMVEGSFD DAVRGVDGVF HA-------- ---------- ---------- ---------- At1g25460    ADLTIEGSFD EAVNGVDGVF HI-------- ---------- ---------- ---------- AtTKPR2      ADLTVEGSFD EAVNGVDGVF HT-------- ---------- ---------- ---------- PoptrDFRL2   ADLLEEGSFD EAIQGVDGVF HT-------- ---------- ---------- ---------- PoptrCCRL1   AELLEEGSFD EAIQGVDGVF HV-------- ---------- ---------- ---------- PoptrDFRL6   ADLREEGSFD EAVRGCDGVF HV-------- ---------- ---------- ---------- At4g27250    ADLRDDGSFD DAVKGCDGVF HV-------- ---------- ---------- ---------- Os01g44260   ---------- ---------- ---------- ---------- ---------- ---------- AtDFR        ADLSEEGSYD DAINGCDGVF HV-------- ---------- ---------- ---------- PoptrDFR1    ADLSVEGSYD EAIQGCTGVF HV-------- ---------- ---------- ---------- PoptrDFR2    ADLSVEGSFD EAVQGCTGVF HV-------- ---------- ---------- ---------- AtANR/BAN    ADLTDEDSFE SSFSGCEYIF HV-------- ---------- ---------- ---------- PoptrANR1    ADLTDEESFN APIAGCELVF HV-------- ---------- ---------- ---------- PoptrANR2    ADLTNEESFN APIACCDLVF HV-------- ---------- ---------- ---------- Os04g53810   ANLEDEGSFD EAVAGCHYAF LV-------- ---------- ---------- ---------- Os04g53800   ADLEEEGSFD EAVAGCDYAF LV-------- ---------- ---------- ---------- Os04g53850   ADMDEEGSFD DAIAGCDYAF LV-------- ---------- ---------- ---------- Os04g53920   ADMDEEGSFD DAVAGCDYAF LV-------- ---------- ---------- ----------               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                 305        315        325        335        345        355 PpDFRL4      --AALV---- ------G-SW LPDS------ ---------- ---------- --------SQ 162  Os03g08624   --AAAV---- ------E-AW LPDP------ ---------- ---------- --------SI At4g33360    --AALV---- ------E-PW LPDP------ ---------- ---------- --------SR PoptrDFRL5   --AAAV---- ------E-PW LPDP------ ---------- ---------- --------SK PoptrDFRL4   --AAIV---- ------E-PW LPDP------ ---------- ---------- --------SK Os02g08420   --ASPM---- ---------- HDDP------ ---------- ---------- --------EE Os09g04050   --ASPV---- ---------- TDDP------ ---------- ---------- --------EK Os08g34280   --ASPV---- ---------- TDDP------ ---------- ---------- --------EQ Os09g25150   --ASPV---- ---------- TDDP------ ---------- ---------- --------EQ PoptrCCR2    --ASPV---- ---------- TDDP------ ---------- ---------- --------EE AtCCR1       --ASPV---- ---------- TDDP------ ---------- ---------- --------EQ AtCCR2       --ASPM---- ---------- TDDP------ ---------- ---------- --------ET PpDFRL3      --ASPF---- ------H-FN ITDP------ ---------- ---------- ------D-SQ PoptrCCRL4   --ASPV---- ------SFSP TDDP------ ---------- ---------- ------Q-VD PoptrCCRL3   --ASPF---- ------Y-FT VNDP------ ---------- ---------- ------Q-AE Os01g34480   --ASPF---- ------Y-HN VKDP------ ---------- ---------- ------K-AE AtCCRL14     --ASPF---- ------F-ND AKDP------ ---------- ---------- ------Q-AE PoptrCCRL1   --ASPF---- ------Y-HD VKDP------ ---------- ---------- ------Q-AE PoptrCCRL2   --ASPF---- ------Y-HD VKDP------ ---------- ---------- ------Q-VE PpDFRL1      --AAAL---- ------V-RI KSDP------ ---------- ---------- ------K-AE AtTKPR1      --ASPV---- ------L-KP TSNP------ ---------- ---------- ------E-EE PoptrDFRL1   --ASPA---- ---------- ---------- ---------- ---------- ---------E Os08g40440   --ASPV---- --------IT ETDS------ ---------- ---------- ------SKAA Os09g32020   EKAPPV---- ---KVDELAK KEEPKFQAFS GTSYSLKRNR DKVSHLWRLP SAKERLQLEE OryzaDFR2    --ASPV---- ------L-AK SDSN------ ---------- ---------- -----CK-EE PpDFRL2      --ACPV---- ------VYDP NGDP------ ---------- ---------- ------E-VS Os01g03670   --ASPVVVVG NSSSNNG-KP NDDDD----- ---------- ---------- --EEEVQ-QR At1g25460    --ASRV---- ------S-VR LDNN------ ---------- ---------- ------N-LD AtTKPR2      --ASPV---- --------LV PQDH------ ---------- ---------- ------NIQE PoptrDFRL2   --ASPV---- ------L-LP HDDN------ ---------- ---------- -----IQ-AM PoptrCCRL1   --AAPV---- ------L-VP YSDR------ ---------- ---------- -----IQ-ET PoptrDFRL6   --AASM---- ------EFYV AGNE------ ---------- ---------- --------DN At4g27250    --AASM---- ------EFDI SSDH------ ---------- ---------- ------V-NL Os01g44260   -----M---- ------D-FE SEDP------ ---------- ---------- ------E-NE AtDFR        --ATPM---- ------D-FE SKDP------ ---------- ---------- ------E-NE PoptrDFR1    --ATPM---- ------D-FE SKDP------ ---------- ---------- ------E-NE PoptrDFR2    --ATPM---- ------D-FE SKDP------ ---------- ---------- ------E-NE AtANR/BAN    --ATPI---- ------N-FK SEDP------ ---------- ---------- ------E-KD PoptrANR1    --ATPV---- ------N-FA SEDP------ ---------- ---------- ------E-ND PoptrANR2    --ATPV---- ------N-FA SEDP------ ---------- ---------- ------E-ND Os04g53810   --AAPV---- ---YDKS-HK SDDL------ ---------- ---------- ------E-KE Os04g53800   --AAPM---- ------N-LK SQNP------ ---------- ---------- ------E-KE Os04g53850   --AAPM---- ------N-FN SENP------ ---------- ---------- ------E-KD Os04g53920   --AAPV---- ------N-FQ SQNP------ ---------- ---------- ------E-KE               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                 365        375        385        395        405        415 PpDFRL4      -------FFK VNVEGFKNVI EAVKAT-PSV KKLIYTSSFF AVGPTDG--- -----YIGDE Os03g08624   -------FIT VNVGGLENVL KAARRT-PTV KKIVYTSSFF AIGPTDG--- -----YVADE At4g33360    -------FIS VNVGGLKNVL EAVKET-KTV QKIIYTSSFF ALGSTDG--- -----SVANE PoptrDFRL5   -------FFS VNVGGLKNVV QAAKET-KMI EKIIYTSSMV ALGSTDG--- -----YVADE PoptrDFRL4   -------FFS VNVEGLNNVL QAAKET-ETI EKIIYTSSFF ALGSTDG--- -----YVADE Os02g08420   -------IIE PVITGTLNVV EVAADA--GV RRVVLSSTIG TMYMDPRR-- DPD--SPLDD Os09g04050   -------MIE PAIRGTRYVI TAAADT--GI KRVVFTSSIG TVYMNPYR-- DPN--KPVDD Os08g34280   -------MVE PAVRGTEYVI NAAAEA-GTV RRVVFTSSIG AVTMDPNR-- GPD--VVVDE Os09g25150   -------MVE PAVRGTEYVI KAAAEA-GTV RRVVFTSSIG AVTMDPNR-- GPD--VVVDE PoptrCCR2    -------MVE PAVNGTKNVI IAAAEA--KV RRVVFTSSIG AVYMDPNK-- GPD--VVIDE AtCCR1       -------MVE PAVNGAKFVI NAAAEA--KV KRVVITSSIG AVYMDPNR-- DPE--AVVDE AtCCR2       -------MLE PAVNGAKFVI DAAAKA--KV KRVVFTSSIG AVYMNPNR-- DTQ--AIVDE PpDFRL3      -------LIE PAVKGTLNVL ESCAKA--GT KKIVLTSSVA AVAYSPK-R- AGA--SVVDE PoptrCCRL4   -------LID PALKGTLNVL RSCAKV-HSI RRVVLTSSAA ACIYSGKPL- NHD--VVIDE PoptrCCRL3   -------LVD PALKGTVNVL RSCTKI-PSI KRVVITSSMA AVVFNGKSL- APD--VVVDE Os01g34480   -------LLD PAVKGTLNVL GSCKKA--SI RRVIVTSSMA AVAYNGKPR- TPD--VVVDE AtCCRL14     -------LID PAVKGTLNVL NSCAKA-SSV KRVVVTSSMA AVGYNGKPR- TPD--VTVDE 163  PoptrCCRL1   -------LLD PAVKGTLNVL GSCARH-PSI KRVVLTSSMA AVAYNRKPR- TPD--VVVDE PoptrCCRL2   -------LLD PAVKGTLNVL GSCAKH-PSI RRVVLTSSVA AVAYNGKPR- TPD--VVVDE PpDFRL1      -------MLD PTILGTLNVL HSCAKS-TTL KRVVLTSSTA AVRFRDDLE- QPGAVTYLDE AtTKPR1      -------ILR PAIEGTLNVL RSCRKN-PSL KRVVLTSSSS TVRIRDDF-- DPK--IPLDE PoptrDFRL1   -------ILE PAIEGTLNVL RSCKRN-PSL KRVILTSSSS TLRVRDDF-- DSN--IPLEE Os08g40440   -------VLD SAINGTLNVL RSCKKN-PSL KRVVLTSSSS TVRLKDEADL PPN--VLLDE Os09g32020   -------MLV PAINGTLNVL KSCKKN-PFL KRVVLTSSSS TVRIRDESK- HPE--ISLDE OryzaDFR2    -------MLV PAINGTLNVL KSCKKN-PFL KRVVLTSSSS TVRIMDESK- HPE--ISLDE PpDFRL2      -------MLN PALKGNLNVL RACTKS-HSI QRVVMTSSCS AIRYDHNRR- PED--PPLSE Os01g03670   -------LVE PIVRGASNVL RSCARASPRP RRVVFTSSCS CVRYGAGAA- -----AALNE At1g25460    -------KFD PNISGTMNVM NSCAKSRNTV KRIVLTSSST AIRYRFDA-- TQV--SPLNE AtTKPR2      T------LVD PIIKGTTNVM SSCAKSKATL KRIVLTSSCS SIRYRFDA-- TEA--SPLNE PoptrDFRL2   -------LID PCINGTLNVL NSCSKA-NTV KRVVLTSSCS SIRYRDDV-- QQV--SPLNE PoptrCCRL1   -------LID PCIKGTLNVL NSCLKA-SSV KRVVFTSSSS TVRYRDDT-- PQI--FSLNE PoptrDFRL6   ENYVQRNIID PAIEGTLNLL TSCSKS-NTV KRVVFTSSIS TLTAKDGAG- KWR--QVVDE At4g27250    ESYVQSKVIE PALKGVRNVL SSCLKS-KSV KRVVFTSSIS TLTAKDENE- RMR--SFVDE Os01g44260   -------VVK PTVEGMLSIM RACRDA-GTV KRIVFTSSAG TVNIEERQR- -----PSYDH AtDFR        -------VIK PTVNGMLGIM KACVKA-KTV RRFVFTSSAG TVNVEEHQK- -----NVYDE PoptrDFR1    -------VIK PTINGVLDIM RACANS-KTV RKIVFTSSAG TVDVEEKRK- -----PVYDE PoptrDFR2    -------VIK PTINGVLDIM KACAKA-KTV RRIVFTSSAG TVDVEEHKK- -----PVYDE AtANR/BAN    -------MIK PAIQGVINVL KSCLKS-KSV KRVIYTSSAA AVSINNLS-- GTG--IVMNE PoptrANR1    -------MIK PAIQGVHNVL KACAKA-KTV KRVILTSSAA ALSINKLN-- GTG--LIMDE PoptrANR2    -------MIK PAIQGVHNVL KACAKA-KTV QRVILTSSAA AVSINKLN-- GTG--LVMDE Os04g53810   -------IVQ GGVEGTLNVM RSCARA-GTV KRVILTSSTA AVSSLRPLE- GAG--HVLDE Os04g53800   -------LLE AGVQGTLNVL RSCVKA-GTV KRVILTSSAA AVSGQPLQGD GNGSSHVLDE Os04g53850   -------LVE AAVNGTLNAM RSCAKV-GTV KRVIITSSDA AISRRPLQ-- GDG--YVLDE Os04g53920   -------LIE AGVQGTMNVM RSCVRA-GTV KRVILTSSAP AVSGRPLQ-- GDG--HVLDE               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                 425        435        445        455        465        475 PpDFRL4      TQFHSMKAFY SP-------- -YEESKAFAD KLACEAAME- GVPIVSLYPG IIYGPGSMTK Os03g08624   TQMHQGKTFC TE-------- -YEKSKVLAD QIALQAAAE- GMPITIVYPG FMYGPGKLTA At4g33360    NQVHNERFFC TE-------- -YERSKAVAD KMALNAASE- GVPIILLYPG VIFGPGKLTS PoptrDFRL5   SQVHHEKYFS TE-------- -YERSKVAAD KVASQAAAE- GLPIVTLYPG VVYGPGKLTT PoptrDFRL4   SQVHCEKRFC TE-------- -YERSKMIAD KIASQAAAE- GVPIVMLYPG VIYGPGKLTT Os02g08420   SFWSDLD-YC KNTK----NW -YCYAKTIAE RKAWEVARGR GVDMAVVIPV VVLGELLQPG Os09g04050   TCWSDLE-YC KRTE----NW -YCYAKTVAE QGAWEVARRR GVDLVVVNPV LVLGPLLQAT Os08g34280   SCWSDLD-YC KETR----NW -YCYGKAVAE QAAWEAARRR GVELVVVNPV LVIGPLLQPT Os09g25150   SCWSDLE-FC KKTK----NW -YCYGKAVAE QEACKAAEER GVDLVVVSPV LVVGPLLQPT PoptrCCR2    SCWSDLE-FC KNTK----NW -YCYGKAVAE QAAWDMAKEK GVDLVVVNPV LVLGPLLQPT AtCCR1       SCWSDLD-FC KNTK----NW -YCYGKMVAE QAAWETAKEK GVDLVVLNPV LVLGPPLQPT AtCCR2       NCWSDLD-FC KNTK----NW -YCYGKMLAE QSAWETAKAK GVDLVVLNPV LVLGPPLQSA PpDFRL3      TFFSDPE-FC QKEQ----RW -YVLSKTLAE SAAWEFVKEH NLNMVAINPT MVIGPLLQSS PoptrCCRL4   TWYSDPA-IC KELK----AW -YALSKTLAE EAAWNFAKEN ATDLVTVHPS FVIGPLLQPT PoptrCCRL3   TWFSDSD-FC EKSK----LW -YHLSKTLAE EAAWKFTKEN GIDMVTLNPG LVIGPLLQPT Os01g34480   TWFSVPE-IC EKHQ----QW -YVLSKTLAE EAAWKFSKDN GFEIVTVNPA MVIGPLLQPS AtCCRL14     TWFSDPE-LC EASK----MW -YVLSKTLAE DAAWKLAKEK GLDIVTINPA MVIGPLLQPT PoptrCCRL1   TWFSDPE-LC RESK----LW -YVLSKTLAE DAAWKFAKEK GMDMVAINPS MVIGPLLQPT PoptrCCRL2   TWFSDPN-LC RESK----VW -YVLSKTLAE DAAWKFAKEK DMDMVAINPA MVIGPLLQPT PpDFRL1      YSWSSIF-FC TKYQ----IW -YSLAKILSE QEAWKFAFLH SIDLVVVLPS FVIGPCLPYP AtTKPR1      SIWTSVE-LC KRFQ----VW -YALSKTLAE QAAWKFSEEN GIDLVTVLPS FLVGPSLPPD PoptrDFRL1   SSWSSVE-LC ERLQ----IW -YALSKTLAE KAAWEFCNGN GIDLITVLPS FVIGPSLSPD Os08g40440   TSWSSME-FC ESLQ----IW -YAIAKTLAE KAAWEFAKEN GIDLVAVLPT FVVGPNLSHE Os09g32020   TIWSSVA-LC EKLQ----LW -YALAKISAE KAAWEFAKEN NIDLVTVLPS FVIGPSLSHE OryzaDFR2    TIWSSVA-LC EKLQ----LW -YALAKISAE KAAWEFAKEN NIDLVTVLPS FVIGPSLSHE PpDFRL2      SVWSSPE-YC RDHK----MW -YALAKTLAE KEAFEFAARE GLNLVVICPS FVIGPSLTPI Os01g03670   SHWSDAA-YC AAHG----LW -YAYAKTLAE REAWRLAKER GLDMVAVNPS FVVGPILSQA At1g25460    SHWTDLE-YC KHFK----IW -YAYKKTLGE KEAWRIAADK KLNLVVVIPS FCIGPILSPK AtTKPR2      SHWSDPE-YC KRFN----LW -YGYAKTLGE REAWRIAEEK GLDLVVVNPS FVVGPLLGPK PoptrDFRL2   SHWSDPE-YC KRYD----LW -YAYAKTIGE KEAWRSAKEN GIDLVVVNPS FVVGPLLAPQ PoptrCCRL1   SHWSDTE-YC KRHN----LW -YAYAKTVAE KEAWRVSKEN GIDLVSFIPS FVVGPLLAPE PoptrDFRL6   TCQTPID-HV WNTK--PPGW IYVLSKRLTE EAAFKYAKDN GIDLISVITT TVAGAFLTSS At4g27250    TCKAHVD-HV LKTQ--ASGW IYVLSKLVSE EEAFRYAKER GMDLVSVITT TVSGPFLTPF 164  Os01g44260   DDWSDID-FC RRVK--MTGW MYFVSKSLAE KAAMEYAREH GLDLISVIPT LVVGPFISNG AtDFR        NDWSDLE-FI MSKK--MTGW MYFVSKTLAE KAAWDFAEEK GLDFISIIPT LVVGPFITTS PoptrDFR1    SCWSDLD-FV QSIK--MTGW MYFVSKTLAE QAAWKFAKEN NLDFISIIPT LVVGPFIMQS PoptrDFR2    SCWSDLE-FV QTVK--MTGW MYFVSKTLAE QAAWKYAKEN NLDFISVIPP LVVGPFIMHS AtANR/BAN    ENWTDVE-FL TEEK--PFNW GYPISKVLAE KTAWEFAKEN KINLVTVIPA LIAGNSLLSD PoptrANR1    KNWTDVE-FL TSEK--PPTW GYPASKTLAE KAAWKFAEEN NIDLITVIPS LMTGPSLTLD PoptrANR2    KNWTDVE-FL TSEK--PPTW GYPASKTLAE KAAWKFAEEN NIDLITVIPS LMTGPSFTPH Os04g53810   SSWSDIE-YL RSMEKLSPTQ AYSISKVLSE KEATKFAEEN GLSLVTLCPV VAVGASPAVR Os04g53800   SSWSDLD-YL RSTNGISPAQ AYAIAKVLSE KEASKLAEEN GISLVAVCPV ATVGASPAPV Os04g53850   ESWSDVD-YL RTEK--PPAW AYSVSKVLLE KAACKFAEEN NMSLVTVFPV FTLGAAPAPV Os04g53920   DSWSDVE-YL TKEK--PPAW AYSVSKVLME KAACKLAEEN NISLITVFPV FTLGAAPTPT               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                 485        495        505        515        525        535 PpDFRL4      GNSLAEMMIE RFNGRMPGYV GYKVK----- -KFSFCHIDD VVVAYLAAIE IGR------- Os03g08624   GNLVSRILIE RFNGRLPGYV GHGHD----- -RESFCHVDD VVAGHVAAME KGR------- At4g33360    ANMVARMLIE RFNGRLPGYI GSGTD----- -RYSFSHVDD VVEGHVAAME KGR------- PoptrDFRL5   GNALAKMLID RFAGRLPGYI GRGND----- -RLSFCHVDD VVGGHIAAMD KGR------- PoptrDFRL4   GNIVAQLLIE RFAGRLPGYI GYGND----- -KFSFCHVDD LVDGHIAAMD KGR------- Os02g08420   MNTSTKHILK YLTGEAKTYV NE-------- -SHAYVHVVD AAEAHVRVLE APG------- Os09g04050   VNASTEHVMK YLTGSAKTYV NA-------- -AQAYVHVRD VAEAHVRVYD CGG------- Os08g34280   VNASVAHILK YLDGSASKFA NA-------- -VQAYVDVRD VAAAHLLVFE SPS------- Os09g25150   VNASAVHILK YLDGSAKKYA NA-------- -VQAYVDVRD VAAAHVRVFE APE------- PoptrCCR2    VNASITHILK YLTGSAKTYA NS-------- -VQAYVHVRD VALAHILVFE TPS------- AtCCR1       INASLYHVLK YLTGSAKTYA NL-------- -TQAYVDVRD VALAHVLVYE APS------- AtCCR2       INASLVHILK YLTGSAKTYA NL-------- -TQVYVDVRD VALGHVLVYE APS------- PpDFRL3      MNTSNELLLG FLNGTAKSFP NQ-------- -AVGWVSVKD VAMAHILAYE KPE------- PoptrCCRL4   LNLSVEMILD LVNG-AETYP NG-------- -YYRCIDVRD VANAHIQAFE IPS------- PoptrCCRL3   LNQSAESVLD LING-AKSYP NT-------- -TYRWVDVRD VANAHIYALE NPS------- Os01g34480   LNTSAEAILK LINGSSSTYP NF-------- -SFGWINVKD VALAHILAYE VPS------- AtCCRL14     LNTSAAAILN LING-AKTFP NL-------- -SFGWVNVKD VANAHIQAFE VPS------- PoptrCCRL1   LNTSAAAILS LIKG-AQTFS NA-------- -SFGWINVKD VANAHIQAFE LSS------- PoptrCCRL2   LNTSAAAILS LIKG-AQTFP NA-------- -SFGWINVKD VANAHIQAFE LSS------- PpDFRL1      LSKTAQDICD LLNGLCRNFG IHG------- -RMGYVHVDD VARAHILVYE TPS------- AtTKPR1      LCSTASDVLG LLKGETEKFQ WHG------- -QMGYVHIDD VARTHIVVFE HEA------- PoptrDFRL1   LCSTATDVLG LLTGESEKFH WHG------- -RMGYVHIDD VALSHILVYE DET------- Os08g40440   LSPTTTDVLG LFQGETTKFT MYG------- -RMGYVHIDD VASCHILLYE TPR------- Os09g32020   LSVTASDILG LLQGDTDRFI SYG------- -RMGYVHIDD VASCHILVYE APQ------- OryzaDFR2    LSVTASDILG LLQGDTDRFI SYG------- -RMGYVHIDD VASCHILVYE APQ------- PpDFRL2      PTSTVFLILD LLRGRAQEYP NK-------- -RIGFVHIDD VVTAHVLAME VPE------- Os01g03670   PTSTALIVLA LLRGELPRYP NT-------- -TVGFVHVDD AVLAHVVAME DAR------- At1g25460    PTSSPLIFLS IIKGTRGTYP NF-------- -RGGFVHIDD VVAAQILAME EPK------- AtTKPR2      PTSTLLMILA IAKGLAGEYP NF-------- -TVGFVHIDD VVAAHVLAME EPK------- PoptrDFRL2   PTSTLLLILA IVKGLRGEYP NM-------- -TIGFVHIDD VVAAHILAME DKK------- PoptrCCRL1   PNSTLLLIQS VVKGSRGEYP NM-------- -TVGFTHIDD VVAGNILAME NSE------- PoptrDFRL6   VPSSIRVLLS PITGDTKFFS ILSAVNARMG -SIALVHIDD ICDAHIFLME QTR------- At4g27250    VPSSVQVLLS PITGDSKLFA ILSAVNKRMG -SIALVHIED ICRAHLFLME QPK------- Os01g44260   MPPSHVTALA LLTGNEAHYS ILK------- -QVQFVHLDD LCDAEIFLFE SPE------- AtDFR        MPPSLITALS PITRNEAHYS IIR------- -QGQYVHLDD LCNAHIFLYE QAA------- PoptrDFR1    MPPSLLTALS LITGNEAHYG ILK------- -QGHYVHLDD LCMSHIFLYE NPK------- PoptrDFR2    MPPSLITALS LITGNEAHYG IIK------- -QGNYVHLDD LCRAHIVLFE NPK------- AtANR/BAN    PPSSLSLSMS FITGKEMHVT GLKEMQKLSG -SISFVHVDD LARAHLFLAE KET------- PoptrANR1    IPSSVHLSMS LITGNEFLKN ALKGMQMLSG -SISITHVED VCRAHIFLAE KES------- PoptrANR2    IPDSINLAMS LITGNKFLIN GLKGMQMLSG -SISITHVED VCRAHIFLAE KES------- Os04g53810   VDTSVPACLS LITGDEEMMN ILKGIEKASG WSMPMVHIED VCRAEIFVAE EES------- Os04g53800   ANESVANVLS LLSGNEEINT LRMIDQYSG- -GLKLVHVDD LCRAEIFLAE KASPS----- Os04g53850   ARTSVPGILS LLSGDETHLE VLKPLQWVTG -SVSIVHVDD LCRAEIFLAE KESSSLSSAE Os04g53920   AATSVSAMLS LLSSDETQLK TLKGLA-ATG -PIPTVHVDD LCRAEVFVAE KES-------               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                 545        555        565        575        585        595 PpDFRL4      VGE-RYMLCG DNMSFHEVFD LAAGLTKTNP AKVTIPMWVL DVAGFLCVQW ARFGAWTGIS Os03g08624   EGE-RYLLTG ENTSLVQIFD MASRITNTKA PRFHVPLWLL EIYGWISVLV SRI------T 165  At4g33360    LGE-RYLLTG ENASFKLVFD MAALITGTKK PNFSIPLWAI NAYGWLSVLI SRV------T PoptrDFRL5   LGE-RYLLTG ENASFSRVLD IAAIITRTEK PRFSIPLWVI EAYGWLSILI FHF------T PoptrDFRL4   QGE-RYLLTG ENASFKLVFD MAAIISETKK PRFSIPLCII ESYGWLLVLV SRL------T Os02g08420   AGGRRYICAE RTLHRG---E L-CRILAGLF PEYPIPTRCR DEI------- ---------N Os09g04050   ARG-RYICAE STLHRG---D L-CRALAKLF PEYPVPSRCK DEA------- ---------A Os08g34280   AAG-RFLCAE SVLHRE---G V-VRILAKLF PEYPVPTRCS DEK------- ---------N Os09g25150   ASG-RHLCAE RVLHRE---D V-VHILGKLF PEYPVPTR-- ---------- ---------- PoptrCCR2    ASG-RYLCSE SVLHRG---E V-VEILAKFF PEYPIPTKCS DEK------- ---------N AtCCR1       ASG-RYLLAE SARHRG---E V-VEILAKLF PEYPLPTKCK DEK------- ---------N AtCCR2       ASG-RYILAE TALHRG---E V-VEILAKFF PEYPLPTKCS DEK------- ---------N PpDFRL3      AEG-RYIINE RLIHYG---E M-VSLLMNRY PQYPIVAKDA DDS------- ---------- PoptrCCRL4   ASG-RYVLTA YVTTFS---E V-LKIIRENY PTLRLPEKST ESM------- ---------- PoptrCCRL3   ANG-RYCLVG TVIHSS---E A-VKILSKLY PDLTIPKQCA DDK------- ---------- Os01g34480   ANG-RYCMVE RVAHYS---E L-VQIIREMY PNIPLPDKCA DDK------- ---------- AtCCRL14     ANG-RYCLVE RVVHHS---E I-VNILRELY PNLPLPERCV DEN------- ---------- PoptrCCRL1   ASG-RYCLVE RVAHHS---E V-VKILRELY PDLQLPEKCA DDK------- ---------- PoptrCCRL2   ASG-RYCLVE RVAHYS---E V-VKILHELY PDLQLPEKCA DDK------- ---------- PpDFRL1      AQG-RYICSA QEATPQ---E L-VQYLADRY PHLQISTKFN DEL------- ---------- AtTKPR1      AQG-RYICSS NVISLE---E L-VSFLSARY PSLPIPKRFE KLN------- ---------- PoptrDFRL1   AGG-RFLCSS IVLDND---E L-ASFLSQRY PSLPIPKRFE QLK------- ---------- Os08g40440   AAG------- ---------- ---------- ---SLPCVYG EQT------- ---------- Os09g32020   ATG-RYLCNS VVLDNN---E L-VALLAKQF PIFPIPRSLR NPY------- ---------- OryzaDFR2    ATG-RYLCNS VVLDNN---E L-VALLAKQF PIFPIPRSLR NPY------- ---------- PpDFRL2      AHG-RYICSS DVAHFG---D I-MSMLKTKY PKLQTPTRCS DMP------- ---------P Os01g03670   ASG-RLICSC HVAHWS---E I-VGSLRERY PGYPIPAECG SHK------- ---------- At1g25460    ASG-RILCSS SVAHWS---E I-IEMLRIKY PLYPFETKCG SEE------- ---------- AtTKPR2      ASG-RIICSS SVAHWS---E I-IELMRNKY PNYPFENKCS NKE------- ---------- PoptrDFRL2   ASG-RLVCSG SVAHWS---E I-IEMLRAKY PSYPYENKCS SQK------- ---------- PoptrCCRL1   ASG-RLVCSG PVAHWS---Q I-IKMLRAKY PSYPYENKCS SQE------- ---------- PoptrDFRL6   AEG-RYICSA HSCVLS---Q L-INHLVEEY PCSNIQRLAE KQG------- ---------- At4g27250    AKG-QYICCV DNIDMH---E LMLHHFSKDY LCKVQKVNED EEE------- ---------- Os01g44260   ARG-RYVCSS HDATIH---G L-ATMLADMF PEYDVPRSFP GID------- ---------A AtDFR        AKG-RYICSS HDATIL---T I-SKFLRPKY PEYNVPSTFE GVD------- ---------- PoptrDFR1    AEG-RYICNS DDANIH---D L-AKLLREKY PEYNVPAKFK DID------- ---------- PoptrDFR2    AEG-RYICSS HEATIH---D L-AKLLREKY PKYNVPAKFK DID------- ---------- AtANR/BAN    ASG-RYICCA YNTSVP---E I-ADFLIQRY PKYNVLSEFE EGL------- ---------- PoptrANR1    ASG-RYICCA VNTSVV---E L-AEFLNKRY PQYQVPTDFG DF-------- ---------- PoptrANR2    ASG-RYICCG VNTSVV---E L-AKFLNKRY PQYQVPTDCG DF-------- ---------- Os04g53810   ASG-RYICGS LNTTVT---E I-AGFLAAKY PQYNVRCDCI EEH------- ---------H Os04g53800   PSG-RYICCA LNTTMR---Q I-ARSLAAKY PHHNVDIDAL GGG------- ---------L Os04g53850   SSA-RYICCS FNTTVL---A L-ARFMAGRY PQYNVKTDRF DGM------- ---------- Os04g53920   ASG-RYICSS LSTTVV---A F-ARFVAGKH PRYNVKTDGF QGF------- ----------               ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|                 605        615        625        635        645        655 PpDFRL4      HQIPFITTHS VNILKHQWAY SSEKAERELG Y-KSR--PLE EGLLQL-LTW LKATGRIKY- Os03g08624   GKLPFISYPA VRVLRHQWAY SCEKAKKELG Y-SPR--SLT EGLSET-LLW LKDSEMIRF- At4g33360    GKLPLISPPT VTVLRHQWSY SCDKAKLELG Y-NPR--SLK EGLEEM-LPW LKSLGVIHY- PoptrDFRL5   GKLPLLCPPS VHVLRHQWEY SCEKARIELD Y-NPR--SLK EGLDEL-LPW LKSLGAITY- PoptrDFRL4   GNLPLISPPT VHVLRHQWEY SCEKAKTELG Y-NPR--GLE DGLKEV-LPW LKSMGVIKY- Os02g08420   PPKKGYKFTN QPL------- ------KDLG I-KFT--PVH EYLYEA-VKS LEDKGFIKKT Os09g04050   PPVKGYLFSN QRL------- ------RDLG M-DFV--PVR QCLYET-VRS LQDKGLLPVL Os08g34280   PRKQPYKMSN QKL------- ------RDLG L-EFR--PAS QSLYET-VKC LQEKGHLPVL Os09g25150   ---------- ---------- ---------- ---------- ---------- ---------- PoptrCCR2    PRKQPYKFSN QKL------- ------RDLG F-EFT--PVK QCLYET-VKS LQEKGHLPIP AtCCR1       PRAKPYKFTN QKI------- ------KDLG L-EFT--STK QSLYDT-VKS LQEKGHLAPP AtCCR2       PRAKPYKFTT QKI------- ------KDLG L-EFK--PIK QSLYES-VKS LQEKGHLPLP PpDFRL3      TRLPSYNLSN EKI------- ------KKLG L-TFQ--PLE EALDET-VAC FKELKLLD-- PoptrCCRL4   --FKPYQVSK EKA------- ------KTLG I-NFT--PLD LSLVDT-IES LKEKGFLKI- PoptrCCRL3   PPMPKYQVSK ERA------- ------ASLG V-KYT--PLE ASLKDT-IES LKEKNFVSF- Os01g34480   PSVPIYQVSK EKI------- ------KSLG L-ELT--PLH TSIKET-IES LKEKGFVTFD AtCCRL14     PYVPTYQVSK DKT------- ------RSLG I-DYI--PLK VSIKET-VES LKEKGFAQF- PoptrCCRL1   PYVPIYQVSK EKA------- ------KSLG I-EFI--PLE ASIKET-VES LKEKGFVSF- 166  PoptrCCRL2   PYVPIYQVSK EKA------- ------KSLG V-EFI--PLE ASVKET-VES LKEKGFVSF- PpDFRL1      PKMPYYKLNT TKL------- ------QRLG L-NCK--PLD VMFDDC-ISF LEEKGLLKRK AtTKPR1      --RLHYDFDT SKI------- ------QSLG L-KFK--SLE EMFDDC-IAS LVEQGYLSTV PoptrDFRL1   --RPYYEFNT SRL------- ------ERLG F-KFK--PIQ EMFDDC-IAS LVEQGHLSSF Os08g40440   -----YGFST AKV------- ------RELG M-KFR--DVE EMFDDA-VDS LRAHGYLLNS Os09g32020   -EKQSYELNT SKI------- ------QQLG F-KFK--GVQ EMFGDC-VES LKDQGHLLEC OryzaDFR2    -EKQSYELNT SKI------- ------QQLG F-KFK--GVQ EMFGDC-VES LKDQGHLLEC PpDFRL2      GDDIHHKMDT TKI------- ------KKLG LTEFK--SIE QMFDDM-LRS LHEKHLESL- Os01g03670   GDDRAHKMDT AKI------- ------RALG FPPFL--SVQ QMFDDC-IKS FQDKGLLPPH At1g25460    GKDMPHSLDT TKI------- ------HELG FASFK--SLT EMFDDC-IKC FQDKGLL--- AtTKPR2      GDNSPHSMDT RKI------- ------HELG FGSFK--SLP EMFDDC-IIS FQKKGLL--- PoptrDFRL2   GDCNPHSMDT TKI------- ------ATLG FPPFK--TLE EMFDDC-IKS FQEKGFL--- PoptrCCRL1   GDNIPHSMDT TKI------- ------AQLG LPPFK--THE QMFDDC-IRS LQEKGFL--- PoptrDFRL6   --SISPEISS KKL------- ------RDMG F-KYKH-SIK DIISET-I-- ---------- At4g27250    RECMKPIISS KKL------- ------RELG F-EYKY-GIE EIVDQT-IDA SIKIKFPTLN Os01g44260   DHLQPVHFSS WKL------- ------LAHG F-RFRY-TLE DMFEAA-VRT CREKGLLPPL AtDFR        ENLKSIEFSS KKL------- ------TDMG F-NFKY-SLE EMFIES-IET CRQKGFLPVS PoptrDFR1    ENLACVAFSS KKL------- ------TDLG F-EFKY-SLE DMFAGA-VET CREKGLIPLS PoptrDFR2    EDLASVVFSS KKL------- ------LDLG F-EFKY-SLE EMFAGA-VET CREKGLIPLS AtANR/BAN    -SIPKLTLSS QKL------- ------INEG F-RFEY-GIN EMYDQM-IEY FESKGLIKAK PoptrANR1    PSKAKLAITS EKL------- ------ISEG F-SFKY-GIE EVYDQT-VEY FKAKGLLN-- PoptrANR2    PSEAKLIITS EKL------- ------SSEG F-SFKY-GIE EIYDQT-VEY FKANGLLN-- Os04g53810   PEKPTISLSS AKL------- ------IGEG F-EFKYKNLD EMYDDL-VAY GKALGLIPN- Os04g53800   PEKPTILLSS EKL------- ------TSEG F-EFMYKTVD EMYDDAFVEY GMALGILHY- Os04g53850   PEKPRVCCSS EKL------- ------IREG F-EFKYTNMG DILDDL-VEY GRALGILPH- Os04g53920   PEKPRVCYSS EKL------- ------VREG F-EFKWTDLD EVFDDL-IEY GNVLGILPQ-               ....|....| ....|....| ....|....| ....|....| ....|....| ....                 665        675        685        695        705 PpDFRL4      ---------- ---------- ---------- ---------- ---------- ---- Os03g08624   ---------- ---------- ---------- ---------- ---------- ---- At4g33360    ---------- ---------- ---------- ---------- ---------- ---- PoptrDFRL5   ---------- ---------- ---------- ---------- ---------- ---- PoptrDFRL4   ---------- ---------- ---------- ---------- ---------- ---- Os02g08420   SNTKELHRQS SPPQNSPASM LMSKL----- ---------- ---------- ---- Os09g04050   PPTADDHHHP SS-------- ---------- ---------- ---------- ---- Os08g34280   AAEKTEEEAG EVQGGIAIRA ---------- ---------- ---------- ---- Os09g25150   ---------- ---------- ---------- ---------- ---------- ---- PoptrCCR2    KQAAEESLKI Q--------- ---------- ---------- ---------- ---- AtCCR1       PPPPSASQES VENGIKIGS- ---------- ---------- ---------- ---- AtCCR2       QDSNQNEVII ES-------- ---------- ---------- ---------- ---- PpDFRL3      ---------- ---------- ---------- ---------- ---------- ---- PoptrCCRL4   ---------- ---------- ---------- ---------- ---------- ---- PoptrCCRL3   ---------- ---------- ---------- ---------- ---------- ---- Os01g34480   SSNL------ ---------- ---------- ---------- ---------- ---- AtCCRL14     ---------- ---------- ---------- ---------- ---------- ---- PoptrCCRL1   ---------- ---------- ---------- ---------- ---------- ---- PoptrCCRL2   ---------- ---------- ---------- ---------- ---------- ---- PpDFRL1      PEKTPTSSST PDEHSKDSVL QNV------- ---------- ---------- ---- AtTKPR1      LP-------- ---------- ---------- ---------- ---------- ---- PoptrDFRL1   SLAIN----- ---------- ---------- ---------- ---------- ---- Os08g40440   VP-------- ---------- ---------- ---------- ---------- ---- Os09g32020   PL-------- ---------- ---------- ---------- ---------- ---- OryzaDFR2    PL-------- ---------- ---------- ---------- ---------- ---- PpDFRL2      ---------- ---------- ---------- ---------- ---------- ---- Os01g03670   A--------- ---------- ---------- ---------- ---------- ---- At1g25460    ---------- ---------- ---------- ---------- ---------- ---- AtTKPR2      ---------- ---------- ---------- ---------- ---------- ---- PoptrDFRL2   ---------- ---------- ---------- ---------- ---------- ---- PoptrCCRL1   ---------- ---------- ---------- ---------- ---------- ---- PoptrDFRL6   ---------- ---------- ---------- ---------- ---------- ---- At4g27250    HKLRQ----- ---------- ---------- ---------- ---------- ---- Os01g44260   PPPPTTAVAG GDGSAGVAGE KEPILGRGTG TAVGAETEAL VK-------- ---- 167  AtDFR        LSYQSISEIK TKNENIDVKT GDGLTDGMKP CNKTETGITG ERTDAPMLAQ QMCA PoptrDFR1    HRKQVVEECK ENEVVPAS-- ---------- ---------- ---------- ---- PoptrDFR2    HEK------- ---------- ---------- ---------- ---------- ---- AtANR/BAN    ---------- ---------- ---------- ---------- ---------- ---- PoptrANR1    ---------- ---------- ---------- ---------- ---------- ---- PoptrANR2    ---------- ---------- ---------- ---------- ---------- ---- Os04g53810   ---------- ---------- ---------- ---------- ---------- ---- Os04g53800   ---------- ---------- ---------- ---------- ---------- ---- Os04g53850   ---------- ---------- ---------- ---------- ---------- ---- Os04g53920   ---------- ---------- ---------- ---------- ---------- ----

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