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Expression patterns of nitrate transporter genes (AtNRT) in Arabidopsis thaliana Okamoto, Mamoru 2002

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Expression Patterns of Nitrate Transporter Genes (AtNRT) in Arabidopsis  thaliana.  by  Mamoru Okamoto  B.Sc, Tokyo University of Agriculture and Technology, 1992 M . S c , Tokyo University of Agriculture and Technology, 1994  A THESIS SUBMITTED IN P A R T I A L F U L F I L M E N T OF THE REQUIREMENTS F O R THE D E G R E E OF  DOCTOR OF PHILOSOPHY in THE F A C U L T Y OF G R A D U A T E STUDIES (Department of Botany) We accept this thesis as conforming to the required standard  THE UNIVERSITY OF BRITISH C O L U M B I A April 2002 © Mamoru Okamoto, 2002  In presenting t h i s t h e s i s in p a r t i a l f u l f i l m e n t of the requirements for an advanced degree at the U n i v e r s i t y of B r i t i s h Columbia, I agree that the L i b r a r y s h a l l make i t f r e e l y a v a i l a b l e for reference and study. I f u r t h e r agree that permission for extensive copying of t h i s t h e s i s f o r s c h o l a r l y purposes may be granted by the head of my department or by h i s or her representatives. It i s understood that copying or p u b l i c a t i o n of t h i s t h e s i s f o r f i n a n c i a l gain s h a l l not be allowed without my w r i t t e n permission.  Department of The U n i v e r s i t y of B r i t i s h Columbia Vancouver, Canada  Date  Aprt/  2.2  ,  Z&oZ.  Abstract  Higher plants possess both high- and low-affinity nitrate transporters. Since the first Arabidopsis thaliana low-affinity nitrate transporter gene, AtNRTl.l (CHL1), was isolated (Tsay et al., 1993), three low-affinity (NRT1), and seven high-affinity (NRT2) nitrate transporter gene homologues have been identified in this species. We investigated the transcript abundances of all eleven genes both in shoot and root tissues in response to NO3" provision, by relative quantitative RT-PCR method. Based upon their patterns of expression following NO3" provision, the genes were classified into three groups: 1. nitrate-inducible, 2. nitrate-repressible, and 3. nitrate-constitutive. AtNRTl.l, 2.1, and 2.2, representatives of the first group, were strongly induced, by 1 m M NO3", peaking at 3 to 12 hours, and declining during 3 subsequent days. B y contrast AtNRT2.4 showed only modest induction both in shoots and roots. Expression of AtNRT2.7, one of the nitrate-repressible genes from the second group, was strongly suppressed by nitrate provision in both roots and shoots. The last group, characterized by a constitutive expression pattern, contains the largest membership, including AtNRTl.2, 1.4, 2.3, 2.5, and 2.6. Tissue-specific expression patterns of limited number of AtNRT genes were observed by using GUS reporter D N A fusion lines. In the root tip regions, AtNRTl.l, 2.1 and 2.4 were expressed, while in the epidermal cells of mature roots, AtNRT2.1, 2.2, 2.4, and 2.6 were expressed. Expression of AtNRT2.1 was also found in the cortex and endodermal cells. In shoots AtNRTl.l showed expression in leaves and flowers, while AtNRT2.6 was specifically expressed in pollen grains. l ^ N C ^  -  influx from 100|iM and 5mM [NO3"], chosen to examine high-affinity and low-affinity transport, respectively, corresponded closely with the expression patterns of AtNRT2.1 and  ii  respectively. These results indicate that despite the close homology among members of the NRT2 and NRT1 families, individual members appear to be differently regulated, and may therefore perform different functions with respect to nitrate transport.  iii  Table of Contents Abstract Table of Contents List of Tables List of Figures List of Abbreviations Acknowledgments Chapter 1. General Introduction.  ii iv v vi viii ix 1  Chapter 2. Gene Structure and Predicted Protein Sequence Analysis of the AtNRT Gene Families 2.1 Introduction 2.2 Methods 2.3 Results and Discussion  8 8 9 11  Chapter 3. Expression Patterns of Nitrate Transporter AtNRT Genes 3.1 Introduction 3.2 Materials and Method 3.3 Results 3.4 Discussion  38 38 40 43 57  Chapter 4. Tissue-Specific Expression Patterns of AtNRT Genes 4.1 Introduction 4.2 Materials and Method 4.3 Results 4.4 Discussion  63 63 65 67 80  Chpater 5. Functional Aspects of Nitrate Transporters 5.1 Introduction 5.2 Materials and Method  86 86 89  5.3 Results and Discussion  91  Chpater 6. Conclusion and Future Prospective  113  References  117  iv  List of Tables Table 2-1. N R T (nitrate transporter) families in Arabidopis.  10  Table 2-2. Prediction of membrane topology on the NRT2 members with seven methods.  23  Table 3-1. Gene specific primers and conditions of RT-PCR.  42  Table 3-2. AtNRT Genes and hypothesized nitrate transport systems.  61  Table 5-1. Coefficients of determination (r ) for the relationships between AtNRT gene expressions and two nitrate transport systems.  95  2  V  List of Figures Figure 2-1. Physical map of AtNRTl and AtNRT2 gene family members.  12  Figure 2-2. D N A and deduced amino acid sequences of the AtNRTl. 1 gene.  13  Figure 2-3. D N A and deduced amino acid sequences of the AtNRTl. 2 gene.  14  Figure 2-4. D N A and deduced amino acid sequences of the AtNRT2.3 gene.  15  Figure 2-5. D N A and deduced amino acid sequences of the AtNRT2.4 gene.  17  Figure 2-6. D N A and deduced amino acid sequences of the AtNRT2.5 gene.  19  Figure 2-7. D N A and deduced amino acid sequences of the AtNRT2.6 gene.  20  Figure 2-8. D N A and deduced amino acid sequences of the AtNRT2.7 gene.  21  Figure 2-9. Amino acid sequence alignments of AtNRT2 family.  24  Figure 2-10. D N A and deduced amino acid sequence of the AtNRTl.l gene.  27  Figure 2-11. D N A and deduced amino acid sequence of the AtNRTl.2 gene.  30  Figure 2-12. D N A and deduced amino acid sequence of the AtNRTl. 3 gene.  32  Figure 2-13. D N A and deduced amino acid sequence of the AtNRTl.4 gene.  33  Figure 2-14. Amino acid sequence alignments of A t N R T l family.  36  Figure 3-1. Estimated relative expression levels of AtNRT genes.  45  Figure 3-2. Expression patterns of nitrate-inducible AtNRT2 genes.  47  Figure 3-3. Expression patterns of nitrate-inducible AtNRTl genes.  49  Figure 3-4. Expression patterns of nitrate-repressible AtNRT genes.  51  Figure 3-5. Expression patterns of nitrate-constitutive AtNRT2 genes.  52  Figure 3-6. Expression patterns of nitrate-constitutive AtNRTl genes.  53  Figure 4-1. Analysis of GUS activity in AtNRT2.1 promoter-GWS' Arabidopsis plants.  70  Figure 4-2. Analysis of GUS activity in AtNRT2.2 promoter-GUS Arabidopsis plants.  73  Figure 4-3. Analysis of GUS activity in AtNRT2.4 promoter-GUS Arabidopsis plants.  74  Figure 4-4. Analysis of GUS activity in AtNRT2.6 promoter-CrMS" Arabidopsis plants.  76  Figure 4-5. Analysis of GUS activity in AtNRTl.l promoter-GcTS Arabidopsis plants.  78  Figure 5-1. Time-course of NC>3" influx into Arabidopsis roots at high-affinity range.  92  Figure 5-2. Time-course of N03 influx into Arabidopsis roots at low-affinity range.  93  n  13  _  Figure 5-3. Phylogenetic tree of NRT2 family.  102  Figure 5-4. Phylogenetic tree of NRT1 family.  103  Figure 5-5. D N A and deduced amino acid sequences of the AtNar2.1 gene.  105  Figure 5-6. D N A and deduced amino acid sequences of the AtNar2.2 gene.  106  Figure 5-7. Amino acid sequence alignment of AtNar2.1 and AtNar2.2.  107  Figure 5-8. Expression patterns of AtNAR2.1 gene.  109  Figure 5-9. Correlation between AtNRT2.1 and AtNAR2.1 expression levels in roots.  110  Figure 5-10. Expression patterns of AtNAR2.1 gene and their correlation with AtNRT2.1 in shoots. Ill  vii  List of Abbreviations C : Carbon cHATS : Constitutive high-affinity transport system CK2 : Casein kinase 2 cLATS : Constitutive low-affinity transport system C R L R : Calcitonin-receptor-like-receptor GFP : Green fluorescent protein G O G A T : Glutamate synthase GS : Glutamine synthetase GUS : (3-glucuronidase iHATS : Inducible high-affinity transport system iLATS : Inducible low-affinity transport system K : Potassium MFS : Major facilitator superfamily N : Nitrogen N i R : Nitrite reductase N N P : Nitrate/nitrite porter NOS : Nopaline synthase N R : Nitrate reductase ORF : Open reading frame P K C : Protein kinase C P T R : Peptide transporter R A M P : Receptor-activity-modifying protein RT-PCR : Reverse transcription-polymerase chain reaction TMS : Trans-membrane-spanner WT : Wild-type X-Gluc: 5-bromo-4-chloro-3-indolyl-P-D-glucoronide cyclohexylamine +  viii  Acknowledgement First of all, I thank God for leading and protecting me during my journey of life. I would like to thank my supervisor professor Anthony D . M . Glass, for his intellectual and financial supports. His encouragement and passion in science and music made my Ph.D. study fruitful and enjoyable. I also would like to thank Dr. M . Yaeesh Siddiqi for his bottomless help. His appropriate advice and feedback were always helpful. I wish to thank members of my committees, professors George Haughn, and Paul J. Harrison for their inspiration; Drs. Yuji Kamiya, and Ken Shirasu for encouraging me to study abroad; and my former supervisor, professor Yasuhiro Arima for introducing me to the scientific path. This work has also been supported with generous help from members of the Glass lab from past and present. Especially, I would like to thank to Brent Kaiser, Anshuman Kumar, Suman Rawat, Salim Silim, Manuela Simon, Degen Zhuo, and John Vidmar. I also thank to collaborators professors Jim Kinghorn, and Sheila Unkles for heterologous AtNRTl.l(CHLl)-GUS  expression  systems,  and professor  Nigel  M . Crawford for providing  line.  I would like to thank my parents for their support and encouragement. This work could not have been done without them. Finally, I wish to thank my wife Julie Okamoto, whose love, belief, and support have kept me strong mentally and physically.  ix  1 General Introduction  Nitrogen (N) constitutes a large proportion (-3-5%) of the dry weight of most plants and hence it is required in large quantities. By virtue of its relative scarcity in natural systems, its availability commonly limits plant growth, while among agricultural species also, nitrogen is the one of the most influential factors controlling rates of plant growth and absolute crop yield. In order to sustain current high levels of crop productivity global N fertilizer use has risen to ~ 1 0 kg per annum, yet estimates of N use efficiency suggest H  values of 30 to 40% for cereals, the major crops with respect to fertilizer consumption (Raun and Johnson, 1999). In temperate agricultural soils, under aerobic conditions nitrate (NO3") is commonly the principal form of available N , since ammonium (NH4 ) is quickly nitrified to NO3" +  under those conditions. Because of its chemical nature (negatively charged), NO3" is hardly retained on soil surfaces, which are usually negatively charged. Therefore NO3" in soil solution would be mobile, moving in soil according to mass flow, which is affected by  1  transpiration and irrigation. Excessive fertilization can cause environmental damage. Unabsorbed free NO3" can leach from soils and contaminate surface and/or ground water, escape to lakes, rivers, and oceans, and cause eutrophication. However, if N fertilizer were reduced by an appropriate amount, it is claimed that plant growth might be maintained with minimum N losses from the soil (Raun and Johnson, 1999; Andersson et al., 2001; Mclsaac et al., 2001). The processes involved in nitrate acquisition by higher plants have therefore been of considerable interest to plant scientists and been extensively studied for several decades. Nitrate utilization by higher plants starts at the root surface where nitrate is absorbed into root cells through the plasma membrane. In many species both roots and shoots have the capability to assimilate nitrate into organic nitrogen compounds. Thus, in those species undertaking significant assimilation of nitrate (NO3") in the shoots, there is a requirement to transfer NO3" to the stele, and on to the leaves, either in the transpirationdriven ascent of sap, or by means of root pressure.  In such cases there is a need to re-  absorb NO3" from the leaf apoplast. Whether in roots or in shoots, NO3" is reduced to nitrite (NO2") by the enzyme nitrate reductase (NR) in the cytosol. Nitrite is then rapidly transported into plastids (i.e., proplastids in non-photosynthetic tissues, chloroplasts in photosynthetic tissues), and converted into ammonium ( N H / ) by the enzyme nitrite reductase (NiR). Ammonium is incorporated into amino acids by glutamine synthetase (GS) and glutamate synthase (GOGAT), and amino acids are the precursors of higher molecular weight organic nitrogen compounds such as" proteins, nucleic acids, coenzymes, or secondary metabolites (Marschner, 1995).  2  Nitrate uptake has been classified according to kinetic criteria as occurring as a result of three discrete transport systems: a constitutive high-affinity transport system (cHATS), an inducible high-affinity transport system (iHATS), and a low-affinity transport system (LATS) (Glass and Siddiqi, 1995; Crawford and Glass, 1998; Forde, 2000). The cHATS and iHATS typically operate in the range of 10 to 250 u,M N 0 " , while the L A T S 3  only becomes evident above these concentrations. A t such concentrations total uptake rates for NO3" are the sum of these three transporter activities (Siddiqi et al., 1990; Glass et al., 1992). The first high-affinity nitrate transporter gene, NrtA  (originally called c r n A ) , was  isolated from a filamentous fungus, A s p e r g i l l u s n i d u l a n s (Unkles et al., 1991). A n A . n i d u l a n s mutant with a defective NrtA  absorbed NO3" at roughly 20% the rate of WT  (Unkles et al., 2001). Although this suggests that NrtA is the principal transporter, a second transporter (NrtB) absorbs NO3" with a much higher affinity (K value of 11 | i M compared m  to 108 | i M for NrtA), suggesting that this transporter may be important for scavenging NO3" from low external concentrations. In C h l a m y d o m o n a s r e i n h a r d t i i there are also two highaffinity NO3" transporters and these exhibit differences in K values of the same magnitude m  as observed in A . n i d u l a n s (Galvan et al., 1996). Genes encoding nitrate-inducible highaffinity transporters have been cloned from various higher plants, including A r a b i d o p s i s t h a l i a n a , using the reported sequences of the A . n i d u l a n s and C. r e i n h a r d t i i high-affinity transporter genes (Forde, 2000). In A . t h a l i a n a , representatives of the high-affinity nitrate transporter family, AtNRT2.1 and AtNRTI.2,  (AtNRTI)  were first isolated by use of degenerate primers based  3  upon the NrtA homologues (Zhuo et al., 1999), and by a differential display method (Zhuo et al., 1999; Filleur and Daniel-Vedele, 1999). The Arabidopsis genome project unveiled five more putative high-affinity nitrate transporters in the family (The Arabidopsis Genome Initiative, 2000). Preliminary experiments showed that all seven members were expressed in roots (Glass et al., 2001). It is well established that AtNRT2.1 is induced by N 0 " (Filleur 3  and Daniel-Vedele, 1999; Lejay et al., 1999; Zhuo et al., 1999; Gansel et al., 2001), as are other NRT2 genes in barley (Trueman et al.; 1996; Vidmar et al., 2000), TV. plumbaginifolia (Quesada et al., 1997; Krapp et al., 1998), soybean (Amarasinghe et al., 1998), and tomato (Ono et al., 2000). The transcript abundances of AtNRT2.1 and the patterns of high-affinity nitrate influx under different conditions of N provision showed high correlations, suggesting that AtNRT2.1 is primarily responsible for iHATS activity (Zhuo et al., 1999; Lejay et al., 1999). This conclusion was substantiated by the recent finding that a T-DNA mutant, lacking AtNRT2.1 and a part of .2.2, lost about 70% of high-affinity NO3" uptake capacity compared to the WT plants, while L A T S transport was unaffected (Filleur et al., 2001).  Studies of expression patterns of AtNRT2.1 and HtNRT2.1, in response to  treatments with amino acids and various inhibitors of NO3" assimilation strongly suggest that NRT2.1 is regulated at the transcript level by glutamine (Zhuo et al., 1999; Vidmar et al., 2000).  Nevertheless, there is evidence to suggest that NO3" influx may be also  regulated at the post-translational level (Forde, 2000; Vidmar et al., 2000). Therefore correlations between transcript abundance and NO3" influx must be interpreted with caution. Characterizations of other members of the NRT2 family (i.e., AtNRT2.3-2.7) and their functional determination await investigation.  4  Low-affinity NO3" transport is thought to be mediated by members of separate (unrelated) family, the NRT1 family, which belongs to a larger peptide transporter family (PTR,  also  called  POP),  which  contains  51  or  52  members  (http://www.cbs.umn.edu/arabidopsis). The first member of this family of putative lowaffinity nitrate transporter genes, AtNRTl.l  (originally designated CHL1), was isolated  from an Arabidopsis mutant that was resistant to chlorate, a toxic NO3" analogue (Tsay et al., 1993). The AtNRTl family contains at least four members, including AtNRTl.2{NTL1),  AtNRTl.3(NTP3),  searches using AtNRTl.l  AtNRTl.l(CHLl),  and AtNRTl .4{NTP2) that were isolated by homology  against the EST database (Hatzfeld and Saito, 1999; Huang et al.,  1999; Forde, 2000). The present study has focused on these four members (i.e.,  AtNRTl.l,  1.2, 1.3, and 1.4). Although the AtNRTl family is generally designated as encoding L A T S , as stated above, it may express both H A T S and L A T S activities (Liu et al., 1999; Wang et al., 1998). Interestingly, the latest findings suggested that AtNRTl.l  might also be involved  in organogenesis (Guo et al., 2001). In this study I have characterized 11 members of NRT gene families in Arabidopsis thaliana (i.e., 4 AtNRTl;  7 AtNRTl).  First of all, gene and predicted protein structures of  AtNRT families were analyzed. These analyses provided the fundamental information upon which subsequent genomic analysis relied. Additional bioinformatics data will be presented in order to predict gene regulation and functional aspects of gene products (Chapter 2). Chapters 3 and 4 will focus on the expression patterns of AtNRT family members in total tissue extraction, and intact tissues, respectively. In Chapter 3, the transcript abundances were analyzed quantitatively by RT-PCR in both roots and shoots, in response to the provision of NO3" following a 7-day period of N 0 " deprivation. Gene expression 3  5  patterns of all 11 NRT genes were revealed with the sensitive RT-PCR method. The patterns were grouped into three categories, namely, nitrate-inducible, nitrate-repressible, and nitrate-constitutive. These expression patterns were then used to predict possible roles in nitrate uptake of the nitrate transporters in the species. In Chapter 4, tissue-specific expression patterns are presented using transgenic plants which carry AtNRT  promoter regions fused with G U S reporter D N A . Previous in situ  hybridization studies showed that A t N R T l . 1(CHL1)  is expressed in epidermal and  endodermal cells in the root tip region, and endodermal cells in mature root region, while expression of A t N R T l . 2 is primarily in epidermal cells and root hairs regardless of the stages of root development (Huang et al., 1996). In N i c o t i a n a p l u m b a g i n i f o l i a affinity nitrate transporter NpNRT2  a high-  expression was found primarily in epidermal and  endodermal cells in root tips, and in lateral root primordia in mature roots. To date, however, no information is available for the NRT2  family of genes in Arabidopsis.  Therefore this is the first report showing the localization of expression of four high-affinity nitrate transporter genes (AtNRT2.1,  2.2, 2.4, and 2.6) in A . t h a l i a n a .  Molecular analysis can predict possible gene and protein structures, and expression analysis provides clues concerning the regulation of genes at the in vitro and in situ levels. Subsequent questions relate to how these genes and/or gene products function. Do they function in isolation, or do they need to be coordinated with other proteins to generate functional transporters? In Chapter 5,  NO3" influx studies were performed in parallel to  compare patterns of influx in response to provision of NO3" after 7 days of N-deprivation, with patterns of gene expression. The kinetic study confirmed that Arabidopsis had four nitrate transport systems (i.e., iHATS, cHATS, inducible L A T S , and constitutive LATS).  6  Nitrate transporter genes were then assigned to these systems based upon their expression patterns. The ultimate goal of this thesis is to elucidate the function of each of the nitrate transporters by integrating molecular and physiological information.  7  2 Gene Structure and Predicted Protein Sequence Analysis of the AtNRT Gene Families  2.1 Introduction Since the first nitrate transporter gene, AtNRTl.l  (previously called CHL1), was isolated  from higher plants (Tsay et al., 1993), three more genes were identified as AtNRTl homologues in A. thaliana. Although A t N R T l proteins are considered to be nitrate transporters, this family also belongs to a family of peptide transporters (PTR) (Pao et al., 1998). Seven AtNRT2 members encode high-affinity nitrate transporters, belonging to the nitrate/nitrite porter (NNP) (Pao et al., 1998) family, which is a subfamily of the major facilitator superfamily (MFS) (Pao et al., 1998). Typical MFS members possess 400-600 amino acid residues with 12-trans-membrane-spanner (TMS) which consists of two sets of 6-TMS.  8  As genome projects have developed, a huge genome information base has been built up from viruses and bacteria to eukaryotes including Homo sapience, and higher plants (e.g., Arabidopsis thaliana, and Oryza sativa). In order to interpret and apply those enormous biological databases, biological informatics (so called bioinformatics) has been developing rapidly. The advantage of bioinformatics is that we can characterize and predict the function of genes and gene products from various perspectives prior to initiating experiments. This is helpful for proteins such as membrane proteins, which are difficult to work with because of their hydrophobicity. In this chapter, gene structures and predicted protein sequences of all 11 members of AtNRT families will be presented. As well, further bioinformatic searches including ciselements, signature motifs, transmembrane topology, and phylogenic analyses were carried out based on the gene and protein sequences using a computational approach.  2.2 Methods Bioinformatics D N A and predicted amino acid sequences were obtained from previous reports or from the online databases (accession numbers are provided in Table 2-1). AtNRTl.l  and 2.2 were  isolated by our group (Zhuo et al., 1999), and Filleur and D-Vedele (1999), and the sequence of AtNRT2.1 was used for a homology search, which was carried out on the BLAST  server (http://www.ncbi.nlm.nih.gov/blast). Nucleotide motifs of exacting  regulatory D N A elements were searched with the P L A C E database (Higo et al., 1999; http://www.dna.affrc.go.jp/htdocs/PLACE). C L U S T A L W or X was used for an initial  9  <" 22 i-  Ol  Z® 3  CD  co 00 00 LO CO  c  CD  p CD  CD  O  = .C Li. N  -4—»  ro  CD  CO Ol  c ro  N  00  oo  LO CO  CD  oo Oi o o T—  O < <  O < <  m < < CO 00  oo  ol Tj-  CN  CO  CM CD 1^00 CO  < o  CM co  o  oi Cl  NCM CO  •<* <y>eo oo CO <  O  CO 00 o  oo CM  CD  .CD  B B ro ro X  Ci Ol o o  oi oi Ol  CM CO CO CM o  I  CM O co LO Oi  AAB  m —  oi Oi Oi  BAB  * J CD  Cl Oi  Oi Oi Oi  AAC  Ol  LO OO  to co CO  CM co CM Oi  T—  LO  o  O  < < <  AAA  CO 0 O c  Ol  E 3 C C  g 'co CO CD o o <  c  I 2  o c  E <  .03  CD  CD  E  o  CO _  Q. CO c  co CD  co co  CM oi Oi CO LO co  oo CM  T— •  o>  LO  LO  o  o  o CO  o CO  < < < < <  O  O O  CO  o Cl  oo  o  O  O  LJ.  Li. <  O  1^  CM oo  oo  co  oo  oo co  TJ-  o  Tt"  CO  LO  O CO LO  CN CM LO  Ol CO LO  1^ CM LO  CO Ol Tj-  CM LO  CM O LO  IO  LO  LO  CO  T -  o  LL  CQ  LO o co o o  O  CO •g o CO  CO CP  I  CM Ol  oi  <  CD T3  CM  LO  LO LO  o  Oi LO  co oo  LO  o  i l  o co <=. o o  O -J  SB  E  or z CM Q) .Q CD  CO c  CD  >  E  co CD E  CM  c  ©5 CD S  z  T~  CM  CM  CM CM  CO  a: a: o o 5.  11  CM  p! P- P2  CO  CO  ii  K  i  AtN  CD  CM  E  >2 i_  CO  .. 1  i-  E z Z <=C  alignment analysis (Thompson et al., 1994). Transmembrane prediction was performed by H M M T O P (Tusnady and Simon, 1998), M E M S T A T (Jones et al., 1994), SOSUI (Hirokawa et al., 1998), T M A P (Persson and Argos, 1994), T M H M M (Sonnhammer et al., 1998), TMpred (Hofmann and Stoffel, 1992), and Toppred2 (Claros and von Heijne, 1994). Other bioinformatic programs including Bioedit (Hall, 1999), GeneDoc (Nicholas and Nicholas, 1997), Sequence Assistant (http://www2s.biglobe.ne.jp/~haruta/), AnnHyb (http://annhyb.fTee.fr), and Altemis (http://www.sanger.ac.uk/Software/altemis) were also employed to support the analysis.  2.3 Results and Discussion Gene Structure of the AtNRT2 Family Besides the first two AtNRT2 genes (AtNRT2.1, and 2.2) cloned experimentally (Filleur and Daniel-Vedele, 1999; Zhuo et al., 1999), five more homologues were retrieved by a homology search against the database generated by the Arabidopsis genome project (Table 2-1). Three genes (i.e., AtNRT2.1, 2.2, and 2.7) are located on chromosome 1, where AtNRT2.1 and 2.2 are closely located in a tail-to-tail configuration (Zhuo et al., 1999). AtNRT2.3, 2.4, and 2.5, were found on chromosome 5, with AtNRT2.3 and 2.4 in tandem 3.8 kb apart (Forde, 2000) (Figure 2-1). The open reading frames (ORF) of AtNRT2.1, 2.2 and 2.3, which were interrupted by two introns in the same positions, encode 530 (57.7 kD), 522 (56.7 kD), and 539 (58.2 kD) amino acid residues, respectively (Figures 2-2, 2-3, and 2-4). The AtNRT2.4 gene has  11  NRT2.7  NRT2.1 NRT2.2 ^~^ —  T6D22  F13K23i  J  1 NRT1.4 F18A8 sssss*avssssssssssssssssssssss, ssssss* r  A/R713  MIL23  NRT2.6 ^  si-  F14D17  ///////////;wx***MMtsf**J7w:f*zf*^ 4  <r7777771^SS7SSSSSSSSSS//S////S//M^  NRT2.5  NRT2.4  NRT2.3  T15N1  Figure 2-1. Physical map of AtNRTl and AtNRTl gene family members. Chromosomes and centromeres are indicated in stripes and dots, respectively. B A C clones are indicated in arrows. 12  1419 GAGCTCATCGAAATAGTTGACTTTTTCACAATTTAGACATGAAATTTTTGTCTTTTATCAAATCCCAACTTGTTGGAAATTT 1337 GACACGTCAGCGAGATTGATCGATACGCACTTAGTCGTTTGACTTTTTCAAATACCCATCGCTACAAGAGTACGGAAATTTG 1255 CGTGCAACCACATTCTAATTATACGCATATCTACATATCAATCCACCGCACCGTCTAATCTACTCTATGATATTTTCAAGAC 1173 CTTTTCAAAAATTCAGATCCGCTAGCTACTACGAAAATCTAAATGACTAAAATAAAACTCTTAATCGTTAACTASA1ATGTT 1091 TCTATAATAATATATGTATATCATACTGTTTTATTTAGTTTGCCGTTTTTCTTTGTTCTAAAGTTTTTTTTTGGTGTGTTTA 1009 ACACTAGTAATTTTTTTGTTCTTTTTAATGTTAAAATA2ATATTTTCACCATCACATATACATTGACATACGTATCTAGGGT - 92 7 TTAGATGAAGACATGTACACACACGATATTGAT^TTTAACTATGTGTTTTTCCTTAATCAACGATTTCAATTTTTCACACCG - 84 5 AAAATGACATATGAAATCAATAAAATAGTTCTACTAAAAGTCCTATATATGCAATCGTAAGCAATTTGAAGAGACAACTAAT - 7 6 3 GTGCAGCTAAGGCCACTCTAAATCCGACCGCCAAGGAGATCAATTAGTTTATTCACTAAAGGATCATCTTCCCCTTTTGTGA - 6 81 ATACTATTTATTACC AAAAC AAAAC AAAAAAAACTATTCACAGTTACAATGAC AAAGATAACCCTCCATAATTAATTAGGAT - 599 PATAGAPTAGTAArC ATTCATATAnAAAATATT'GTPGPPGTTAPTTAPf^TAGCr'TR AATGATAACTPATCyAGTPATGCTGT  - 517 -435 -353 - 2 71 -18 9 -10 7  TACAGCAGTTCAAATTAAGTGTCCAGGTTATGACTTGGTGAAAGAGGACCAAACTTTTAAACCTTAAGAAAAGAAGAGGAAA AAAACAATTAGCCTATCCTGTATCACTGTATGTAACCAGACTTATGTTTGGTTTCCACGCAATTTGACGGATACATGTTTCT ATGAT^TAATAATGATAGTTTTATTACTAACACAACCATATTGTTGACTATCCATCCATAAATCATTAAATCGCAAGATGA GGGAAGGGTAGAGCGGTCATTTGGAAGG^TATCGGCAACCTTTGGTG^TAAGCGAGAGACTAGGAAGATGCTTGCGGCGAAA ATGGATTCCTCGAAAATTAATATTTAAATCGM^GTTAACCGTTGAGAATCTCCAAAGAATGCTTTTTTCATTGTCAACACT  GGCTAGGAACCCiaiAXSAGCCATCGTGTGATTAATATTCAGACATCGATCAAATAAACTTGAATCAAATCTCAAACTTGCA  - 2 5 AAGAAACTTGAAATATTTTATAACAATGGGTGATTCTACTGGTGAGCCGGGGAGCTCCATGC ATGGAGTCACCGGTAGAGAA M G D S T G E P G S S M H G V T G R E 19 58 CAAAGCTTTGCTTTCTCGGTGCAATCACCAATTGTGCATACCGACAAGACGGCCAAGTTCGACCTTCCGGTGGACACAGAGC Q S F A F S V Q S P I V H T D K T A K F D L P V D T E H 4 7 140 ATAAGGCAACGGTTTTCAAGCTCTTCTCCTTCGCCAAACCTCACATGAGAACGTTCCATCTCTCGTGGATCTCTTTCTCCAC K A T V F K L F S F A K P H M R T F H L S W I S F S T 74 222 ATGTTTTGTCTCGACTTTCGCAGCTGCACCACTTGTCCCTATCATCCGGGAGAATCTCAACCTCACCAAACAAGACATTGGA C F V S T F A A A P L V P I I R E N L N L T K Q D I G 101 304 AACGCCGGAGTTGCCTCTGTCTCTGGGAGTATCTTCTCTAGGCTCGTGATGGGAGCCGTGTGTGATCTTTTGGGTCCCCGTT N A G V A S V S G S I F S R L V M G A V C D L . L G P R Y 129 386 ACGGTTGTGCCTTCCTTGTGATGTTGTCTGCCCCAACGGTGTTCTCCATGAGCTTCGTGAGTGACGCAGCAGGCTTCATAAC G C A F L V M L S A P T V F S M S F V S D A A G F I T 156 468 GGTGAGGTTCATGATTGGTTTTTGCCTGGCGACGTTTGTGTCTTGTCAATACTGGATGAGCACTATGTTCAACAGTCAGATC V R F M I G F C L A T F V S C Q Y W M S T M F N S Q I 183 550 ATTGGTCTGGTGAATGGGACAGCAGCCGGATGGGGAAACATGGGTGGCGGCATAACGCAGTTGCTCATGCCCATTGTGTATG I G L V N G T A A G W G N M G G G I T Q L L M P I V Y E 211 632 AAATCATTAGGCGCTGCGGTTCCACAGCCTTCACGGCCTGGAGGATCGCCTTCTTTGTACCCGGTTGGTTGCACATCATCAT I I R R C G S T A F T A W R I A F F V P G W L H I I M 238 714 GGGAATCTTGGTGCTCAATCTAGGTCAAGATCTGCCAGATGGAAATCGAGCTACCTTGGAGAAAGCGGGAGAAGTTGCCAAA G I L V L N L G Q D L P D G N R A T L E K A G E V A K 265 796 GACAAATTCGGAAAGgtatatttatctatataaatatatattccttaataatttaggctgcttatgttacagatggatcaaa D K F G K intron I 270 878 agattaactcgtgatatcgtataaatgttgtagATTCTGTGGTATGCCGTTACAAACTACAGGACTTGGATCTTCGTTCTTC I L W Y A V T N Y R T W I F V L L 2 87 960 TCTACGGATACTCCATGGGAGTTGAGTTGAGCACTGATAATGTTATCGCCGAGTACTTCTTTGACAGgtttgtttttgatct Y G Y S M G V E L S T D N V I A E Y F F D R 309 1042 cgattggaaaatagaagaattaaattataacataagagtaaaactaatgtatacatcatacatggtttgtccagGTTTCACT intron II F H L 312 1124 TGAAGCTCCACACAGCAGGGCTCATAGCAGCATGTTTCGGAATGGCCAATTTCTTTGCTCGTCCAGCAGGAGGCTACGCATC K L H T A G L I A A C F G M A N F F A R P A G G Y A S 339 1206 TGACTTTGCAGCCAAGTACTTCGGGATGAGAGGGAGGTTGTGGACGTTGTGGATCATACAGACGGCTGGTGGCCTCTTCTGT D F A A K Y F G M R G R L W T L W I I Q T A G G L F C 366 1288 GTGTGGCTCGGCCGCGCCAACACCCTTGTAACTGCCGTTGTGGCTATGGTGCTCTTCTCTATGGGGGCACAAGCTGCTTGCG V W L G R A N T L V T A V V A M V L F S M G A Q A A C G 394 1370 GAGCCACCTTTGCAATTGTGCCCTTTGTCTCCCGGCGAGCTCTAGGCATCATCTCGGGTTTAACCGGGGCTGGAGGGAACTT A T F A I V P F V S R R A L G I I S G L T G A G G N F 421 1452 TGGATCAGGGCTCACACAACTCCTCTTCTTCTCGACCTCACACTTCACAACTGAACAAGGGCTAACGTGGATGGGAGTGATG G S G L T Q L L F F S T S H F T T E Q G L T W M G V M 448 1534 ATAGTCGCTTGCACGTTACCTGTGACCTTAGTTCACTTTCCTCAATGGGGAAGCATGTTCTTGCCTCCTTCCACAGATCCAG I V A C T L P V T L V H F P Q W G S M F L P P S T D P V 476 1616 TGAAAGGTACAGAGGCTCATTATTATGGTTCTGAGTGGAATGAGCAGGAGAAGCAGAAGAACATGCATCAAGGAAGCCTCCG K G T E A H Y Y G S E W N E Q E K Q K N M H Q G S L R 503 1698 GTTTGCCGAGAACGCCAAGTCAGAGGGTGGACGCCGCGTCCGCTCTGCTGCTACGCCGCCTGAGAACACACCCAACAATGTT F A E N A K S E G G R R V R S A A T P P E N T P N N V 530 1780 TGATCATACATTCCACCCACGGTGGAATGGTGAAGGATGATCGCATATAAGAATATGTCACACAGTGAAAAAAAAAAATGCA * 1862 AATGTTATCAATGCTTGCATAACATTACTATCTATCTTTCATTTACTAAACAAACCTTTTGCTTTTTGCCTTGAAATCTTTT 1944 TATTATATATCAAAATATATCTCTATGTCTTGAGATTTG  Figure 2-2. D N A and deduced amino acid sequences of the AtNRT2.1 gene. The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined.  13  -13 2 6 TCAAACCCCAACAGGCCTCAACAGAGGGAACACCGGCCACGTCACCAAGATTGATGTATATACGCTAGTGGCACGGAAATGG -12 4 4 TACGGCATAAAATATACGAATACAACTACTTTTTCTTGTTATATTTAAGACGTCATCTACAACTACATTGTAATATATTTTG -116 2 GGTTATAATTTAGAACAAGACGTATAGCTCTACCTATCAATTCGCAGGAGTCGATTTAATACCTACCTATTTCTTTATGTAA - 9 9 8 GTCTGAGTTGTTTAATCAAATTTCCAAAGCAGCAACCATTTTTCCAGCAACTGAAACCATTTAAAACAAAATTTACCCAAAA - 916 AATTAAGAAGATTTTGAATTTCGAAATCAGACCACCTCAAAAGTCAAATCTTATATATTTTATGTTTATATCCAAGCATAAT - 8 3 4 C y T A T A T A T T T T C A T A G T T T G T f l G G A A A T C C A A A G T T T C T A A A T T T A T T P AAATTAAAGTCATTAATTAATCCATGTTTAAAT  -7 5 2 AATCAAAGGACATGTGAAATTGCTAATGCCAGTCAAATTACATTACAACCAACTAAAATATCGAACAAATTAAGTTATGTCT -67 0 ATATGTGCTATACAAAATTATCTAATTTTTACAGTGTTATATATGGAAAATATATGATAAGTTTGTTGAAGTAATAAGCTTA -5 8 8 TTGATTTTTTAGAGACAACTAATGTGCAGCTAAGGCCACAACAAATTAAATCGTCCAGGAGACAGCAGTTTATTCACCACAA - 5 0 6 TCATTCCTATTCTTGATACGATGTGATATAGAATTACATTGATACCCTTAAGAAATTATGAAGAATATATGGTCTAAAAGAG - 4 2 4 AATCACAATGACATCGCTTAAAAATTATTTAAATATGGATTTTAATGAGTTCACGATGTGGTGCTTGATCCTGTTATAAGAT -342 AATATGTATTACAGACATGTAAAAAAAAAATCCACTTCTGAAACACAAAAGGAGAAAAGGATACAGTTGTCACTTGTCATCT -260 GAGAGGTGAATATCGGTAACCTTTGGGGATTAGCGAGAGAGTGGGAAAGATGCTTGCGGCGAATATGGATTCCTCGAAAAAA -17 8 ATGTATTTTTAATATTGTTTAGTTAGCCGTTGAGAATCTCCAAAGAATACTTTTTCTTTTTTTTTTTGAAATTGTCAAAGCT - 9 6 ATACGAATCCTATATAATCCCTCGTGTGACTAATATCTAGTACATCAATCAXAJ^MCTTGAATTTTCTCAAAGGAACTTGA -14 TACGTTTAAAATACATGGGTTCTACTGATGAGCCCGGAAGTTCCATGCATGGAGTTACCGGTAGAGAACAGAGCTATGCTTT M G S T D E P G S S M H G V T G R E Q S Y A F 23 69 CTCGGTAGATGGTAGTGAGCCGACCAACACAAAGAAAAAGTACAATCTGCCGGTGGACGCGGAGGATAAGGCAACGGTTTTC S V D G S E P T N T K K K Y N L P V D A E D K A T V F 50 151 AAGCTCTTCTCCTTCGCCAAACCTCACATGAGAACGTTCCACCTCTCGTGGATCTCTTTCTCCACATGTTTTGTTTCGACGT K L F S F A K P H M R T F H L S W I S F S T C F V S T F 7 8 233 TCGCAGCTGCACCACTTATCCCGATCATCAGGGAGAATCTTAACCTCACCAAACATGACATTGGAAACGCTGGAGTTGCCTC A A A P L I P I I R E N L N L T K H D I G N A G V A S 105 315 CGTCTCGGGGAGTATCTTCTCTAGGCTCGTGATGGGAGCCGTGTGTGATCTTTTGGGTCCTCGTTACGGTTGTGCCTTCCTT V S G S I F S R L V M G A V C D L L G P R Y G C A F L 132 397 GTGATGTTGTCTGCCCCAACGGTGTTCTCCATGAGCTTCGTGAGTGACGCAGCAGGCTTCATAACGGTGAGGTTCATGATTG V M L S A P T V F S M S F V S D A A G F I T V R F M I G 160 479 GTTTTTGCCTGGCGACGTTTGTGTCTTGTCAATACTGGATGAGCACTATGTTCAACAGTCAGATCATCGGTCTGGTGAACGG F C L A T F V S C Q Y W M S T M F N S Q I I G L V N G 187 561 GAC AGC AGCCGGATGGGGAAACATGGGTGGCGGCATAACGCAGTTGCTCATGCCC ATTGTGTATGAAATCATTAGGCGCTGC T A A G W G N M G G G I T Q L L M P I V Y E I I R R C 214 643 GGATCAACAGCGTTCACGGCCTGGAGGATCGCCTTCTTTGTCCCCGGTTGGTTGCACATCATCATGGGAATCTTGGTGCTCA G S T A F T A W R I A F F V P G W L H I I M G I L V L T 242 725 CGCTAGGTCAAGATCTGCCAGGTGGAAACAGAGCTGCCATGGAGAAAGCGGGAGAAGTTGCCAAAGACAAATTCGGAAAGgt L G Q D L P G G N R A A M E K A G E V A K D K F G K 268 807 atatctctatctacatgaatatgtcaaaacaagttaggctaactatgtcatagatggatcggatataataggctaactcgtg intron I 889 atatcgtataaatcgtgtagATTCTATGGTACGCCGTTACAAATTACAGGACTTGGATTTTCGTTCTTCTGTATGGATATTC I L W Y A V T N Y R T W I F V L L Y G Y S 2 89 971 CATGGGAGTTGAGTTAAGCACAGACAATGTTATCGCCGAGTACTTCTTTGATAGgtttgttttctgtctcgattggaaattg M G V E L S T D N V I A E Y F F D R 308 1053 acaacttcacatatattcaggaataacataagagtaaaatttatattcccttttatttttattttgtcaatcgttccctttt intron II 1135 atttaaaataaaaaaatggtatgttcagGTTTCACTTGAAGCTTCACACAGCGGGGATTATAGCAGCATGTTTCGGAATGGC F H L K L H T A G I I A A C F G M A 325 1217 CAATTTCTTTGCTCGTCCAGCAGGAGGCTGGGCATCTGACATTGCAGCCAAGCGCTTCGGAATGCGAGGGAGGTTGTGGACT N F F A R P A G G W A S D I A A K R F G M R G R L W T 352 1299 TTGTGGATCATTCAGACGTCCGGTGGTCTCTTTTGTGTGTGGCTCGGACGTGCCAACACCCTCGTCACTGCCGTTGTATCTA L W I I Q T S G G L F C V W L G R A N T L V T A V V S M 380 1381 TGGTCCTCTTCTCTTTAGGAGCACAAGCCGCTTGCGGAGCCACCTTTGCTATCGTGCCCTTTGTCTCCCGGCGAGCTCTAGG V L F S L G A Q A A C G A T F A I V P F V S R R A L G 407 1463 CATTATCTCGGGTTTAACCGGGGCTGGAGGGAACTTTGGGTCAGGACTCACACAGCTCGTCTTTTTCTCGACTTCGCGCTTC I I S G L T G A G G N F G S G L T Q L V F F S T S R F 434 1545 ACAACTGAAGAAGGGCTAACGTGGATGGGAGTGATGATAGTTGCTTGCACGTTGCCTGTTACCTTAATCCACTTTCCTCAGT T T E E G L . T W M G . V M I V A C T L P V T L I H F P Q W 462 1627 GGGGAAGCATGTTCTTCCCTCCTTCCAACGATTCGGTCGACGCTACGGAGCACTATTATGTTGGCGAATATAGTAAGGAGGA G S M F F P P S N D S . V D A T E H Y Y V G E Y S K E E 489 1709 GCAGCAGATTGGCATGCATTTAAAAAGCAAACTGTTTGCTGATGGAGCCAAGACCGAGGGAGGCAGCAGCGTCCACAAAGGG Q Q I G M H L K S K L F A D G A K T E G G S S V H K G 516 1791 AACGCAACCAACAATGCTTGATCATGTGTCATTGATATC AAGAAATTAATAATTTCACTTATGTGAAATGGACATAAACTGT N A T N N A * .522 1873 TGGAAAATAAAGAACCATTTCTTTCATCATTTGCTTTTA  Figure 2-3. DNA and deduced amino acid sequences of the AtNRT2.2 gene. The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined.  14  • 14 6 2 •13 8 0 • 12 9 8 -121 6 -113 4 -10 5 2  TATATATATAGAACTAAAACCATTACAAAAAGAAAAGATTTCGCCTTTTTAATGATGGATAATTCTAAAGCCTATAAGACTT AAACTTTTATTTAAAATCTACAGTTTGTTGCCCAAATAAAATGTGATAAGTATAGAGATAACAAAATATAAAATTATTTCTT ACCAAAAAAAAATATATATATATATATATAAGACTATTTTACCGTAATTTATTGATGATTGCAGACAATACAAGATATCTCT AGTTTACAAAAATATCATCAACAATATTCGAGAGAATAGTTCTTTTGAGTATTTGCGGATGGCCGGAAACAACAACACTTAG AAATCATATTTAGTAAAGAATTATGTTTAGAGTTTAGACTTTATAGCTTATATATTATATTGAGATGATAGATGATTATAAG GAAAAACATAAGGAAGTCAACTTATCATAACGCTTCATTGTAAGGATATGCGAATATCAAAGGCGGAAAGATTTAGAATAAG  - 97 0 - 88 8 - 806 - 724 - 64 2 - 56 0 -47 8 - 396 - 314 - 232 -15 0 - 68  TGAATAACCCATAATTTCATAAACGTTAGAGCATTTTTTTAGGAAATTATTTTAAGATAGCAATTATTTCATTTGGTGAGTC GACCACATGGAATCCTCAAGAGACAAATGAAAAATAATTAGACTTTTTGACGATTTTTGCCTTCATTGATACGTACGGCCTC TTAGGCTTTTTAGCTATTTCCAATGCCAACTGTCAACATTCGTATCTCTTTCGCCATTTTAGTGAAATTCCACAAAGTCATT ATCTTTGATGTATATAACTTGCCAGGCTGCTACTATACCAAATAGATTTATAAATATTATTTTTAGATTTCTTTTCCATACT TTTTAATTCTCAAACGAAACTTTATGCAAAGTTGAAATAAAGTTTTCTTCTGCATTTCACTTAAAATTATAATTTGTCAAAC AGAAGTGCAAACATTGATTTTCTGACTGAAAATTTTTCAACCTTACAAAAGTTGCTTGAACTTTGTTTAGAAAAAAGAAAAT ACTAATACTTGATAAACCCTCACGGTTCCTATTTTAAAACCAAAACCTTCAAATCAAAGACTCAAGAATCAATTCATAAATG TGTGAGACAAAACTCATAACCCAAATATGGTACACGTACGTATGAAACGTACTTAAATGCTACAAAAGAATAATATGTTTAG TTCTCAAATTTAAATAATTTTTTCCTTCTATCATTACTAATCAAAATTACAACTCATATCTATACTAAATGCTATTATCAGC TAACAATAATAAAATTTTCACAAATTGGTAAAGTCCTTATTAACTTTTACTTATCTTATTCAAATCTCATTATTGGACCCAC CTAACCCTACCCACCATATGATATTGGTATCCCCTCTGGCCTCTATATAAACTTTGCATTTCTCTAATCTCCAACTTACACC AACAAAACACAACAAAGACCATTAGCCTTCTCTCCCACTCAGAGTCTTTCATCTCACTCTCGCCTTAAATGACTCACAACCA  15  TTCTAATGAAGAAGGCTCCATTGGAACCTCCTTGCATGGAGTTACAGCAAGAGAACAAGTCTTCTCTTTCTCCGTCGATGCT S N E E G S I G T S L H G V T A R E Q V F S F S V D A TCGTCTCAAACAGTCCAATCAGACGATCCAACAGCTAAATTCGCCCTTCCGGTTGATTCCGAACATCGAGCCAAAGTGTTCA S S Q T V Q S D D P T A K F A L P V D S E H R A K V F N 6 ACCCACTCTCTTTTGCTAAACCTCACATGAGAGCCTTCCACTTAGGATGGCTCTCATTCTTCACATGCTTCATCTCCACCTT P L S F A K P H M R A F H L G W L S F F T C F I S T F CGCGGCAGCACCATTAGTCCCC ATC ATCCGCGACAACCTCGACCTCACTAAAACCGAC ATTGGAAACGCCGGAGTCGCATCC A A A P L V P I I R D N L D L T K T D I G N A G V A S GTCTCTGGTGCCATTTTCTCAAGGTTAGCCATGGGAGCGGTTTGTGATCTCCTCGGTGCACGATATGGGACTGCCTTCTCCC V S G A I F S R L A M G A V C D L L G A R Y G T A F S L TCATGCTAACCGCCCCAACCGTCTTCTCAATGTCGTTTGTGGGTGGCCCTAGCGGATACTTAGGCGTCCGGTTCATGATCGG M L T A P T V F S M S F V G G P S ' G Y L G V R F M I G ATTCTGTCTCGCCACGTTTGTATCATGCCAGTATTGGACCAGCGTTATGTTCAACGGTAAGATCATAGGACTAGTGAACGGC F C L A T F V S C Q Y W T S V M F N G K I I G L V N G TGTGCAGGCGGGTGGGGTGATATGGGCGGTGGAGTGACTCAACTCCTAATGCCGATGGTCTTCCACGTCATCAAACTTGCCG C A G G W G D M G G G V T Q L L M P M V F H V I K L A G GAGCCACTCCGTTCATGGCCTGGCGGATAGCTTTCTTCGTTCCCGGATTTCTTCAAGTTGTTATGGGCATTCTCGTCCTCAG A T P F M A W R I A F F V P G F L Q V V M G I L ' V L S TCTCGGCCAAGATCTCCCTGACGGTAACCTAAGTACCCTTCAGAAGAGTGGTCAAGTCTCTAAAGACAAATTCTCCAAGGTA L G Q D L P D G N L S T L Q K S G Q V S K D K F S K  M 97 179 261 343 425 507 589 671 753  T  H  N  H  5 32 0 87 114 142 169 196 224 251 277  83 5 cttttctatatatatatatttctgtctcatcttcaaatatataacaaatccagaccaagaagaatatggctctcattaaaag intron I 9 1 7 aatcttgcaaacattaaacatactcatgaagttttgcaataaattcgtgaagaactatttcgtttatttagttaaataaatt 9 9 9 tctagtgtctaaaggtttttcttgttatagGTTTTCTGGTTTGCTGTGAAGAACTACAGAACATGGATTTTATTCGTTCTTT V  F  W  F  A  V  K  N  Y  R  T  W  I  L  F  V  L  Y  295  1 0 8 1 ATGGATCTTCCATGGGAATTGAATTAACTATCAACAACGTTATCTCCGGATATTTTTACGACAGg t t c g a t t t c t t a t t c g t G  S  S  M  G  I  E  L  T  I  N  N  V  I  S  G  Y  F  Y  D  R  316  1 1 6 3 taaaacccaactgatgaacttacttacttctgtcacaaggtaataaccttaatttgttttcttgttctctacgtatttatca intron I I 1245 gGTTTAACCTTAAGCTTCAAACAGCTGGTATAGTAGCAGCCAGCTTTGGAATGGCTAACTTCATCGCCCGTCCCTTCGGTGG F N L K L Q T A G I V A A S F G M A N F I A R P F G G TTACGCTTCTGATGTAGCGGCTCGGGTTTTTGGCATGAGAGGCCGGTTATGGACCTTATGGATCTTTCAAACCGTAGGAGCT  343  Y A S D V A A R V F G M R G R L W T L W I F Q T V G A CTTTTCTGTATCTGGCTAGGTCGAGCTAGTTCACTTCCCATAGCAATCCTAGCAATGATGCTCTTCTCAATCGGTACACAAG L F C I W L G R A S S L P I A I L A M M L F S I G T Q A 1491 CAGCTTGCGGAGCCCTCTTCGGAGTTGCACCTTTTGTCTCGCGCCGCTCTCTAGGGCTCATATCGGGACTAACCGGCGCAGG A C G A L F G V A P F V S R R S L G L I S G L T G A G 1573 AGGAAACTTCGGGTCCGGTTTGACTCAACTGCTTTTCTTCTCATCAGCGAGGTTTAGTACAGCTGAGGGACTCTCATTGATG G N F G S G L T Q L L F F S S A R F S T A E G L S L M 1655 GGCGTTATGGCGGTTTTGTGCACACTCCCAGTTGCGTTTATACATTTTCCGCAATGGGGAAGCATGTTTTTAAGACCGTCGA G V M A V L C T L P V A F I H F P Q W G S M F L R P S T 1737 CCGATGGAGAAAGATCACAGGAGGAATATTATTACGGTTCTGAGTGGACGGAGAATGAGAAACAACAAGGATTGCACGAAGG D G E R S O . E E Y Y Y G S E W T E N E K Q Q G L H E G 1819 AAGCATCAAATTTGCAGAGAATAGTAGGTCAGAGAGAGGCCGGAAAGTAGCTTTGGCTAACATTCCAACGCCGGAGAACGGA S I K F A E N S R S E R G R K V A L A N I P T P E N G 1901 ACTCCAAGTCATGTTTGAAGACAAAACTTACAAGAGATTTTCCTTTTACATTAAATCCCTTTTTAATAGTTTCATACTCCAC T P S H V * 1983 TCATATATGTACCGAGTAAGACCTTTTCTGTGATAGGTAAGGATCGATGAGCTTGGTACTTTAGTATAAATTATTGTAATGT 2065 CATCAGAATGTTCAACTACTCTTTTTTCTGCACCAATAAGCTTTATGTTCAATCAGATTTACATGTCAAGTGAAAAAAACAA 2147 AAAAAGTCTCTGTTTACGGTGTGTGAAATGCTAAGAGAGTCCACATGAAGAAAACTTTATGGACAAGGACCA  370  1327 1409  398 425 452 480 507 534 539 '  Figure 2-4. D N A and deduced amino acid sequences of the AtNRT2.3 gene. The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined. 15  3 introns and 4 exons, containing introns 2 and 3 in the same position as those of AtNRT2.1-2.3 (Figure 2-5). AtNRT2.5 and 2.6 have one short intron (Figures 2-6 and 2-7). The ORF of AtNRT2.5 encodes 493 amino acids (52.7 kD) which is the smallest protein among the N R T families, whereas AtNRT2.6 encodes the largest transporter (58.6 kD) in the NRT2 family. AtNRT2.6 shares the same intron position as the first intron of AtNRT2.12.3. Two introns were found in the AtNRT2.7 gene, the second intron having the same position as that of AtNRT2.5, while the first one is unique (Figure 2-8). Putative T A T A and G A T A boxes were found in the promoter regions of all members of the NRT2 genes. Some G A T A boxes were separated by 2-22 bp except in AtNRT2.7. Rastogi et al. (1997) found that the important region of spinach N i R promoter contained G A T A consensus sequences located 24 bp apart, harboring a potential binding site for a NIT2-like transcriptional factor. Nitrate-dependent transcription motifs (an A T rich region followed by [AG]-[CG]-T-C-A) (Hwang et al., 1997) were observed in all AtNRT2 family members at -500 to -1000 bp from the start codon. However, those positions might be too far upstream. In the cases of nitrate reductase (NR) and nitrite reductase(NiR), the motifs were found at -140 to -250 bp upstream in Arabidopsis (Hwang etal., 1997). The seven AtNRT2 members encode predicted proteins consisting of 493-539 amino acids, which are typical membrane proteins. Membrane spanning regions and topologies were analyzed with prediction programs including H M M T O P (Tusnady and Simon, 1998), M E M S T A T (Jones et al., 1994), T M H M M (Sonnhammer et al., 1998), TMpred (Hofmann and Stoffel, 1992), and Toppred2 (Claros and Von Heijne, 1994). Although it is generally  16  1666 AAAACTCATCATTCCACAATATGTACATACGAAATAAGTTATGGAATAGM^TTTATCTTAATGAAGATTTCTCTTTTAAAA 1584 AAAAAACTAAAGCACAAAAGTGCTAACTAGAAAAAAGTTCTCGTTCACA&AArRTAAA&GTPATTAACTCATTACGAATTAA 1502 GAATAATGGACTTAATATAATGTTAAAGGTAAACAAGATCAAACAATAGCACTGTTGCACGTTTCCTCTGGAGTTTCTTAAG 1420 GACAAAAAAGGTTTTTATTTGTGAAGGTACAACTGTTATTGCTGTTACAATCTTCCTAAGCATAATTAGGGATCTGATTACA 133 8 TCATCACAACTTTAGTTTAATAAGTGAAAATCTATATATTATTTTGTTTATTTCAATAACATTCTATTATATTAACAAAAAA 1256 AAAAAAAAAATCAAATGGAACCTTTGAATCCATGCAAAGACATAGTCACATAGAGAGAGAGAGGACCCACCGGACTCGTTCA 1174 CATGTATGAATATGGATTGATTTTTATTTCTCTTTTTAAAAAAAAATATGGATCGATTATTGCATCCCATCATGTGGAAATA 1092 GCTCATTACCAAGAAAAAAAAAATTACAATGAAATTTTCTTAGATTAATCTCCGAAGTCTGTAGTAGTTAAGCTTACAAACT 1010 TCAAGGAAAATCACCTAATAAAAATTCGTGGATTTATTCCATGAGTATGGAGCTATAATTATAAACTTATTAAATAGAGAAT - 92 8 AGACTTGATAACTCGCAGTTGATAATGCCTCATGGTACAATCTCTGAAAACATCGATCGAGGTTCGAAATACCACCACAGCA - 84 6 ACGCAAAAAGCGTTGGCAAAATGCCAAAATCTCATGATTCTTTGGATTTAATTACTTCACCCAAGTTTAACGATTTTTATCG - 7 6 4 TTAATTTTCTTTAGGTAATGCTCTTTTGTAATATCTTTACATTTCATTTTCATGATACTAACATTCATAGCAAAACAAAATT - 6 8 2 ATATATTAAATAATGATTTTAAGAAGTAAACATGATTTTTTTTTTCTGTAACTGTAAGACTATGTTATTTATTTTTTATCTG - 600 AGAAAAAAAAACTTAGAAAGAAAAGGAATCATATAGAAAAGAGATTACATCATGCGCTGCGACATATAAAGTTTCAAATTAT - 51 8 ACCGCCGATCTTTATTATATTG_A|£AGTAAACTCTATGAGGATTTGCTGTATTAGACATGAAAAGAAATCGTTGTAAACAGAA - 43 6 CCAGAAAGTAGTTTCTCGTTTGAGAAAAAAAAAAAAAAAAAAAACTTCCTAGATATATGGACAGTTTAGTAATATTATATTG - 354 TTGATAAATACTAAATTGGAATATAAGTGAAAGTGAACCTTTGGGACGTATGACCAGGCTAAATTCTCGTGTTTGCATGCTC - 272 GCGGCGAAAGTGAATATTCCATACTATTAATATAAAGACACAACTTGTATAATTGTAATCAATCTCACATAAACAACTTTGA -19 0 ATCATTAATTATCGTTAAGAACTATACTATTATAGTATCATTTACGTAAAACGAATCCCACTTATAGCCTTTTCGAATCTCC -10 8 ATCGGCTCTTACGAAGTCAACTTTCGTATCTCT^IAXMAACCATTCTTCTCCTTCTTGTTCCCTAAACCAAGACCACAAGA -2 6 AAAAAACATAAAAAAATATTCACAAAATGGCCGATGGTTTTGGTGAACCGGGAAGCTCAATGCATGGAGTCACCGGCAGAGA M A D G F G E P G S S M H G V T G R E 19 57 ACAAAGCTATGCATTCTCTGTCGAGTCTCCGGCAGTTCCTTCCGACTCATCAGCAAAATTTTCTCTCCCCGTGGACACCGAA Q S Y A F S V E S P A V P S D S S A K F S L P V D T E 46 13 6 CACAAAGCCAAAGTCTTCAAACTCTTATCCTTTGAAGCTCCACATATGAGAACTTTCCATCTTGCTTGGATCTCATTCTTCA H K A K V F K L L S F E A P H M R T F H L A W I S F F T 7 4 221 CTTGCTTC ATTTCCACTTTCGCTGCTGCTCCTCTTGTCCCCATC ATTAGAGATAACCTTAATCTCACAAGACAAGATGTCGG C F I S T F A A A P L V P I I R D N L N L T R Q D V G 101 303 AAATGCTGGTGTTGCTTCTGTCTCTGGCAGTATCTTCTCTAGGCTTGTTATGGGAGCAGTTTGTGATCTCCTTGGGCCACGT N A G V A S V S G S I F S R L V M G A V C D L L G P R 128 385 TATGGCTGTGCTTTCCTCGTCATGCTCTCTGCTCCAACCGTCTTCTCCATGTCTTTCGTTGGTGGTGCCGGAGGgtaagcat Y G C A F L V M L S A P T V F S M S F V G G A G G 153 467 tcttgtgaattgtaaaatttctcaaaaaacttaagattaacttcacttagtcctatataaatatatgtactaatgtacatat 54 9 gatatgcagttattgaaacaattttaaaagcatttttctaaaaaaccaaaggatttcatctcaaaattaattgacaataagg 631 a a a g t a g t t t a t a t a a t g g a t t a t t c t t a a t g t g g g t t t c t a a c a a t a t t t t g g c c a t a t a t a g G T A C A T A A C G G T G A G G T T intron I Y I T V R F 159 713 CATGATCGGGTTCTGCCTGGCGACTTTCGTGTCATGCCAGTATTGGATGAGCACAATGTTCAATGGTCAGATCATAGGTCTA M I G F C L A T F V S C Q Y W M S T M F N G Q I I G L 186 795 GTGAACGGGACAGCGGCAGGGTGGGGGAACATGGGCGGTGGGGTCACTCAGTTGCTCATGCCAATGGTCTATGAGATCATCC V N G T A A G W G N M G G G V T Q L L M P M V Y E I I R 214 877 GACGGTTAGGGTCCACGTCCTTCACCGCATGGAGGATGGCTTTCTTCGTCCCCGGGTGGATGCACATCATCATGGGGATCTT R L G S T S F T A W R M A F F V P G W M H I I M G I L 241 959 GGTCTTGACTCTAGGGCAAGACCTCCCTGATGGTAATAGAAGCACACTCGAGAAGAAAGGTGCAGTTACTAAAGACAAGTTC V L T L G Q D L P D G N R S T L E K K G A V T K D K F 268 1041 TCAAAGgtactttattagtacttaagtaaaataaatgttaattcttcttggatcctttgattcttagtcttatatattaggg S K intron II 270 1123 tctgcagatcgttgtctaaattatattattttcattgaatatataaagaaggttgttctgatatagatcttagattaacatt 1205 t a g a t a g a g a c a t t a a a t t a a t c c a a g a a a g c g a t t c g a c t a a c t a a a a a a a a a a a a a a a a a a c a a t t a c g t t t t c a t a t a g 1287 a a a a a g c g a a a t c c t t a t a a t a c t c t t c c a t a g a t t t t t t g t t t t c t c t t t t t t t t t t t t g t t a t a g a t c t t t t t a t t t g g t 1369 taagagtaagactcacagttttctggtggacaaattaaccagGTTTTATGGTACGCGATCACGAACTATAGGACATGGGTTT V L W. Y A I T N Y R T W V F 284 1451 TCGTGCTGCTATATGGATACTCCATGGGAGTAGAGCTCACAACCGATAACGTCATCGCTGAGTACTTTTTCGACAGgtataa V L L Y G Y S M G V E L T T D N V I A E Y F F D R 309 1533 ttattaaaactggtatataatttatcgaatccatagtcagtcagtctctaaagtataaacaataataacaagggtttgattg 1615 c t t t t a g c a t a t a t a g t a c t a t t a t t a t t g c a a t a t a c a a g g a t t t t g g t t t t t t c c t a a c c a t t a a a a t c a a t t t a a t t a a 1697 cgtcaatgccgcgtgttaattgtagtagacagtaaaactcaaactcaaatttgttgataccttgcatgtcgatttactacca intron I I I 1779 c a a t g t t t t a g c c a a a a a a c a t a t a t t t t t g a a a a a t g t a t t c t a c t c a t g a a a a t g a t t c t t g t t a a g c t t t c t t t a c a t t 1861 t c t g t t t t t g t a a a t c c a c t a c t t a c a t t t c a t t t a t t t g t t a c c g a g t a g a c c c t a a a t a t a t a a a t t a c t t c t a t g g a t c 1943 aaagactcaatacatggcgatcatttttcagGTTCCATCTTAAGCTTCATACCGCCGGTATAATCGCGGCAAGCTTTGGTAT F H L K L H T A G I I A A S F G M 326 2 025 GGCAAACTTCTTTGCCCGTCCTATTGGTGGTTGGGCCTCAGATATTGCGGCTAGACGCTTCGGCATGAGAGGCCGTCTCTGG A N F F A R P I G G W A S D I A A R R F G M R G R L W 353 2107 ACCCTATGGATCATCCAAACCTTAGGCGGTTTCTTCTGCCTATGGCTAGGCCGAGCCACCACGCTCCCGACCGCGGTTGTCT T L W I I Q T L G G F F C L W L G R A T T L P T A V V F 3 8 1 2189 TCATGATCCTCTTCTCTCTCGGCGCTCAAGCCGCTTGTGGAGCTACCTTTGCTATCATACCTTTCATCTCACGCCGCTCCTT M I L F S L G A Q A A C G A T F A I I P F I S R R S L 408 2 271 AGGGATCATCTCTGGTCTTACTGGAGCTGGTGGAAACTTCGGCTCTGGTTTGACCCAACTCGTATTCTTCTCGACCTCAACG G l I S G L T G A G G N F G S G L T Q L V F F S T S T 435 2353 F  TTCTCCACGGAACAAGGGCTGACATGGATGGGGGTGATGATTATGGCGTGTACATTACCCGTCACTTTAGTGCACTTCCCGC S T E Q G L T W M G V M I M A C T L P V T L V H F P Q 4  Figure 2-5 D N A and deduced amino acid sequences of the AtNRT2.4 gene.  17  63  2435 2517 2 599 2 681 2763  AATGGGGAAGCATGTTTTTGCCTTCCACGGAAGATGAAGTGAAGTCTACGGAGGAGTATTATTACATGAAAGAGTGGACAGA W G S M F L P S T E D E V K S T E E Y Y Y M K E W T E 490 GACCGAGAAGCGAAAGGGTATGCATGAAGGGAGTTTGAAGTTCGCCGTGAATAGTAGATCGGAGCGTGGACGGCGCGTGGCT T E K R K G M H E G S L K F A V N S R S E R G R R V A 517 TCTGCACCGTCTCCTCCGCCGGAACACGTTTAAGAGTTTTTAAATGTACATGTTGTATCAGTTTCTATATATTTCTCCAAAT S A P S P P P E H V * GTGTAATTAGTTGATCGAATTGCATGCTTTAATTTCTTTTAAAGGATATGCTACTCTTCATGTAATTTCGTAACAATTATAT TGTTTTTTTAAATTTCGTA 5  2  7  Figure 2-5. (continued). The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined.  18  1426 CTAGATTATCAGTTCCTGCAGTTGTCATCCGTACTGCTGTGGAGTGTAATGAGGCAGAGAAATCTTCCCCTGTGAACGACAA 1344 CGACAAACCCAGACGCGCTGCTACATCAAAGCCAGACCGGAAACCCAAATCCACAGCCTCTAAACTGATTGCGACACAGAAG 1262 GAAGAGGAGGCACTCGAATCCATTGCTCCAGAAGAAACTTCAGCTGAATGTGGTGAGATACTGAAGCAGGACGGGAAGCTAA 1180 AATCCGTTTCTCCCAAAAACAATAGCACTGCTTCTAACCTAGTATCATTTTCAAAAGCTAAGAAATCAACTATGAAGGAGAA 1098 TCTATCAGAGAACAAGGCTGAAGAGAGTGCATCGGTTAGTACCCGAAAACTGAAAATAGGAACGGAGATGACAGCCACGGTC 1016 GACCATGTTCGAGCCCTTGGATTGGTTCTTGATTTAGGTGGTGAAATCCGCGGTATGTACATATTCCAGGTATGTTTCAGTA -9 3 4 AATTCTCCTTTGACTTGTTCTCCCATTTTCTTGAGTTAACTTTTGAGGCGATATACTTAATTCTTGCTTTGTATTGATATTG - 8 5 2 TGTACTATGAATGAGTACAGGGAGATAAAGATAAGTTCAAAAAAGGAGACACATTGCGAGTGAAATGTACAAGTTTTAACAC - 77 0 CAAAGGAGTCCCTGTGATGGCTTTGGTTGACGAAGAGGGAGAAGAATAGTGGTAAACTCTCTTTCCTTTCTACAAGGTTTTT - 688 TCAACCCAAGGGATCATGTGGAGTCGATCATATGGATCATACGAGAGTTTTGCTTGAAATGTTTTTATCATACGGATCGAAT - 606 CAAGAGATGCTCGTTAGCTGCTTTTGGTGAGCAAATCTTGGTAGATGGATAGATTCATTGGCGTCACAACTTGAGGAAAGCT -524 AATGAACTCGGTTAGGTAACTAGTCTTTTACTTTGGCCTTGTGATGTGCCATTTTGTTTCTCTTTTATTGGGGGGGTTTTGT - 442 GGAACCGAAAGTGGATTGTATTGTTTAGTGTCTTAGTAACTGACGTCTGAAAGGTGCGTAACGCAAGTTTCATCATTTTTGT - 360 CCAATTTTTACAAAAATACAAAAGCACCAAAAACCCAAGTCGGCAGCTAAAGATAGAAACTACGCATCCCAATGGCATTCTT - 2 7 8 GATAGATATTATTTGTCCGAATATATTTTCTTCTAAATTACAAATTCATTTCAACAATTGACGTCAAAAATTAATTTAAGCC -19 6 AAGAGACGAGGAACTAAAATTGAATTTCACATTTTGATTGAGCATTTGGGTTTGAATTAAGATTACTCGAAAGTTGCCAAAA -114 GTTTGCCTCTGAGTCATTTTATTGTTCATGAAAGATTTAAATTCAAAGATAATGTTCATTGATTGGGTGGTCGTGTAAGTAA - 3 2 GAGTCGTCAGCGAGTTTTCTTCTCCGAGAGTAATGGAGCCATCTCAACGCAACACCAAACCGCCGTCGTTTTCAGATTCCAC M E P S Q R N T K P P S F S D S T . 1 51 TATCCCGGTTGATTCCGATGGTCGAGCCACCGTCTTCCGACCATTCTCTCTCTCCTCGCCACACTCACGAGCCTTTCACCTA I P V D S D G R A T V F R P F S L S S P H S R A F H L 133 GCTTGGCTCTCACTCTTCTCATGCTTCTTCTCCACCTTCTCCATCCCTCCTCTGGTCCCCGTCATCTCCTCCGACCTCAACC A W L S L F S C F F S T F S I P P L V P V I S S D L N L 7 215 TCTCTGCCTCCACCGTATCCGCCGCCGGAATCGCTTCCTTCGCTGGCTCCATCTTCTCTCGCCTCGCTATGGGACCACTCTG S A S T V S A A G I A S F A G S I F S R L A M G P L C 297 TGATCTCATCGGACCACGTACTTCCTCAGCGATTCTCTCTTTTCTCACCGCTCCTGTAATCCTCTCCGCCTCACTCGTCTCC D L I G P R T S S A I L S F L T A P V I L S A S L V S 379 TCTCCGACGTCCTTCATCCTCGTCCGTTTCTTCGTCGGCTTCTCGCTCGCTAATTTCGTAGCCAATCAATACTGGATGTCCT S P T S F I L V R F F V G F S L A N F V A N Q Y W M S S 461 CCATGTTCTCCGGTAACGTCATTGGTCTCGCTAACGGTGTCTCAGCCGGTTGGGCTAACGTCGGCGCCGGTATCTCTCAGCT M F S G N V I G L A N G V S A G W A N V G A G I S Q L 543 CCTTATGCCTCTCATATACTCCACCATAGCCGAATTCCTTCCACGCGCCGTCGCCTGGCGCGTGTCCTTCGTATTTCCCGCC L M P L I Y S T I A E F L P R A V A W R V S F V F P A 625 ATTTTTCAGGTTACAACGGCCGTCCTCGTTCTCCTCTACGGCCAAGATACTCCCCACGGTAACAGAAAAAACTCGAACCAGA I F Q V T T A V L V L L Y G Q D T P H G N R K N S N Q N 707 ACAAACTCACAATTCCTGAAGAAGAAGAAGTACTAGTAGTTGAAGAAGACGAACGTTCCAGTTTCGTCGAGATCCTAATCGG K L T I P E E E E V L V V E E D E R S S F V E I L I G 789 CGGACTTGGAAATTACAGAGCGTGGATCTTAGCGCTGCTCTACGGATACTCGTACGGCGTCGAGCTAACGACGGACAACGTG G L G N Y R A W I L A L L Y G Y S Y G V E L T T D N V 871 ATCGCCGGATATTTCTACGAGAGATTTGGAGTGAATCTGGAGGCGGCGGGGACGATCGCGGCGAGTTTCGGGATATCGAACA I A G Y F Y E R F G V N L E A A G T I A A S F G I S N I 953 TTGCGTCGCGACCGGCGGGAGGGATGATATCGGATGCGCTGGGGAAGAGATTCGGTATGAGAGGGAGGCTGTGGGGGCTATG A S R P A G G M I S D A L G K R F G M R G R L W G L W 1035 GATCGTGCAATCGGTGGCTGGGTTGTTGTGCGTGTTACTCGGACGAGTCAACTCGCTCTGGGGATCAATCCTCGTCATGTGG I V Q S V A G L L C V L L G R V N S L W G S I L V M W 1117 GTCTTCTCTGTTTTCGTTCAAGCTGCTTCTGGCCTTGTATTTGGCGTGGTCCCTTTCGTCTCCACGCGgCtagtttaaagtC V F S V F V Q A A S G L V F G V V P F V S T R 1199 taccaatccggtttttgctaataatttcggtttggttttaatttggttttgtttataatgacagATCGTTAGGAGTGGTGGC intron S L G V V A 1281 GGGAATTACGGGAAGCGGCGGTACGGTTGGTGCGGTGGTGACGCAGTTTCTGTTGTTTTCCGGTGATGATGTTCGAAAACAG G I T G S G G T V G A V V T Q F L L F S G D D V R K Q 1363 AGAAGCATTTCACTTATGGGTTTGATGACTTTTGTGTTTGCTCTTTCTGTTACATCAATTTACTTTCCACAATGGGGTGGAA R S I S L M G L M T F V F A L S V T S I Y F P Q W G G M 1445 TGTGTTGTGGGCCTTCGTCATCTTCCGAAGAAGAAGATATTTCTCGGGGACTCCTTGTAGAAGACGAAGATGAAGAAGGTAA C C G P S S S S E E E D I S R G L L V E D E D E E G K 1527 AGTGGTTAGTGGTAGTCTACGTCCCGTTTGTTGAGTTAGTTTAAAGTCTACCAATCCGGTTTTTGCTAATAATTTCGGTTTG V V S G S L R P V C * 1609 GTTTTAATTTGGTTTTGTTTATAATGACAGATCGTTAGGAGTGGTGGCGGGAATTACGGGAAGCGGCGGTACGGTTGGTGCG 1691 GTGGTGACGCAGTTTCTGTTGTTTTCCGGTGATGATGTTCGAAAAC AGAGAAGCATTTCACTTATGGGTTTGATGACTTTTG 1773 TGTTTGCTCTTTCTGTTACATCAATTTACTTTCCACAATGGGGTGGAATGTGTTGTGGGCCTTCGTCATCTTCCGAAGAAGA 1855 AGATATTTCTCGGGGACTCCTTGTAGAAGACGAAGATGAAGAAGGTAAAGTGGTTAGTGGTAGTCTACGTCCCGTTTGTTGA 1937 TGTCGCATTTGAACTGCTGGCCCA  7 44 2 99 126 154 181 208 236 263 290 318 345 372 3 95 401 428 456 483 493  Figure 2-6. DNA and deduced amino acid sequences of the AtNRT2.5 gene. The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined. 19  142 6 TTTCATATCTTATGGTATTATTGGGTAATTGAAAGCAAAAAAAAAAAAATGAATTTTTGAATAAAGTTGATACAACTATTTC 1344 CAAAAGTAAAATTAATTTGATGAGTCGACCACATGGAATACACAAAAGACAAACTGCAATTATTTTTAGAAGAATGAGCTTT 1262 TTACAATGAACCGTACGATCTCATAGTCTCATTGACCTTTGGTTGATGTCAAATGTCAAACATTTGTCTCTCCATAAAGATA -118 0 TTCTTGTACTTAGATGACTCTATAACAAAAAAATAAAAAGAATAAGAAGATATTCTCGTAAATTAACAATATTTATATATAA -10 9 8 TGTATAAGTATAACCATTAAACAAAAAGATCAACAATATTTTCAAAATATTATAGTAAGCTGGAAACATCAATGCATTAGGT -1016 AAGACACATGCATGTTGTACATTAGCTACGGATGCGCAAAATGGACGCTAAGCCGGCGGTGAAAGAGACACGTTGTTCTTCT - 9 3 4 GCATTTTATTCCATTCGTACGTAATAGTTAATTCTATAAAGTTATATAATGTTTCGACTTGATAGAGATATGGTACAAGTAG - 8 5 2 ICAATGAAACGTATTTTCTAATTAAGTTAAGTTATAAACATTTTAATAGTAAATGGAGCACGTAATTTGCATTATGCAAAAA - 7 7 0 CACACATATGCTTAGTTCTAATAGGATATTCTCTTTTCCGAATGAACTATTTTTGGAGCGGTGGACTTTTTTTTTTTATTAA - 6 8 8 CCGATATTAATTAGATAAAATTTAGGAGAGCCATTCATAATAATGTTATTTATATATGTTATATGATGCAGTTCGGTATAGA - 6 0 6 TTTTTCGTGTCAAATTGTCCGTTTTGATATTTGCACTACGAAAGATTAAAGATAAAGAAAAGCTAGTGAACTTTCTCTTATC - 52 4 GTTTCGTAATTTTTCTTCTGATCATTCGGTTATACGTGAACTTTCTCTTATCCTTCGTAATTTTTCTTCTGATAATTCGGTT - 3 6 0 TGCTATTGAAAACGTTTGCAAAAACCTACAAAGAGACTACATCTAAAATGTACAAGAGACTTTACATATTGATTGTTTTCTA - 2 7 8 CCAATAAATTTCGTAATACTATTTCACCAAAAAAAAAATTAAAACAAAAAGCCATCGCTCATTTCATTTCACGTAGTATTAT -19 6 TCAACTCTTATTATTGGATCCACCTAACCGTACCCACCAAAAATCTCTATAAATACTATGCAACTCATCTTCTCCAACTTAC -114 ACCAAAAACAGAAAACAACAAAGGCCACAAAGAAGAAGAAAACCTTCTTCAACGTTTAAAGTCTCTTCTCTCTCTCTCTCTT - 3 2 AACTTCTCCCATTTTCTTTGAACTAAAGATCAATGGCTCACAACCATTCTAATGAAGACGGCTCTATTGGAACCTCCTTGCA M A H N H S N E D G S I G T S L H 51 TGGAGTCACGGCAAGGGAGC AAGTCTTCTCCTTCTCCGTCCAAGAAGATGTCCCTTCATCTCAAGCCGTCCGAACAAACGAT G V T A R E Q V F S F S V Q E D V P S S Q A V R T N D 133 CCAACGGCTAAGTTTGCCCTACCAGTGGACTCCGAACATAGGGCAAAAGTGTTCAAACCACTATCATTCGCTAAACCACATA P T A K F A L P V D S E H R A K V F K P L S F A K P H M 7 215 TGAGAGCCTTCCACTTAGGATGGATCTCTTTCTTCACTTGCTTCATCTCCACCTTCGCAGCCGCACCTCTAGTCCCCGTCAT R A F H L G W I S F F T C F I S T F A A A P L V P V I 297 TCGCGACAATCTCGACCTGACCAAAACCGACATCGGAAATGCTGGAGTTGCATCAGTTTCCGGCGCCATTTTCTCGAGACTC R D N L D L T K T D I G N A G V A S V S G A I F S R L 379 GCTATGGGTGCTGTATGTGACCTTCTAGGGGCACGTTATGGAACCGCCTTCTCACTTATGCTTACAGCTCCAGCAGTTTTCT A M G A V C D L L G A R Y G T A F S L M L T A P A V F S 461 CCATGTCGTTCGTAGCTGACGCGGGAAGCTACTTAGCCGTAAGGTTCATGATCGGTTTTTGCTTAGCAACGTTCGTATCATG M S F V A D A G S Y L A V R F M I G F C L A T F V S C 543 TCAGTACTGGACGAGTGTTATGTTCACTGGAAAGATTATCGGACTCGTTAACGGATGTGCTGGAGGGTGGGGAGATATGGGA Q Y W T S V M F T G K I I G L V N G C A G G W G D M G 625 GGAGGAGTGACTCAGCTACTAATGCCAATGGTCTTCCACGTCATCAAACTCACCGGAGCCACTCCCTTCACGGCTTGGAGGT G G V T Q L L M P M V F H V I K L T G A T P F T A W R F 707 TCGCCTTCTTCATCCCCGGCATTCTTCAGATAGTTATGGGTATTCTCGTTCTCACTCTCGGCCAAGATCTTCCCGATGGTAA A F F I P G I L Q I V M G I L V L T L G Q D L P D G N 789 CCTCAGTACTCTCCAAAAGAGTGGTCAAGTTTCTAAAGACAAATTCTCCAAGgtaatatatt'aaacatgatcaatattttta L S T L Q K S G Q V S K D K F S K 871 ggacaatactagcaataatgcatgtggttctaattacaattttgttttgtttaatagGTCTTTTGGTTCGCTGTGAAAAACT intron V F W F A V K N Y 953 ATAGAACATGGATCTTATTCATGCTCTATGGATTTTCTATGGGAGTTGAATTAACGATCAACAACGTTATATCTGGATACTT R T W I L F M L Y G F S M G V E L T I N N V I S G Y F 1035 CTACGATAGGTTTAACCTTACGCTTCACACAGCTGGTATTATAGCAGCCAGCTTTGGTATGGCAAACTTCTTTGCCCGTCCT Y D R F N L T L H T A G I I A A S F G M A N F F A R P 1117 TTTGGTGGCTACGCTTCAGATGTAGCTGCACGGCTCTTCGGTATGAGGGGACGGTTATGGATCTTGTGGATCTTACAAACTG F G G Y A S D V A A R L F G M R G R L W I L W I L Q T V 1199 TTGGAGCTCTCTTTTGCATCTGGCTTGGTCGTGCTAGTTCACTACCTATAGCTATCTTAGCCATGATGCTTTTTTCCATGGG G A L F C I W L G R A S S L P I A I L A M M L F S M G 1281 CACACAAGCTGCTTGTGGAGCTCTCTTTGGTGTTGCTCCTTTTGTTTCCCGCCGTTCTCTTGGACTTATCTCGGGATTAACT T Q A A C G A L F G V A P F V S R R S L G L I S G L T 1363 GGTGCTGGTGGAAATTTTGGGTCGGGAGTTACTCAACTTCTTTTCTTCTCTTCCTCGAGGTTTAGTACGGCGGAAGGACTAT G A G G N F G S G V T Q L L F F S S S R F S T A E G L S 1445 CGTTGATGGGCGTTATGGCTGTTGTGTGCTCTCTTCCGGTTGCGTTTATACATTTTCCGCAGTGGGGAAGCATGTTCTTGAG L M G V M A V V C S L P V A F I H F P Q W G S M F L ' R 1527 GCCATCACAAGATGGAGAGAAATCAAAGGAAGAGCATTACTATGGAGCGGAATGGACAGAGGAAGAGAAGAGCTTAGGACTA P S Q D G E K S K E E H Y Y G A E W T E E E K S L G L 1609 CACGAAGGAAGCATTAAATTTGCTGAAAACAGCCGGTCAGAGAGAGGCCGCAAGGCGATGTTGGCTGATATTCCAACGCCGG H E G S I K F A E N S R S E R G R K A M L A D I P T P E 1691 AAACCGGATCTCCGGCTCATGTCTAGTGAAGGATAGTCAC ATTACATCTTTTTCCACATATAAATAACCCTC AAACTTAGCT T G S P A H V * 1773 TTATGTTTGCATGTTTTATGTTCCTCTTATGAGAGATGTACCGAGTAAGATCCTGACTTGATAAGTGAGGTTCAGTGAGCTC 1855 GGTGCTCATGATGTACAATGTCGTTTGATATAAGACTTATGCATCAGTTTTCTCTCTGTTTTATCAACAAGCCGTGTCTTTA 1937 AAAGTCTTCCAAGATCATATTATTGATTTAACAAAATCGATCAAATACTGAAAATGAGAAGAGTGTTTTGAGGCACAACTAG 2 019 TCATACCTTAAGAAGAAGCAATTGACTTTAGTAATCTTTACGTCTCAGAAACAGATCACATTAAAGAATCTGGAAAGAGTAA 2101 GAAGCAACTTAACTAG  17 44 2 99 126 154 181 208 236 263 280 289 316 343 371 398 425 453 480 507 535 542  Figure 2-7. D N A and deduced amino acid sequences of the AtNRT2.6 gene. The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined. 20  -14 2 6 ACATATATATATATATATATATATATATGTAAAGCATATTAATTGATATGTAAATAACTATTATAAGATTTTAAGAGTAAAT -13 4 4 AAATAGTATGCCAAAACAATAATTTGAATACTTATACTACTATTTTGAGTTTTTGATTTTCAATTAAACATTCAATGACAAA -12 6 2 AAC AAAAAGGGAACT AATTGAATTATTGCATCTTATGC AT AT ACTATATTTCATAGATCCAACATTAAAATAAACTAACTGT -118 0 TATTTTAGACCATTGTTTTCTTTAAAATAATTGTTGCTTTTTGCCCACAGAAATTAATAATGTXjTTGTTTTAGGATTTTAGT -1098 GTAAATTCTGATAAATAATGTCTAAACTTTCTCTATATAAATTAATGAAAATATGAAATAAATTTTTTCTTCTTAATTCGCT -1016 TGAAAATAAAAAAAAATGACATGAATATGGAAAACATCATTGTGAATTTTTTTGTTAGTTAGTCAGTTAAAGTAAAGATTAT - 9 3 4 GGAAGTTTTGTTTTGGTAAACTTACAAAAACAAATATTAATTGTAACAAAAATTGATTTCAAACTCTCTCTCTTTCTCATTT - 85 2 ATATAACTTTATTTTTCACAAATCACAATGCACAACTCAAAAAAATTAGAATGTTTAAAGTAGATAATGCAAACAAAAAACT - 77 0 CTCAAATCGATTTGATATTAATTAAATGAATCTCTTGATCTTCAAATTGAGTTACAATCTAACCTTTTCTATTTAGATAAAA -688 TGTGAAAATTTATTTTAGAACTTATACTGAACACAGAGACGTAACGAAGAGAAACAGAAAACTAAAAAATATGTTGTAAATA - 6 0 6 CGACAAAAGACTATAAAAGTTAATGACATTCACGAAATTTACACGTTCTAATGGTCGATGACACAAGGAAACTTTCAATGTT - 5 2 4 GCCACAAGTGAATTGAGATCTCAAGTCAGCCTCCAATACTTCTGAAAGAGCGGTGCTAACCCTCTTAATACAAAATTTATAT - 4 4 2 ATCTAAACAAAACACCGTACTAAACCAAACAATCTTAGATTCAATCGCGGTGCTTACAATCTAACTTAGTTATAACAAAATT - 3 6 0 TATATATCTAAACGAAAACTAAACACC ACATTAAACTCAACCATCTTAGATTCAATCAAAACCAAGATTTAATATATTTTAT - 2 7 8 TTTTCATCTAGAAAGAAAAACCAGAAAACCTTTATGTAATGATTCAAGTTTTTTTTTATACCATCACACTAAAAATAAAAAG -19 6 ATAGCATTCAAAATCCAAAAATAAATAAATATTAAAATGATTACATCAACGCTTCACAAGAACATAAATCCATGAAAATGTC -114  -32 51 133 215 297 379 461 543 625 707 789 871 953 1035 1117 1199 1281 1363 1445 1527 1609 1691 1773 1855 1937 2019 2101 2183 2265 2347  ACAGCTTTAACACTCTCCTTCTCTATAAATACTCATAACCTCAAACCTGAGATTCCTCATTCCTTAAACCCCTAAACCTCCA  AAATTCTCTGAACCTTCACAAAGATCACAAAAATGGAGGTCGAAGGCAAAGGAGGAGAAGCTGGAACCACCACCACAACCGC M E V E G K G G E A G T T T T T A 17 ACCTCGGAGGTTCGCACTTCCGGTGGACGCGGAGAACAAAGCAACAACTTTCCGACTATTCTCAGTCGCTAAACCTCACATG P. R R F A L ' P V D A E N K A T T F R L F S V A K P H M 44 AGAGCTTTCCATCTCTCATGGTTTCAATTCTTTTGCTGCTTCGTCTCCACTTTCGCAGCTCCGCCTCTCCTCCCTGTTATCC R A F H L S W F Q F F C C F V S T F A A P P L L P V I R 7 2 GTGAAAATCTTAACCTCACCGCCACCGACATCGGAAACGCCGGAATAGCCTCTGTCTCCGGCGCTGTTTTCGCTCGTATCGT E N L N L T A T D I G N A G I A S V S G A V F A R I V 99 CATGGGCACGGCATGTGATCTTTTCGGTCCACGTCTAGCCTCCGCCGCTTTGACGCTCTCCACCGCTCCCGCCGTCTATTTC M G T A C D L F G P R L A S A A L T L S T A P A V Y F 126 ACCGCCGGGATAAAGTCTCCGATCGGGTTTATCATGGTGAGATTCTTCGCCGGATTCTCTCTCGCCACTTTCGTCTCGACTC T A G I K S P I G F I M V R F F A G F S L A T F V S T Q 15.4 AGTTCTGGATGAGCTCCATGTTCTCTGGACCCGTCGTGGGTTCGGCTAACGGAATCGCCGCCGGGTGGGGTAACCTCGGAGG F W M S S M F S G P V V G S A N G I A A G W G N L G G 181 AGGCGCGACGCAGCTGATCATGCCCATCGTGTTCTCGTTGATTCGTAATATGGGAGCCACCAAGTTCACCGCGTGGAGGATC G A T Q L I M P I V F S L I R N M G A T K F T A W R I 208 GCTTTTTTCATCCCCGGTCTCTTTCAGACTCTCTCTGCTTTCGCCGTTCTCTTGTTCGGTCAGgtaacaaaccaatcacact A F F I P G L F Q T L S A F A V L L F G Q 229 caccggttcagttattttggttttttcaactaatccggttttgagaatttatcaccaagttattttttgttttggttaaatt tactttctttgtatagtcagtttatcctgttctatataaatgattaaaccgattcgtttaggtgcaaacccggtttattgat intron I accggtttgggtcgtctagtagagtctttagtcggttaatcatggtcgagtttcagtggatatggacaataactgtttaatc atctaagttgtgtctattacaaggaatagtaaaaggatacatttgttttgtcttatgtttgctatatgtttttggaaatgag tagGATCTTCCTGATGGAGATTATTGGGCGATGCATAAATCTGGAGAGAGGGAGAAAGATGATGTGGGGAAAGTGATATCTA D L P D G D Y W A M H K S G E R E K D D V G K V I S N 256 ATGGAATCAAAAACTATAGGGGATGGATAACAGCATTAGCATATGGCTATTGTTTTGGAGTAGAGCTTACCATTGACAACAT G I K N Y R G W I T A L A Y G Y C F G V E L T I D N I 283 CATCGCAGAATATTTCTTCGATAGATTCCATTTAAAGCTCCAGACAGCAGGGATTATAGCAGCGAGTTTTGGACTAGCCAAT I A E Y F F D R F H L K L Q T A G I I A A S F G L A N 310 TTTTTCGCTAGACCTGGAGGAGGAATTTTCTCTGATTTTATGTCGAGACGGTTTGGGATGAGAGGAAGGTTGTGGGCTTGGT F F A R P G G G I F S D F . M S R R F G M R G R L W A W W 338 GGATTGTGCAAACATCAGGAGGTGTATTATGCGCATGTCTTGGCCAGATTTCTTCCTTGACAGTGTCTATAATTGTTATGCT I V Q T S G G V L C A C L G Q I S S L T V S I I V M L 365 TGTCTTCTCTGTATTCGTCCAAGCCGCTTGTGGACTTACCTTTGGCGTTGTTCCCTTTATTTCTAGAAGgtaacatacattt V F S V F V Q A A C G L T F G V V P F I S R R 388 tggtattgagttgcttgattggttattcaacatttttgcttacaaaagtttgtttatgcagATCTCTTGGGGTGGTATCGGG intronll S h G V V S G 395 AATGACTGGTGCGGGAGGCAATGTAGGCGCGGTCTTAACACAGTTGATATTCTTCAAAGGATCGACATACACGAGAGAGACG M T G A G G N V G A V L T Q L I F F K G S T Y T R E T 422 GGTATAACTCTAATGGGGGTAATGTCAATCGCATGTTCATTACCAATATGCTTGATTTACTTTCCGCAATGGGGAGGTATGT G I T L M G V M S I A C S L P I C L I Y F P Q W G G M F 450 TTTGTGGACCCTCTTCCAAAAAAGTAACTGAAGAAGACTATTATCTCGCCGAATGGAACGATGAAGAGAAAGAAAAGAACTT C G P S S K K V T E E D Y Y L A E W N D E E K E K N L 477 ACATATCGGAAGCCAAAAATTTGCGGAAACCAGCATTAGCGAAAGAGGTCGAGCCACAACGACTCATCCCCAAACTTGAAAT H I G S Q K F A E T S I S E R G R A T T T H P Q T * 502 ATATAAATTCCAAAAGGTTGATATCACCGTTTCCAAAAAATAAACAAGCAAAAAGACAGATTTACGTGATAATACTTCATAA TAGGATGCGAGATGTTAGTTTCAAAGTTATAGATCAAATCAGTGAAATGAGATTTTGGTAAGTGTGTTATATAGTTCTTAAA AATCTGGAATCCCGTATCATCTTTTCTTATATAGTTCTTACATCTTAACATATATATTTGTTATTTCTATATTGGTGGTTTT ATATTTGCTTGAGTTCATAAACTTCTTGATAAGATTCATAAACCGTCTTTGAAAACAAACCATCAAAATGGTCCCTCTTCTT GTTTCTTTGAAAAGATCATTTCATACAAGCGATATAGACAAAGCATTTAAGAAACAACAAGTTGAGAAGTTTTGTAACACGT ACGTTGTTGTAACAAAAAAAAAAAAAAAAAAGAGTAAAGACTTTGCCAAAGTTTTCGAAGACTTTACCTTTGCCATGGTTAA  Figure 2-8. DNA and deduced amino acid sequences of the AtNRT2.7 gene. The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. GATA boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined. 21  accepted that the MFS has 12 TMS and a cytoplasmic N-terminus, predicted T M S numbers varied from 9 to 12 (Table 2-2). The average numbers settled between 11 and 12. AtNRT2.1, 2.2 and 2.4 are highly homologous at the protein level, sharing 89% and 82% identity between AtNRT2.1 and 2.2, or 2.1 and 2.4, respectively (Table 1). AtNRT2.3 and 2.6 proteins also show high homology, with values of 89% identity and 93% similarity between the two. The middle regions of the proteins have even higher degrees of similarities, whereas N - and C-termini, which mostly consist of hydrophilic residues, share less homology within the family (Figure 2-9). In TMS5 all AtNRT2 family members have a sequence, [AG]-G-W-[GA]-[ND]-x-G, which is highly related to a signature motif found in the NNP family (Pao et al., 1998;Trueman et al., 1996). Another conserved sequence, R[PA]-x-G-G-x-x-[SA]-D, was identified between TMS8 and TMS9. This is not only found within plant members of the NRT2 family but it is also well conserved in all known NNP family members including NrtA (formerly called crnA) in Aspergillus nidulans (Unkles et al., 1991), YNT1 in Hansenula polymorpha  (Perez et al., 1997), and narK from E.coli  (Rowe et al., 1994). Half of this sequence (G-x-x-[SA]-D) is closely related to a part of the M S F specific sequence motif, G-[RKPATY]-L-[GAS]-[DN]-[RK]-[FY]-G-R-[RK]-[RKP][LIVGST]-[LIM], which is located between TMS2 and TMS3 (Pao et al., 1998). It is notable that the longest conserved sequence, F-G-M-R-G-R-L-W, was found at the beginning of TMS9 in all AtNRT2 members (Figure 2-9). This sequence is also well conserved in other photosynthetic species including Chlamydomonas Chlorella sorokiniana  reinhardtii,  and  (data not shown), suggesting that the sequence could be applied to  clone the homologues from other species. AtNRT2.5 protein, the least homologous among the seven AtNRT2 members, has the longest hydrophilic loop predicted between TMS6 and  22  \  Table 2-2 Prediction of membrane topology of the NRT members by seven methods  Protein  AtNRT2.1 AtNRT2.2 AtNRT2.3 AtNRT2.4 AtNRT2.5 AtNRT2.6 AtNRT2.7 AtNRTl. 1 AtNRTl .2 AtNRTl.3 AtNRTl .4  HMMTOP  12 out 10 out 12 in 12 in 12 in 12 in 12 out 12 in 12 in 12 in 12 in  MEMSTAT  SOSUI  TMAP  12 out 12 out 11 out 12 out 12 out 11 out 11 out 11 out 9 out 10 out 11 out  8 n/a 8 n/a 10 n/a 9 n/a 10 n/a 11 n/a 8 n/a 12 n/a 13 n/a 12 n/a 12 n/a  10 n/a 10 n/a 10 n/a 10 n/a 10 n/a 10 n/a 10 n/a 12 n/a 12 n/a 12 n/a 12 n/a  TMHMM  TMpred*  11 in 11 in 11 in 12 in 10 in 11 in 11 out 11 out 12 in 11 out 12 in  12 out 12 out 11 in 12 in 12 out 12 out 11 in 12 in 12 in 12 out 12 out  Toppred  12 in 12 in 12 in 12 in 12 in 12 in 12 in 12 in 12 in 12 in 12 in  Predicted number of transmembrane helixes and the location of N-terminus (in=cytoplasmic, out=exoplasmic). * With minimum length of 17, maximum length of 29, other programs were used with default setting.  23  H  Ul  o  iH  H  CD H  rH  i—l  o\ o  Cl  CO  o iH co rH  ^ H (N  (N H O  "I H M  1  H f OJ O) N M  VO H Ul Cfi rl H  <J H  (N rH  H  rl  1<  OJ  (N  m m cn cn m  IO CTl OJ  n O  cn  r-  LO  r~- r- o~t  UJ  (N  (N  IN  r-1  fl  fl  O'  o CM c^ cn C N oj m n CN CN -a* o cn m in cn L O in in fl  ft ft ft ft ft ft ft >ca> > >KI>  j jjjjj ft ft  OJ  CM  CU  ft  c+-t <N  H E a a i n co l H i B. I  I 0.  O o o  o  [fl  I  CQ O  <+H  o •*-> S3  OC3 w < ft O n i a i Q > u w I I I I Q E. 2 i  i  i  i  ww OS  • i-H  u o a CD c/l O o c  '§ <: ON I  H  n * n w > ui  OJ OJ OJ CN OJ CNJ CN H fn H H H H H Oi CU Cr! B! Bi Oi Oi  S3 2 2 2 2 2  2  U  i J JJ OJ 4J JJ 4J < < < < < < <  OJ OJ OJ OJ OJ OJ OJ Ir" EH H H H H H  CN CN OJ CN OJ OJ OJ H H H H H H E-> Bi 01 Oi  .. .. 2.. g  4J J J <  JJ  2  -U JJ <  < < 2<  2  4J  <  4J 4J 4J 4J 4J 4J 4J < < < < < < <  OJ OJ OJ OJ OJ OJ OJ EH H E-! H E-; H , Bi Bi  E-i  2  2  4J U 4J 4J OJ J J U < < a: < < < <  W VH  3) 24  CD  •  CO CD  CD  53  IS CN +u  s, indi ed v hreon ine,/serine:  n  a a U  +^  o  CD  '3 H fl o O  CD  O  .g  cn O i-i  o 'So o  CO  Cl O CJO CD )H CD O Id  , and .expa :rved quei  5  PH  <u  >> CO  CD CO  cd  c,  CD -4-* 'm-t I CCS CD  a o CD CD  CD CD  ~0 CD  1 O  CD  as i CN  CD lH  25  TMS7 (Figure 2-9). This long loop is more evident in NrtA (Unkles et al., 1991), and YNT1 (Perez etal., 1997). Some protein kinase C (PKC) phosphorylation sites (motif: [ST]-x-[RK]), and casein kinase 2 (CK2) phosphorylation sites (motif: [ST]-x-x-[DE]), were found in the cytosolic domains (Figure 2-9). The P K C sites before TMS11 and at the N - and C-termini were well conserved, whereas most of the C K 2 sites were restricted to both termini with less conservation. It is intriguing that the conserved threonine residue in the N-terminus (i.e., Thr-16 in AtNRT2.1) is a phosphorylation site of both P K C and CK2. N-glycosylation sites, where the consensus pattern is (N-{P}-[ST]-{P}), were found among TMS1 and TMS2 in five of the proteins (Figure 2-9). Neither PSORT (Nakai and Kanehisa, 1992) nor SignalP (Nielsen et al., 1999) were able to find N-terminal signal sequences within the AtNRT2 members.  Gene Structure of the A t N R T l Family  The gene structures of AtNRTl. 1(CHL1) and 1.2(NTL1) had been characterized previously (Tsay et al., 1993; Huang et al., 1999), and a brief characterization of AtNRTl. 3 (NTP3) and 1.4(NTP2) was also reported earlier (Hatzfeld and Saito, 1999). Briefly, AtNRTl.l are located on chromosome 1, whereas AtNRTl.3  and 1.2  and 1.4 are on chromosome 3 and 2,  respectively (Figure 2-1). The AtNRTl.l  gene possesses four introns in which the first three are 94 to 185 bp  in length, whereas the fourth is 1650 bp (Figure 2-10). The nitrate-dependent transcription motif was found, at 237 and 246 bp upstream from the start codon. The promoter region  26  -17 5 4 -16 7 2 -15 9 0 -15 0 8 -14 2 6 -13 4 4 -12 6 2 -118 0 -10 9 8 -1016 - 934 - 852 - 77 0 - 68 8 - 606 - 524 - 442 - 360  GGGACTCTTCATTGTGACTTTTTTGTTCTCGCTCTTCCACAATCTTTGGATGTGTACAAAATAATCGATTGTTGGGGATATT ATAGTAAATTTAGCAATATGAAACTAGCAACGAAGAAAGTGTTTATTGATGGGTTCAAAATTTCATCGATCTGCATATCAAT AACTCGGAAAGAGATGGATCATGACACATAGTATACAATAAATTTTATAAATTTCGAAAATTAACTAATTGAGGATAGAAAT TCATCAATTACTTAATAAATAAATAAAAAACTGATTCAAATGTATGTTTTACTTCTGTAACATACAATTTCTTGCTTTTCTT GAAAATTGACTCGTTTTTTATATTGGATATTTTACATAGACTTTGAGACTTATTAATAAAACTAACTAACCATCTCTTACAA ATTGTTGGAATAAATTATTTTTATTTTTCTGTTGGCTCTATAAAATGAAAATGACCTTTGTTCTTCTTCTTTATACTCCTAT ATATGTTTTCTCCAGAGAGAAAGAGAACCATTGAAGTTGCGAGACTTCCAATTATATATATAGTTCATGAAAGTCCTGTGAC CATGCTCTTTATTTATTTTATTTCACTATACGTTAAATAAATGGAAAGTAGGGTAATAATCATATTGCAGCATGATTCATTT TAGTGGCGTCTAAGAAGCATTCATTTTGAGCCATTAAATCTCAAGGTAGACTTTCCCATTAACACAAAAGAAGAAAAAATTG GTACGTAATCATACCAACATCTACAAATCTTTGGTTTCAATTTTGTAACAAAGACCTAGATTGTTGACAAACAAAAAGCAAA TACCTAAAAGGACTTTTATTGACTTCTATAAAGATGTTTTGATTGAAATTTCATATAATTTAATAGTTTCCTCAAACTATAT GCAATAAAATTATAATTTGATAATTACATGTGAAAGAAAACATGACTCTCAAATTAATATGAGTCGATTATCAATAAATTTT TGTGATATGGCTGTGCTGCAGAACAACTGAATGGGCCTAGAAGTAAAGTTGATATTGAGCAAACAAAAAACGAAATAGATTT TTTTTTTCTTTTGGGCAAACTCAAAAAACGAAATAGATATGCCTCGACAATACTACAAAATCTCAAATGAACAATATTGATG AAAATGCGTTTGTAACACAGAAATCAATTATTTTGAATTATTTTCCATATATAGTACAGACGTAAAAAACATACTGTATTAT CTTTCATGGAAGTAAAATAATTTTCCAAGAAATAGAACAAATGTAAAACAGGTGGTGGCTAAAACTGGTGCTTTTAATGGCT AATGCCATTGAATCACTGACAAAATGACCGATGACTTCAACTTAAAAGTTCAAGCCCACAGTTCCAAAGGTAGAGGAAGTGG TAAAATTTAGGTATGGTCTCTTTCTCTCTCTCTCAATTTTCTCTTTCTACAAATATATACTACAGTTACAGTAGTAGTTATT  -19 6  ATGAATAAAAAATCAAAATAAAACAATAAAAACTTTTTTAACTTGGCTAGTTTCCCAGTATAAATAGATGTATCAACGAACA  -114 - 32  1363 1445 1527 1609 1691 1773 1855 1937 2019 2101 2183  CATTTAAGACCACAAAAGAAACCAAGAGCTCTCAAACAAAACAGCCTTTTACATAAGAACAAACACCCCCAAAAACTGCAAA AAAAAGAGAGAGATCATTAATCCATCTTCAAGATGTCTCTTCCTGAAACTAAATCTGATGATATCCTTCTTGATGCTTGGGA M S L P E T K S D D I L L D A W D CTTCCAAGGCCGTCCCGCCGATCGCTCAAAAACCGGCGGCTGGGCCAGCGCCGCCATGATTCTTTgtaagtataatcacata F Q G R P A D R S K T G G W A S A A M I L C ataaaagttctagagaaaagctaccaacaatatacatgctgaagacaagaattgaaactttttaatggcatttactaagtta intron I taagtttcttatggctatcattcttattcttttatgtattctcgatgtatccaactttatcattaacaaaattttattgtgt gaagGTATTGAGGCCGTGGAGAGGCTGACGACGTTAGGTATCGGAGTTAATCTGGTGACGTATTTGACGGGAACTATGCATT I E A V E R L T T L G I G V N L V T Y L T G T M H L 6 TAGGCAATGCAACTGCGGCTAACACCGTTACCAATTTCCTCGGAACTTCTTTCATGCTCTGTCTCCTCGGTGGCTTCATCGC G N A T A A N T V T N F L G T S F M L C L L G G F I A CGATACCTTTCTCGGCAGgtttgtctataaatatatttatatttacttaactaaaatcattcagattctttttaaaatatta D T F L G R i n t r o n II atttgagttcattcattttgttttgtatagGTACCTAACGATTGCTATATTCGCCGCAATCCAAGCCACGgtaaggacctca Y L T I A I F A A I Q A T aaagtccctttctccttaccaaaacttatacccaagaaaacgaagaaaataaaaatattgtctagtcaataaacaaatcgaa atagtaaacagcataagtcgttatttttgttatagttttccgaaaaataatatccgtgttatgaactatgatgctatcagGG intron III G TGTTTCAATCTTAACTCTATCAACAATCATACCGGGACTTCGACCACCAAGATGCAATCCAACAACGTCGTCTCACTGCGAA V S I L T L S T ' I I P G L R P P R C N P T T S S H C E CAAGC AAGTGGAATACAACTGACGGTCCTATACTTAGCCTTATACCTCACCGCTCTAGGAACGGGAGGCGTGAAGGCTAGTG Q A S G I Q L T V L Y L A L Y L T A L G T G G V K A S V TCTCGGGTTTCGGGTCGGACCAATTCGATGAGACCGAACCAAAAGAACGATCGAAAATGACATATTTCTTCAACCGTTTCTT S G F G S D Q F D E T E P K E R S K M T Y F F N . R F F CTTTTGTATCAACGTTGGCTCTCTTTTAGCTGTGACGGTCCTTGTCTACGTACAAGACGATGTTGGACGCAAATGGGGCTAT F C I N V G S L L A V T V L V Y V Q D D V G R K W G Y GGAATTTGCGCGTTTGCGATCGTGCTTGCACTCAGCGTTTTCTTGGCCGGAACAAACCGCTACCGTTTCAAGAAGTTGATCG G I C A F A I V L A L S V F L A G T N R Y R F K K L I G GTAGCCCGATGACGCAGGTTGCTGCGGTTATCGTGGCGGCGTGGAGGAATAGGAAGCTCGAGCTGCCGGCAGATCCGTCCTA S P M T Q V A A V I V A A W R N R K L E L P A D P S Y TCTCTACGATGTGGATGATATTATTGCGGCGGAAGGTTCGATGAAGGGTAAAC AAAAGCTGCCACACACTGAACAATTCCGg L Y D V D D I I A A E G S M K G K Q K L P H T E Q F R tacgattcttttaattaactcatcatttgctttccacgtacgatcctcaaaacttacaatgatttaaattttaagataaaag ttttaaaatttttctttttcttttccatttaagggttaattgaaataattgaggtactggttcccttaattaaatgtgatag tatcagtagactttaaaaatgtgaaattaaaagtggggttgtgtgggtgagaaataactcgaaatgctcgtgtcctttaatt atagtgggaccgtaaatatttctcattatatgcctacttggcattagaaatcatttttttttgacagccattataaattaat taaaaggtgttgaatatctttctttgtcttttgttacggggaaaataaattattttcataatattattactcgaccatacag cgaaactggtccaggatacgaattatacagctaattacaacatttttggatttttgggttcaaagtccctactttggcattt tatattgtatattttttccttaaaatcctatgtgtgtgtgcatgtgtatatctttgttagataacacgttaagttcggttca tagaataggtaggaaaataaaagtagtctctcggaattagtcggaaagataaagtaattcagataaacaaatgaataagtat atgcaagtgatatcaagtggggtaaaattctccatctttactttttgcctataaaaaatttcacacccactcgtagaatatt tggtttttacagaaagagtatcttcatcattgcggaaaattaaatacaccaatttgctattttatctttattatagtattat aattatgattatgattctaatgccttataactttaaatacacatacactgacacacatatatctatatttatattcccctga  2265 2347 242 9 2511 2593  i n t r o n IV ctcgtgagttttccccctttaagtacggtatcttttatttttgctaacttaagtacagtatcttttatccatcaatccctat gcatacctacatagaaataaaagaatccaaaggaatcaatttttctttataccagataatttatggaaaatctatttagcat ctctagatattggaatccctttctcggaaataaaactaataaagaagaagagacgagaagttagggtagggaggcaggtgtt ttgtctgtagtgaaaacgatcaaatatcgtgtcgtagcacctccactactttacaccttcaccgggacagacccaaagttag gcataattaagaaccctagcgtcacatgcacgacacgtgctttgcgtgctcggtgctteattaaatttctctttcgtttggg  51 133 215 297 37 9 461 543 625 707 789 871 953 1035 1117 1199 1281  17 39  5 92 98 111  112 139 167 194 221 249 276 303  Figure 2-10. D N A and deduced amino acid sequence of the AtNRTl. 1 gene. 27  2 675 2757 2 839 2921 3 003 3 085 3167 3249 3331 3495 3 57 7 3 659 3741 3 823 3 905 3 987 4069 4151 4233 4315 4397  tctctctaaaaggtagttgaaaactaaagaaaaaaccttttacacttttccataaattcaaactcttaacttttttttgcct acactattttaaaagcaattacgtatttgtcatgcatgtgtgtgaaggatataccatcttgaaaagattccacgtaactatc tccacaacatgttgattcaaatattcaatgcgtaagctatattccaaaaaaagaaacaatgtattattgatatgaaatttca ataaatagggacacttcataattttctaagaaacacacaaaagatctttggtttgaaaaatcagatacttatctttaatcca atatatgtaaaatattttatctccattttacataatttactattatattctaattattccttatatcatttttgatgccaca gTTCATTAGATAAGGCAGCAATAAGGGATCAGGAAGCGGGAGTTACCTCGAATGTATTCAACAAGTGGACACTCTCAACACT S L D K A A I R D Q E A G V T S N V F N K W T L S T L 330 AACAGATGTTGAGGAAGTGAAACAAATCGTGCGAATGTTACCAATTTGGGCAACATGCATCCTCTTCTGGACCGTCCACGCT T D V E E V K Q I V R M L P I W A T C I L F W T V H A 357 CAATTAACGACATTATCAGTCGCACAATCCGAGACATTGGACCGTTCCATCGGGAGCTTCGAGATCCCTCCAGCATCGATGG Q L T T L S V A Q S E T L D R S I G S F E I P P A S M A 385 CAGTCTTCTACGTCGGTGGCCTCCTCCTAACCACCGCCGTCTATGACCGCGTCGCCATTCGTCTATGCAAAAAGCTATTCAA ~ V F Y V G G L L L T T A V Y D R V A I R L C K K L F N 412 CTACCCCCATGGTCTAAGACCGCTTCAACGGATCGGTTTGGGGCTTTTCTTCGGATCAATGGCTATGGCTGTGGCTGCTTTG Y P H G L R P L Q R I G L G L F F G S M A M A V A A L 439 GTCGAGCTCAAACGTCTTAGAACTGCACACGCTCATGGTCCAACAGTCAAAACGCTTCCTCTAGGGTTTTATCTACTCATCC V E L K R L R T A H A H G P T V K T L P L G F Y L L I P 467 CACAATATCTTATTGTCGGTATCGGCGAAGCGTTAATCTACACAGGACAGTTAGATTTCTTCTTGAGAGAGTGCCCTAAAGG Q Y L I V G I G E A L I Y T G Q L D F F L R E C P K G 494 TATGAAAGGGATGAGCACGGGTCTATTGTTGAGCACATTGGCATTAGGCTTTTTCTTCAGCTCGGTTCTCGTGACAATCGTC M K G M S T G L L L S T L A L G F F F S S V L V T I V 521 GAGAAATTCACCGGGAAAGCTCATCCATGGATTGCCGATGATCTCAACAAGGGCCGTCTTTACAATTTCTACTGGCTTGTGG E K F T G K A H P W I A D D L N K G R L Y N F Y W L V A 549 CCGTACTTGTTGCCTTGAACTTCCTCATTTTCCTAGTTTTCTCCAAGTGGTACGTTTACAAGGAAAAAAGACTAGCTGAGGT V L V A L N F L I F L V F S K W Y V Y K E K R L A E V 576 GGGGATTGAGTTGGATGATGAGCCGAGTATTCCAATGGGTCATTGATCATGAATTCATGATCATGATCATGATGATGAACAT G I E L D D E P S I P M G H * 590 TATGCATGTCTATGTTGATATGTTTGAATTTGATTTTGAGTTTTGTTTGTATATTTTATGATGCTTTTCTTAATTACCTCTT GTTTCCGAGTCGACAAATAATGGACCGACCGATAAGGGATAAAAGTTAAAGTTTTCCC ATCAGGTTCTGTATAAAAGCAGAA ATTGTAACATTTCTTAAGATTTGACGCAATTAACGTCTTTTTGTCTTCAATTTCCATTTTTCATTTTTTCCCAGTAAATTAT CATACCATTCAACGTTTGTTTTCTCACTTGTTTTGGTATCGTTTGTTTTCGAATATGTGAATAATTTGGACCAGAACTAGGC GTCTAGGCCACTAGCTAGTGCCTAGTGGACTATCAC  Figure 2-10. (continued). The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined.  28  also contains a putative T A T A box (-138) and several G A T A boxes. The open reading frame (ORF) of AtNRTl.1  consists of 1770 bp, encoding 585 amino acids (64.9kD).  By comparison between the genomic D N A (AC010675) from the B A C clone (T17F3) and the cDNA (AF073361) sequences, the AtNRTl.2  is interrupted by four introns  (130, 135, 1365, and 75 bp from 5'to 3'), and the ORF which consists of five exons (3, 106, 219, 431, and 996 bp) encodes 585 amino acids with a predicted M W of 63.9 kD (Figure 211). The promoter region of AtNRTl.2  also contains two nitrate-dependent transcription  motifs, as well as putative T A T A and G A T A boxes. In AtNRTl.3  three introns (83, 78, 79 bp from 5'to 3') are located at the beginning  of the gene, resulting in four exons of 3, 118, 218, and 1431 bp (Figure 2-12). The ORF encodes 590 amino acids (65.2 kD), which is same length as that of AtNRTl. 1. Five potential nitrate-dependent transcriptional motifs were observed in the 5' upstream region between -893 and -635 bp. The AtNRTl.4  gene consists of 6 introns and 7 exons, spanning about 4.1 kb in the  genome (Figure 2-13). The ORF of the gene is 22 bp longer than was originally reported (Hutzfeld and Saito, 1999). The full length of 1758 bp encodes a sequence of 586 amino acids with M W of 64.5 kD. Among the four A t N R T l members, sequence identities (between 33 to 51 % at the protein level), were not particularly high (Table 2-1). A t N R T l . 1 and 1.2 are the most dissimilar, and AtNRT 1.3 and 1.4 are located between 1.1 and 1.2. The A t N R T l members share only 3-10 % identities with members of the AtNRT2 family at the protein level. Membrane spanning regions and topologies were also analyzed. Four programs (i.e., H M M T O P , T M A P , TMpred, and Toppred) predicted 12 TMS in all NRT1 members. Two  29  1423 TCTTGTATCCATGCCATGATAATGGTTACTTTGTTGTTTTATTGTCTATTATTTCTATTATATATGAACTTTCAATTTGAAT 1341 TTTAGATATATTGGCAGTACAAATACAAAAATTACTTTAACCACTATAGCTCCTCCGAGCATTCGTCACTGATC AGTGAGTG 1259 TGTGTTTATATATGCGATATTAAATTAAATAAGTTTTTCTTCACACTGTGTGTGTGTGTGTGTTTGTGTGCGTGGTAACAAT 1177 AAAGTTCTGCGTAGACGACACGTATCCAATATTAATGGAGTTCCGAAAGAAAGATCTTCTGGCAAAACCATCATATATAGAG 1095 ACAACAGTTTATTTTATCTTTTAAACAAAAATACGATCACATTTTTTTTACCTAAATTGCTAATAAAAAGTACATAGAAAAT 1013 GGTTTACAAATATCAGCCATTAACATATATAGTTCAATATTACCCGACAAACAAAAACATAGTTTATTTATGATTCTATCTC - 9 31 AAAAGAATTTAAGACGTCAAAAGAGGTAATTAGTAACATCATTTTATTGGAGATATTTTGCAATGAAAACTGCCATGAATAG -84 9 AAAGAGGAGGAATCAGTAGGTCTAGATTAAGTGAATGTTCTACTTCA3TTTTGTTTTAGg^AAAAGATAGTTTCACTAAAT - 7 6 7 TTATTTTAAAGCCATTAAGTGGAGGGCTTGATTCCTTCCATCACCTTTATCTTGCCCTCAACTTTTTTTTTTTGGATTTACT -685 TGCATCCTTCTCCATTAAACAAACCAAACCCAAATATAGTGTGTATTTTATTTAATAATTATGACCAGATAAATGTGGTAGA - 6 0 3 CTAAAAGTTTATTTTACGTGAAACAATCTATGTCATTCTTTAACTATCTAGAAGAATTTAGTGTTCATTAACATGTAAATGT - 521 GAACGAATAATATAATGTGAGTAATCGATATGCAATCAATCCTTAAACTTTGTTACCACTATACCTTGTAGAGAATAATAGA -43 9 ACAAAATCAATTCTCATATGTTAATTGGTATTGGAAACCCCATTTCAAAATCAACTTGCATATTAAGTAAAGGGAAAACAAA - 3 5 7 CATGATTGATTAGTCTTTATTCCACCACTATATTACTAGCTTTATAAATTCTTGGAATTAATATCATCTTTAGTGCCCTAAA -275 AACAAAGAAATAAAGCTAGTTTTCTCTAGAGGAGAAGAAAACAATGTTATTTCCTAAGAAGAGCATAAAGAAAAC^^AACA -19 3 TGAAGTCATTTTCTAATAATAAAGAGGGCCCAAATTCTTCTTTCTTCTCACCCAATTGGACCCTTCCTCAATCCCTTCTCCT -111 CTCCTCTCTTTAAATTCCGCTAATACCCTTCTCACTTTCACTCTTATATTTCATAAAAACCTTTTTTTATATCTCCTCTACC -29 TCAAAGTTTGAGAGAAAGAAAGAGAGAGAATGgtgggttcttgaagcttctcacattattttcCtcatcgttcaagaaatca M 1 54 a t a t t t g a t g a t g t t t c c t t t t a t a g a a a t a t a t g t c t t t t t c t c a a a g t c t t g t t t t g t t c t t t g c c a t a t t a t t a c a g G A intron I E 2 136 AGTGGAAGAAGAGGTCTCAAGATGGGAAGGCTACGCCGATTGGAGAAACAGAGCAGCCGTGAAAGGCCGTCACGGTGGCATG V E E E V S R W E G Y A D W R N R A A V K G R H G G M 29 218 C T C G C C G C C T C T T T C G T C T T A G g t c a g t t t c a a a a t t c c a a a t t t a c c c c t c g a t t c t c t t a a t g c a t c t t t t t c t t t a t c a L A A S F V L V 37 300 tccacacatttatattaagaacgattctctaatggatcattgtgattgattcatatatatttgtctcttatgaagTGGTGGA intron II V E 39 382 GATATTAGAGAATCTAGCGTATTTGGCGAATGCGAGTAATCTTGTGCTATACCTAAGAGAATACATGCACATGTCTCCATCA I L E N L A Y L A N A S N L V L Y L R E . Y M H M S P S 66 464 AAATCGGCAAATGACGTCACCAATTTCATGGGCACAGCTTTTCTCCTAGCTCTCCTCGGTGGTTTCCTCTCCGACGCTTTCT K S A N D V T N F M G T A F L L A L L G G F L S D A F F 9 4 546 TCTCCACTTTTCAAATCTTCCTCATCTCAGCTTCCATCGAGTTTTTGGtaaacctctcttaatcattcttataatcacttca S T F Q I F L I S A S I E F L G 110 628 t t t t t t t a c a t t t t g t t a a t c t t t a a a a t t t c t a a a c t t a a c a a g g a a c a a c a a a t c a a a c t c c a c t t a t a a a a a t a t t c a g 710 a a a c t t t g t t a t c c a t t a g a t t a c t t t a g t t t t c t t t t c t c t a t c g c t t a a g t t t t a a g t t a c t a c c g t t g a c t t t t g t t t t 792 taatggctaagccaccacaatcataaatccgttcacattaaaatagatcccacatgtatatctatacaattattagcataaa 874 a g a a a a t t a t c a c a c a t g a a a a t a t g g t t g t a g c a a a a a a a a a t c c a a c g a a c c a t g c g t g c a t t a g g a t g c t g a t a a a a a g 956 gacaaaagcaaagaggagcgtgactttgatacggtaccgtatccgtatctataagcaatgctttgttttgatcctaacacga 1038 c a c a t a c g t g a t a a c a t c t a t a a a a a a t c c g t a t g t t a a g g t c g g g a c c c a a a c g t a t t t t t a t c a g t t t t a a c t g t c a c t g 1120 t c t c a g g g t t a a a a g a g g a a a t t t a a a a a c t c t t t c t t g g g t t t c a g t a a c a c a g c a a g c t t t t t a t t t t a t t t t g t t a t c t 1202 t g t c t t t a c g t a t g a t a g g g t a t g a a a c t a t a a t g t c c a c t t a t a t a a c a t c t g c c a c t c g t a c c c t c g t g a c t c t g c a a c t intron III 1284 taatgttacaaaagacaaaacaaacttgtagttctaaagtacagttggggctcttaatgctttgtgggtagcgtttggccgg 1366 a c g c a a a c g c a a a c g c t c a c t c t t c t a c t t c c c a t t a t g g a t a g a g a t a t t g a t g g t t c a t g t a t a c c t a t a c a c t a t c a t a 1448 a c t t c a t t a g a a a a c t t a t a a c a g a t t a c a a g a a a a t a t a t a t a g c t g a c t t a a c t t a t a a t c t c c t t g t c a c t t t t t a t a g 1530 a t t t g a g t c a t t t a c t t g t a t g a t a t g a a g t a t t t a t a t t c c a t a t a c a t t c a t c t a g a a t c a a c a t a t a t c a a t a t a t g a t 1612 tggataatgtatactagagtccaaaacttttaaaaccctggtgttacgtcagtgtaaccgaagttatttcttcaagaaaagg 1694 cagtggccaatgaggcgaccacacgaaaattaggctttgtccatacctcatttaataacgaacgacgtttcatcgttcataa 1776 c g g t t t c a a t t a t t t g t a t c a c g t c g c t g a t c t g a c t c t c a c g a a c c a c a a g g g t t a a a a t c t c t c a c g t g c c c c t g g t c c c 1858 a t t c c c a t a c t a t t c t t t g c t a a t c c c a a a a a a a t a a c c g t c t c t a g t t a a t g a t t t t a a c a a a t c a a t a g g a t t a a a a t t t 1940 tatttgggaaacgtgcaggGATTGATCATACTCACAATTCAAGCTCGGACACCATCCTTAATGCCTCCATCGTGCGATAGTC L I I L T I Q A R T P S L M P P S C D S P 131 2022 CCACATGTGAAGAAGTGAGTGGTTCGAAGGCAGCGATGCTATTCGTGGGGTTGTACCTTGTAGCTTTGGGTGTGGGAGGGAT T C E E V S G S K A A M L F V G L Y L V A L G V G G I 158 2104 CAAAGGTTCATTAGCATCTCACGGAGCAGAACAGTTTGATGAGAGTACACCTAAAGGTCGGAAACAAAGGTCAACGTTCTTT K G S L A S H G A E Q F D E S T P K G R K Q R S T F F 185 2186 AACTACTTCGTGTTTTGTCTTGCTTGTGGAGCACTAGTTGCTGTCACGTTTGTAGTTTGGTTAGAAGACAACAAAGGATGGG N Y F V F C L A C G A L V A V T F V V W L E D N K G W E 213 2268 AATGGGGATTCGGTGTTTCTACCATTGCTATCTTCGTCTCTATTCTCATCTTTCTCTCTGGATCAAGATTTTATAGGAACAA W G F G V S T I A I F V S I L I F L S G S R F Y R N K 240 2350 GATTCCATGTGGAAGTCCTCTCACCACAATCTTGAAGGTTtgttttgacctctttagctcttattggagattgacgtgtgcc I P C G S P L T T I L K V i n t r o n IV 253 2432 ctaagttatgtatatgatttctttattcaggttCTTCTTGCGGCTTCGGTTAAGTGCTGCTCGAGTGGAAGTTCAAGCAATG L L A A S V K C C S S G S S S N A 270 2514 CGGTTGCGAGTATGTCCGTGAGTCCCTCAAATCATTGCGTATCAAAGGGGAAAAAAGAAGTTGAATCACAAGGAGAATTGGA V A S M S V S P S N H C V S K G K K E V E S Q G E L E 297 2596 AAAGCCACGTCAAGAAGAAGCTTTGCCTCCTCGGGCACAACTAACTAACAGTTTGAAAGTATTAAATGGAGCTGCGGATGAA K P R Q E E A L P P R A Q L T N S L K V L N G A A D E 324 2678 AAACCTGTCCATAGATTGTTAGAATGCACAGTCCAACAAGTGGAAGATGTGAAGATTGTCTTGAAAATGCTTCCGATATTTG K P V H R L L E C T V Q Q V E D V K I V L K M L P I F A 352 2760 CTTGCACTATCATGCTTAACTGTTGCTTAGCTCAGCTCTCTACATTCTCCGTCCAACAAGCTGCTTCCATGAACACAAAGAT C T I M L N C C L A Q L S T F S V Q Q A A S M N T K I 379  Figure 2-11. DNA and deduced amino acid sequence of the AtNRT1.2 gene. 30  2 842 2 924 3 006 3 088 3170 3252 3334 3416 3498 3580 3 662  AGGAAGCCTAAAGATACCTCCAGCTTCCTTACCGATCTTCCCCGTCGTTTTCATAATGATCCTCGCACCTATCTACGACCAT G S L K I P P A S L P I L P V V F I M I L A P I Y D H CTCATTATCCCATTCGCTAGAAAAGCTACCAAGACCGAAACAGGAGTCACTCATCTACAAAGAATCGGAGTAGGTTTAGTTC L I I P F A R K A T K T E T G V T H L Q R I G V G L V L TTTCGATATTAGCAATGGCGGTTGCAGCTCTAGTTGAGATTAAACGAAAGGGAGTGGCTAAAGACTCCGGCTTGCTTGACTC S I L A M A V A A L V E I K R K G V A K D S G L L D S GAAAGAAACCTTACCCGTGACTTTCCTATGGATCGCACTTCAGTATCTTTTCCTAGGGTCAGCCGATCTATTCACACTAGCT K E T L P V T F L W I G L Q Y L F L G S A D L F T L A GGACTACTAGAGTATTTCTTCACGGAAGCACCTTCCTCAATGAGATCTCTCGCAACATCGCTCTCGTGGGCTTCTTTGGCTA G L L E Y F F T E A P S S M R S L A T S L S W A S L A M TGGGGTATTACCTAAGCTCAGTGATCGTGTCCATAGTAAACAGCATCACAGGAAGCTCAGGGAACACACCTTGGCTCAGAGG G Y Y L S S V I . V S I V N S I T G S S G N T P W L R G AAAAAGCATAAACCGTTACAAACTAGACTACTTCTATTGGCTAATGTGTGTTCTTAGTGCAGCTAACTTCTTGCACTACCTC K S I N R Y K L D Y F Y W L M C V L S A A N F L H Y L TTTTGGGCAATGCGTTACAAGTATAGATCAACTGGTTCAAGAAGCTAAAATTGGATGGGCAACTTTTGAGTTTTTTTTTTGT F W A M R Y K Y R S T G S R S * TTTTAATTAGAGCAGAAAATGTTTTTACTTGAGCGGCTGTTATATAAGAGATGATAAATGGGGGTAAGTAGTAATGTTGTGA TCAGGTATATATTGGGGTTTGAAGTTTTTATCGTTGGACAAGTAATGTACAGCGAATGATATTAACTTGCTTTAAGTCTTTC TTTTGTT  406 434 461 4 88 516 543 570 585  Figure 2-11. (continued). The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. T A T A box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined.  31  -13 4 4 TTTAATGTATTTGCTGCTTTCTTGACTTATATTGCTAACATCATTTCAAGTAGAGGGATCAATTCATTAACATGTACAGCTT -12 6 2 TTTAATCAGTGGATCTCTCTAAGTAAATATCTTCCTCCATTTCATGGATTTTTTTACATGTCATATTCACCTTGATTACAGT -118 0 CACTTTCGAATATTACTTATAACGGAAATAATATGTTTTTTTTTTGCTTTACACATCTCTGGTTGAATACGCAATTCGTAAT -10 9 8 TTCCTATGTGACACCTGAAATCTTGTATCTTTCTTAAAAGTTATAGACTAGCTTCTTGTGGATCTAACAAATCCTTTTAGCT -1016 AAAAATAATCCATTAAACCTAGTTCCAAATGATTCAACATTTTGGTATACTAAATTACTAAGTGTATGTCCTAGGGATGTTG - 9 3 4 TGAACAAAAACCAGTCTGATTTAAACATACTCTTGGTGATATATATATATAGTCATAATTTTCTTAATCAAGTACAAATTGG -852 TTCATGATTTTTTGATCCACCAAAACATTTCTAATGAAACGAAATACTCATTAAAGAACAACACTCACACTAATGATTGAAC -770 ATTAATATGAACCATGTGATATTGAAGTGAAAGCACTAACTTTAATGCTTAACAAGT£A,TCCCAAAATATTAGAGACCATGC - 6 8 8 ATATTTGTACCAGTGAGAGTTCAGATTAATCTTGAACCTTj^GTGTATAACECAGTAAAAACTGTCCACGTGGTAGATCAAT -606 AAACAACCACAATCTGGCACACATGATATAAAGACAAAGATTTTTGATATGTCTCCAATTAATGTAAAATCTTAACAATAAA -524 AAACAATTCTATAGTATGGATGGTAAGAGATTTGTTGAAGGAGAAGAGGACGTGGGAAAAATACAAAGAAGCTAAAAAAAAA -442 CTCATTGCAACCACAAACAAAATGGTATAAAGAGACAAAAGAGAGTAATGGACATGGGGAATTACAAAGAAGCAGAAAACCT - 3 6 0 TGCAACCACATGAAATAAACAAATGTCTTTGTCATAAGATAATGAAATCACACTGTTGTCTCAATGTTTGTTTAGATCTATC -27 8 TGATCATATATCGCTGAAACAACCACACAAAAAGCAAAGCCACATTTTATATAAAGACCCATCATATATCAATCAATCCCCA -19 6 TCTCTCTTCACATGCCCATTTGAATCGTATCTCCTCTCATTTCTTCTTTTGTTTTGTTGGAGTTAGATAAAATCAAAGGTCT -114 AATAAAAGTGTCAAAACCCTTATCGCTATAACCTCCACTACCATCTTAAACTTCTCCTTATAACTCACGCTTCTCTGCTTTC -32 TTCTCTCAGAGTCTAACTGCTCAAATAAGAAAATGgtgagttaaaaagttttttctctctgttttttttttgtttcctctgt M intron I 1 51 ttcttatgttCttaatggttttgcttgtctCtaaagGTTCATGTGTCATCATCTCATGGAGCCAAAGATGGCTCTGAAGAAG V H V S S S H G A K D G S E E A 1 7 133 CCTATGATTACAGAGGAAACCCACCAGATAAGTCTAAAACCGGTGGATGGTTAGGCGCCGGTTTAATTTTAGgtaaagtctt Y D Y R G N P P D K S K T G G W L G A G L I L G 41 215 aattcttaatgtgaaaaaagagtgactcctctgtttctaacactcctctgtatcttcttaatgtgaagGGAGCGAGCTATCA intron II S E L S 45 297 GAGAGAATATGCGTGATGGGCATATCAATGAATCTAGTGACGTACCTTGTTGGAGATTTACACATCTCATCAGCTAAATCAG E R I C V M G I S M N L V T Y L V G D L H I S S A K S A 7 3 379 CGACCATAGTCACCAACTTCATGGGAACTCTTAACCTTCTAGGGCTTCTCGGTGGTTTTTTGGCTGACGCTAAACTCGGTCG T I V T N F M G T L N L L G L L G G F L A D A K L G R 100 461 CTACAAGATGGTTGCAATCTCAGCTTCTGTCACAGCTCTGgtaagctcttaaaccacgtacttgtagctcgattggcttgag Y K M V A I S A S V T A L intron III 113 543 actttCtagctCtaattccttgtttctgtgaaaacagGGAGTGTTGCTTTTGACGGTGGCTACAACTATCTCAAGCATGAGA G V L L L T V A T T I S S M R 128 625 CCACCAATATGTGACGATTTCAGGAGACTTCATCATCAGTGCATAGAAGCAAACGGACACCAGTTGGCTCTTCTCTATGTTG P P I C D D F R R L H H Q C I E A N G H Q L A L L Y V A 156 707 CTCTCTATACC ATAGCTCTAGGCGGAGGAGGAATCAAATCCAACGTCTCTGGTTTTGGGTCTGACCAGTTCGATACTAGTGA L Y T I A L G G G G I K S N V S G F G S D Q F D T S D 183 789 TCCTAAAGAAGAGAAACAGATGATTTTCTTCTTCAACAGATTCTATTTCTCCATCAGCGTCGGCTCTCTCTTCGCCGTGATT P K E E K Q M I F F F N R F Y F S I S V G S L F A V I 210 871 GCTCTTGTTTACGTTCAGGACAACGTCGGGAGAGGCTGGGGTTACGGGATCTCTGCCGCGACTATGGTGGTTGC AGCCATTG A L V Y V Q D N V G R G W G Y G I S A A T M V V A A I V 238 953 TTTTACTCTGCGGAACGAAACGGTACCGTTTCAAGAAACCTAAAGGAAGCCCTTTTACAACAATATGGAGGGTTGGTTTCTT L L C G T K R Y R F K K P K G S P F T T I W R V G F L 265 1035 GGCTTGGAAGAAAAGAAAGGAGAGTTACCCTGCGCATCCAAGTCTTTTGAACGGTTATGACAACACCACGGTTCCACACACA A W K K R K E S Y P A H P S L L N G Y D N T T V P H T 292 1117 GAGATGCTTAAGTGTTTAGACAAAGCCGCAATTTCCAAGAACGAGAGCTCTCCTAGCTCGAAGGACTTCGAAGAGAAGGATC E M L K C L D K A A I S K N E S S P S S K D F E E K D P 320 1199 CGTGGATCGTTTCGACTGTTACACAAGTCGAAGAAGTGAAACTCGTGATGAAATTGGTACCGATTTGGGCAACGAACATTCT W I V S T V T Q V E E V K L V M K L V P I W A T N I L 347 1281 TTTCTGGACGATTTACTCCC AAATGACGACTTTCACGGTCGAACAAGCGACGTTTATGGACCGAAAACTCGGATCTTTCACT F W T I Y S Q M T T F T V E Q A T F M D R K L G S F T 374 1 3 6 3 GTTCCTGCAGGCTCTTACTCTGCTTTCCTCATACTCACAATTCTCCTCTTCACTTCCCTTAACGAGAGAGTCTTTGTTCCTT V P A G S Y S A F L I L T I L L F T S L N E R V F V P L 402 1445 TAACAAGAAGGCTCACAAAAAAGCCTCAAGGAATCACAAGCCTACAGAGAATCGGAGTAGGGCTAGTATTCTCAATGGCTGC T R R L T K K P Q G I T S L Q R I G V G L V F S M A A 429 1527 AATGGCTGTAGCCGCGGTTATAGAGAACGCTAGACGCGAGGCAGCGGTTAACAACGATAAGAAAATAAGCGCGTTTTGGTTG M A V A A V I E N A R R E A A V N N D K K I S A F W L 456 1609 GTTCCACAATATTTCTTAGTCGGTGCGGGTGAGGCCTTTGCTTACGTTGGACAGCTTGAGTTCTTTATAAGAGAAGCACCAG V P Q Y F L V G A G E A F A Y V G Q L E F F I R E A P E 484 1691 AGAGGATGAAATCGATGAGCACCGGATTGTTTCTAAGCACGATATCGATGGGATTCTTCGTGAGTAGCTTGCTTGTTTCGCT R M K S M S T G L F L S T I S M G F F V S S L L V S L 511 1773 TGTTGATAGGGTTACAGACAAAAGCTGGCTTAGAAGTAACCTTAACAAAGCGAGATTGAACTACTTCTACTGGTTACTTGTT V D R V T D K S W L R S N L N K A R L N Y F Y W L L V 538 1855 GTCTTGGGAGCATTGAACTTCTTGATTTTTATTGTGTTTGCCATGAAACATCAGTATAAAGCTGATGTGATTACTGTTGTTG V L G A L N F L I F I V F A M K H Q Y K A D V I T V V V 566 1937 TGACTGATGATGATTCAGTGGAGAAGGAAGTGACGAAGAAAGAGAGCTCTGAATTTGAGCTTAAGGACATTCCTTGAAACCA T D D D S V E K E V T K K E S S E F E L K D I P * 590 2019 GATTTAGAAGAAGAAAAAAAACCTCTGGTTTTGTTATTTGCTTTGAAGATTTCATTTTGTCTTTGTATTTTTAGTATATTGT 2101 GTGTATGAAATAGAAAGATTACTATATGGTTTGGATTGTATTTTTTTTTGTAAGATTTTTAAAAATTTAGTTACTATAGTTT  Figure 2-12. D N A and deduced amino acid sequence of the AtNRTl.3 gene. The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. T A T A box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined. ^ 7  -17 5 4 -16 7 2 -15 9 0 -15 0 8 -14 2 6 -13 4 4 -12 6 2 -118 0 -10 9 8 -1016 -934 -85 2  TGAATGGATAGTTGATAGTTCAATCCGGAGAACTTTTGAGCTATATACCAATAAAAGGGAGTTTAATGTTGTCTAGCTTAAA GGGAATTTAGTTTTGGGACTTGAAAAGAAAAAATATGTTCGACAAGATTGTAAATTTAACATCAAAACTTTAGCTCGTAATG TCTATCTAGCTTATAGGGAAATTTAGTTTTGGGATTTAAAAAGAGTAAAAATGTTCGACAAGGATTTAACACTCCAGAAGAC ATTGTACATTTCGACAAAAAAAAAGAAGACATTGTACATTTTTGTCTCTCTTTTTTCTTTTTCTTTTTTTCTTGGTGAACCC CGTAACTTGCATTAATTATCTTGTTTGTTTAGTTTTTTTTCACAAAGCTGTATAAGGCGTGACTGGTACTCTTTCGGC AT A T TTTTGATTGATTTCGAGAGTTTCTTTTGGTCTCGGCATTTAGAGTAAAATCTGATTTGGGATGATTTTTTTGAAGAACACTA ATGTAGTAGAGTCAAAGCTTACATATTTTTAGTAGTTGGAAAATTATTTGAACATCTTTAATATGAATGCAAGTTCCCGTCT GCAAGCCTCTTTATTTGCCTTTGTTTTCATTTTTGGTTTGAATACAAGCAAATGTCAAATATGGAACATATTGATATCTGTA CTTTGTTTTTAATATCAATTGGGACAAACAAAACCAAATAGTCGACCGTGCATTTAAAGGATTTTTAGAAATATTTGGCTCC TTTGCACATTTCCACATTACCTCATCCATTTTTGCTCCGTGCATATATTCATTATATTACTTTTGAGTAACTTTCTCGTGCC TTCTCCGAATTCCGTCATGTATTTCTCATATTATTTCCTAGTGATTCTCAACAGCCATGCAATCCAAATTACCTCAGAAACT TTCCTTTGATATGATCCGATCCATATCAAGCCAAATAGACCTAGTTTGACCCCTATTACTATGTAAGAAGCTCCAGACAATT  - 77 0 TTTAACCTAGTATTTGTTTACGCTTTTTCTTCTAAGTTTTGTCTAAGTGTTTAAGAGGGACTTACAAGACTTCAACTACATT - 6 8 8 TGTGATGACGATCTTATCATTTCATCCAGCTTAGTAATATAATGTTATGCTCGAAACGTGTTTGATAAAGGGGTTAGACCAA - 606 ATTTCAAAAACGTTTTTTCTTACTTAACCAGTATGAATTAGTGGACTACTAAGTGACATTGTTTTCAATGCTCTAGTTAGCA - 52 4 A A T C A A A G T T T A G C T A A T T A A G T G A T C A A T G A A G T T A T T T G T C A T G A A A G T G G A T T A A T C T T G T T T G A G C G T T K X : A A G A T T A - 4 4 2 TATAACACTACGTTGTTGCTTAATGAATGTCTTAGCATGAAAATTATTTTTTCTATCTTATCTTACGAATTATCTTCCCCAT - 3 6 o GATCAATTGTTTGTTTATTTCTTGATTTGCCTAGTAAACCTTCTAGTTTTTGGTTATAAATTTATAAGTTTCACCCTCCAGG - 2 7 8 GTTTGAGTCTTCTTGGAAACAAATATCACATCCTTGTGGAAAGTTTGGGTTTAGGCCAAAGGCCAAAACATTCCAGAAATTA -19 6 T T C C A A A T T A G G C G G G T A A A G C C C T T T T C T A C T A G T A T A T G T T C G A T A T T C T T C T T A T T T G G A A A A A A A A A C A T A T G T C A T A -114 TTCTACTATATGTTCTCATTCCTATTCTTCTTAGTTAGGCAAAAGATCTCATTGCTATTCTTCTTCTTATTTAGGCAAAAGA -32 TATATATATATATATTTATATTTATATCAAATATGGTTCGTTTTTCAATAGTTAGTGGAGAAataaaaaaaaaataaaaatt M V R F S I V S G E 10 51 g g a a a c t a a t a g t a a t g a a c c t c g t t g a g a a t c t t t a t t t g a t c t c g c c a a a t a t t t t a t g g a a a a a t a t g c a a g t g t t g t t 133 tcatgatccaaagttctcgctctatgtatgtgtctttgggacccagagtttgggtcgaataaataagttatcatcataaaag 215 a g a a a a t t t a c a a c a a a t a a g a a a a t a g a a a a t t a a a g a a a a a a a t t a a a a a g a g c c a a a a a t a a t t t c g a a a t a t a a a t t a 297 a g a a a t a t t t t a a a g t t g g g g a a a a a a g t g t g a t g a a c c t a t c t c a a a g a t t t c a c g t t t t t g c g a t a t g t c c c a a a t c a c a intron I 379 tatagtggaaggtcggtgctagccctctttcattcattttgtggctataaaaaggcagtctcctgtccatcattatttgctt 461 c t g t g g c t a a c a a a g a g c a a a c a a a c a c t t a g a a g a a a c t a a g a a t a c t c t c a t c a a g g c g a t a t a g a a a a a a a t g g t t t g g 543 a t a a t c t t t t t c t t c t t a c t c g t a a a c t a t t g g t t a t a a g a t t c g g g a a c t t t g g a t t g a c g t a c g t c g t t g t t t t c a g G A G E 11 625 AGCAAAGGGAGTTGGACAGTGGCTGATGCCGTAGACTACAAAGGACGACCTGCCGACAAATCCAAAACCGGTGGTTGGATCA S K G S W T V A D A V D Y K G R P A D K S K T G G W I T 3 9 707 C T G C C G C T C T C A T T C T T G g t t c g t c t t c t t c t t t t c t a c t t g a c a t a t a t a t a t a t a t a t a t a t a t a c a t t t g g t c c t c a t g A A L I L G 45 789 t a c a t a a t a g a t a t g c c a t t t t t t t t g t g t g t g c a c a t a t a c t t a t g c c a t t a t c a a t a a g a a t c t g t g t g a a a t t t a t t c a 871 c a g a a g t c c t a g t t a a t t a g c t a a a a a t g a a c t c t t t t t t t a t a g c t a a a a a c g a a c t t c t t t t t c t t c t t t a t t t a a c t g c 953 atgcttttttatctttctttttttactaaaatcttcgtttcttacttcatgtgacatgcattactactatatatttatatta 1035 t t t a a t a t t c t g t a a a t g a a g a a a a t a c a t c t a t c a t c c a c a t a t t g g c a g a g t a g t c a t t a g t g a a t a c a t a c a t a c a a c t 1117 tatacgtaattaatttgatcaagagggtgtagttcatgcgtataagttttaaattccataagttgtataatttgtgaataca 1199 t g g t g a g a a a c a a a a g a g a c t c a t t t t c a a a t c a g t c a c a c t c a c a c a t g c a t g a t a t g a t t g a a a t a a a t a t a t t t g t a t a 1281 t a a a a a t a t g a a a t g t c g t t g t t c t g a a t c t c g c t g a t t g a a a g a a a g a t a a a g a g a a a a g g a a c a c g c c a c a t g g c t c c c c i n t r o n II 1363 a t c t c g c t t a t c c a a t c a t a a t a a c a t t t t t t t t t c t t t t t t a a a a t t t a a t c a t t c t g a a a a a c a a t a t t g a t t a g a a a g a 1445 g a a a a a c g a a a a c t g g a t t t a t a t c t g t a t t c a c g t g t c t a c t t a g g g a g c a g a a a a t g c c g a c c t c c a a a c c c t t g t t t t g 1527 ttccttaatattctcttacaaaaagtaccagttgtcttaattaaaattagtccggataatccaaaatttagttttgttgctt 1609 c t a a g t t t a a a a c t g a t a a t a t a t c t c c t t c a c t t c c t t a c t t t t t t a a a g g a c a a a a a g a t t g a a t g t t a c a t c c a t a a c t 1691 tatcatgaatattcatttatgtttatcaatactttatattttattttgttggccaaattaatagttggagaatgaaaggtct 1773 atgttattttcgtattaatttaccttaaaacaatcaaacttgttaatcagcttatggctgcttactagttaaggattattct 1855 a c t t a t a t g t a t g a a a t g g a c t c a c c a a t t a a c t t g g a a c a t a t g t a c a a a a c t a c a a a t g t t g a c a c a t t a a a a a t g a a a c 1937 atatattgcagGGATAGAAGTTGTGGAGAGGCTATCAACAATGGGAATAGCAGTGAATTTGGTAACATATTTGATGGAGACA I E V V E R L S T M G I A V N L V T Y L M E T 2 019 ATGCATCTCCCAAGTTCAACCTCTGCCAACATTGTCACTGATTTCATGGGCACTTCCTTCCTCCTATGCTTGCTCGGTGGTT M H L P S S T S A N I V T D F M G T S F L L C L L G G F 9 2101 TTCTCGCTGACTCCTTCCTCGGCCGTTTCAAAACCATCGGCATTTTCTCAACCATTCAAGCTCTGg taagac t c t a t c t a a a L A D S F L G R F K T I G I F S T I Q A L 2183 atcttatatatagttttaaaaaggtcattgtgattagttggttttaccatctagtagtagatgcgtctaagagaataaataa 2265 c c t g t a t t t t t c t c c a a g a t c t c c g a t t c t a a a a c t a c t a t t a t a a g c a a a t t a t c a a t t a g a g c t c t a t t a a a a a a a t t c a intron III 2347 c t t a g a a a a a a t c a a a c a a a a t g t t c g c t a t c a a a t c t g c t a a g g t c g t t a a c t t a g t t g g a g t c t t g g a g a c g g t t t t a a t 242 9 atCttgtatacagGGAACTGGTGCTCTAGCGGTAGCAACTAAGCTGCCAGAGCTACGTCCACCAACATGCCATCATGGAGAA G T G A L A V A T K L P E L R P P T C H H G E 2511 GCTTGCATACCCGCGACCGCCTTCCAAATGACAATTCTTTATGTTTCGCTTTACCTTATAGCCCTTGGAACTGGTGGTCTTA A C I P A T A F Q M T I L Y V S L Y L I A L G T G G L K 2593 AATCTAGTATCTCTGGATTTGGGTCTGACCAGTTTGATGACAAAGATCCTAAAGAGAAAGCTCACATGGCTTTCTTCTTCAA S S I S G F G S D Q F D D K D P K E K A H M A F F F N 2675 C A G g t t a g g t t t a g a g t t t a t t t t c a t g c a t g g a a t t a t a a c a t t g t t a t a g t g t t c c c t t t t t c a a a t a a a a t t t t a a t t g R i n t r o n IV 2757 gcacatgcagGTTCTTCTTCTTTATTAGTATGGGGACATTATTGGCTGTGACTGTTTTAGTTTACATGCAAGATGAAGTGGG F F F F I S M G T L L A V T V L V Y M Q D E V G  Figure 2-13. D N A and deduced amino acid sequence of the AtNRTl.4 gene. 33  68 6 117  140 168 195 196 220  2 83 9 2921 3 003 3085 3167 3249 3331 3413 3495 3577 3659 3741 3 823 3905 3 987 4069 4151 4233 4315 4397 A inn  AAGATCTTGGGCTTATGGAATCTGCACTGTCTCTATGGCTATAGCTATTGTAATATTCTTGTGTGGGACTAAGAGATACCGT R S W A Y G I C T V S M A I A I V I F L C G T K R Y R 247 TATAAGAAGAGCCAAGGAAGTCCCGTTGTGCAAATATTTCAGGTCATAGCAGCTGCGTTCCGAAAGAGGAAAATGGAACTAC Y K K S Q G S P V V Q I F Q V I A A A F R K R K M E L P 275 CTCAAAGCATTGTTTATCTTTATGAAGATAACCCTGAAGGCATTAGAATTGAACATACTGATCAGTTTCAgtgagtttCtca Q S I V Y L Y E D N P E G I R I E H T D Q F H 298 gttcaatctttacaaagaggaagtaaattaaagtaaattttgtatctaataaaatcttgtgtgtagCTTGTTGGACAAGGCG intron V L L D K A 303 GCCATAGTTGCAGAAGGAGATTTTGAACAAACCCTTGATGGAGTTGCAATCCCAAACCCTTGGAAGCTAAGCTCAGTGACCA A I V A E G D F E Q T L D G V A I P N P W K L S S V T K 331 AAGTTGAGGAAGTAAAAATGATGGTTAGGCTTTTGCCTATTTGGGCAACAACTATAATTTTTTGGACAACATATGCCCAAAT V E E V K M M V R L L P I W A T T I I F W T T Y A Q M 358 GATTAC ATTCTCTGTTGAGCAAGCTTCAACTATGAGACGTAACATTGGAAGCTTTAAGATCCCAGCTGGTTCCCTCACCGTG I T F S V E Q A S T M R R N I G S F K I P A G S L T V 385 TTTTTCGTTGCGGCTATTCTCATAACTCTAGCTGTCTACGACCGTGCCATAATGCCTTTTTGGAAGAAATGGAAAGGAAAAC F F V A A I L I T L A V Y D R A I M P F W K K W K G K P 413 CAGgtgacataagattcatagattcatatatctattcttttttcatatatgtctctcagctatatattcacatgcattaaca G i n t r o n VI 414 tttcagGTTTCTCTAGCCTACAAAGAATAGCTATTGGATTGGTCTTATCAACCGCTGGAATGGCAGCTGCAGCTCTAGTAGA F S S L Q R I A I G L V L S T A G M A A A A L V E 439 GCAAAAGCGTTTATCCGTTGCGAAATCTAGTTCACAAAAAACATTGCCTATAAGTGTGTTTTTACTTGTTCCACAATTCTTC Q K R L S V A K S S S Q K T L P I S V F L L V P Q F F 466 TTAGTAGGAGCTGGGGAAGCCTTTATCTAC ACTGGCCAACTTGATTTCTTCATAACACAATCGCCTAAGGGAATGAAAACTA L V G A G E A F I Y T G Q L D F F I T Q S P K G M K T M 494 TGAGCACTGGACTCTTCTTGACCACTTTATCACTAGGTTTCTTTGTCAGCAGTTTCTTGGTCTCAATCGTCAAGAGGGTCAC S T G L F L T T L S L G F F V S S F L V S I V K R V T 521 TTCAACTTCTACTGATGTAGGATGGCTGGCTGATAACATTAACCACGGCCGACTCGATTACTTTTATTGGCTTTTAGTCATT S T S T D V G W L A D N I N H G R L D Y F Y W L L V I 548 CTCAGTGGAATTAACTTCGTTGTCTATATCATATGTGCCTTGTGGTTTAAGCCAACGAAGGGTAAAGACTCAGTAGAGAAGG L G II NN FF VV V V Y Y I I I C I A C L A W L F WK Fl 'K TP i T \ K 576 L SS G < jG ^ K i DJ So vV i E , K^ E^ AAAATGGCAAGGGATTTTCAGTTGAAGACTGCTGAATTTTGTTTTGCAATAATTGTCTTGTGTACAATATTATCTTGCAACA 586 N G K G F S V E D C * ATGTCGCTTTCC AATTATGTTTCTTGTATATTAAGCAATTGGCTTGTTTTTAGATTCCTCCCGGTCTCAAATATTGTGTCTT TACCGTTTATGTTATTCACTCTTTTTTTTTGCATCGTGAAAAATAATTATTTAACGAAGTATACTTTTAATTTTCTW3TTAC GTCCTGTCGCGATCCGATTAATCTCCTTTTTTTTTCGATTAATCTTTTAGGTTTTATGCTTTAGTAGGTCGAGAAGATGAGA TCCACATTTAGGCCTTTAGCTATTTCATATCTCTTTACCTTTGTGATCTAGTGTCCGGAACATTGTAGAACTGTGGAGAACA mnmmili-i it n » MTliTlR J\ HPiMTir'l'IfPP'T'Tl  Figure 2-13. (continued). The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined.  34  PTR  signature  sequences:  PTR1:  [GA]-[GAS]-[LIVMFWAHLIVM]-[GAS]-D-x-  [LIVMFYWT]-[LIVMFYW]-G-x -[TAV]-[IV]-x -[GSTAV]-x-[LIVMF]-x -[GA] between 3  TMS2 and TMS3,  and PTR2:  [LIVMAG]-G-[GSA]-[LIMF]  3  3  [FYT]-x -[LMFY]-[FYV]-[LIVMFYWA]-x-[IVG]-N2  [FYT]-x -[LMFY]-[FYV]-[LIVMFYWA]-x-[IVG]-N2  [LIVMAG]-G-[GSA]-[LIMF] within TMS5, are well conserved among the four A t N R T l members (Figure 2-14). The PTR family was not included within the M F S because of insufficient homology between the two families (Pao et al., 1998). However, PTR members possess some features in common with those of MFS: The four A t N R T l members possess sequences of 592 amino acids on average, which are 70 residues longer than those of AtNRT2 proteins, and they are also predicted to have 12 TMS. The A t N R T l members commonly have cytosolic N - and C-termini and a relatively long cytosolic loop, approximately 100 amino acids, between TMS6 and TMS7.  In the loops at least one  phosphorylation site was found in each protein. A conserved protein kinase C (PKC) phosphorylation site was also found at the end of TMS6. Putative N-glycosylation sites were found between TMS1 and TMS2 of A t N R T l . 1 and 1.2. Because predicted TMS1 of AtNRTl.2, M-34 to A-53, is shifted upstream compared to A t N R T l . 1, the N-54 becomes a possible glycosylation site (Figure 2-14). T M H M M and M E M S T A T were evaluated as the finest performance prediction programs for known and un-known proteins (Moller et al., 2001). However, both programs predicted that only one third of NRT members should possess 12 TMS. Rather, Toppred, considered to be one of the less powerful performance programs, predicted that all of 11 members  should have  12 T M S and cytoplasmic N-terminus (Table 2-2). These  35  oq vo ro o o cn OJ  OJ  OJ  rH  oj r- t/i oj o cn cn o ro OJ OJ ro  cd  3  <  CN  •H  *r ro 01  JJ  OJ J J  H  T  n 01  i-i ^  m  OJ  JJ  4J  4J  H  ^ m  (N  r-t  ro  j j xJ  JJ  E-« JJ  < < < <  OJ  rl  n  CJ  Ci JJ  < < <<  JJ  < < *C <  discrepancies might be due to insufficient information of the MFS proteins. Clearly larger data sets and experimental evidence are essential for more accurate predictions. Introns found in the AtNRT gene families carry conserved sequences at 5' and 3' ends, G-T[AT]-[ATC] and [CTJ-A-G, respectively. These sequences match with the consensus sequences for splicing in eukaryotes (Keller and Noon, 1984; Padgett et al., 1986). The position and length of introns become a key factor for designing primers of RT-PCR. This detail will be discussed in the next chapter.'  37  3 Expression patterns of Nitrate Transporter A tNRT Genes 3.1 Introduction  It has been demonstrated that genes belonging to the NRT2 family are induced in response to nitrate provided externally. Among lower eukaryotes, this family includes representation in Aspergillus  nidulans NrtA and NrtB (Unkles et al., 2001), Chlamydomonas  reinhardtii  CrNRT2.1 and 2.2 (Quesada et al., 1998), and the diatom Cylindrotheca fusiformis NAT1 and NAT2 (Hildebrand and Dahlin, 2000). In higher plants, the barley HvNRT2.1 (BCH1) was one of the earliest identified NRT2 members that showed rapid induction in response to nitrate provision. In this species the transcript was detectable within 30 min of NO3" provision (Trueman et al., 1996). Subsequently, cloned NRT2 genes from other species also showed nitrate inducibility with 1 to 4 h for the peak of induction. These include Arabidopsis  thaliana AtNRT2.1 and AtNRT2.2 (Filleur and Daniel-Vedele, 1999; Lejey et  al., 1999; Zhuo et al., 1999), Nicotiana plumbaginifolia  NpNRT2.1 (Quesada et a l , 1997;  38  Krapp et al., 1998), Glycine max GmNRT2 (Amarasinghe et al., 1998), and  Lycopersicon  esculentum LeNRT2 (Ono et al., 2000). However, additional members of the NRT2 family from A. thaliana, identified from searches of the Arabidopsis genome data bank, AtNRT2.32.7, have not been characterized yet. NRT1 family genes, on the other hand, respond to nitrate provision in two ways, either they are nitrate-inducible, or nitrate-constitutive. AtNRTl.1  (CHL1), the first nitrate  transporter gene isolated from higher plants, was induced by nitrate and acidic pH (Tsay et al., 1993). Nitrate-inducible NRT1 genes have also been identified from Brassica napus BnNRT1.2  (Zhou et al., 1998), G. max GmNRT1.2  esculentum LeNRT1.2  (Yokoyama et al., 2001), and L.  (Lauter et al., 1996; Ono et al., 2000). B y contrast, nitrate-  constitutive genes, such as AtNRTl.2,  are expressed independently of external nitrate.  These genes were also observed in G. max GmNRT1.3 esculentum LeNRTl.l  (Yokoyama et al., 2001), L.  (Lauter et al., 1996; Ono et al., 2000), and Oryza sativa  OsNRTl  (Lin et al., 2000). The expression patterns of AtNRTl.3 and 1.4 are unknown. Significant portions of incoming NO3 proceed from roots to shoots to be reduced and metabolized and/or stored (Marschner, 1995). Indeed, in some species virtually all nitrate reduction occurs in leaf tissue, and hence NO3" absorption by leaf cells is of crucial importance. Yet, there is little information concerning NO3" transport systems in shoots. Although loading of NO3" into xylem vessels is considered to be passive, the absorption of NO3" from the leaf apoplast by leaf mesophyll cells is necessarily against  the  electrochemical potential gradient (Glass and Siddiqi, 1995). This NO3" flux might be anticipated to involve L A T S based upon typical values of xylem N 0 " (Glass and Siddiqi, 3  1995). Notwithstanding the importance of absorbing NO3" into leaf cells, expression levels  39  of AtNRTl.1,1.2,  and 2.1 in shoots were shown to be significantly lower than those in roots  (Tsay et al., 1993; Huang et al., 1999; Zhuo et al., 1999). However, Guo et al. (Guo et al., 2001) showed strong expression of AtNRTl. 1 in shoots using GFP/GUS fusion lines. The foregoing emphasizes the importance of NO3" transport systems in shoots. Therefore, I have characterized the expression patterns of 11 AtNRT  family  members in both roots and shoots, in response to the provision of NO3" following a 7-day period of NO3" deprivation. The transcript abundances were analyzed quantitatively by RTPCR.  3.2 Materials and Method Plant growth condition  Arabidopsis plants (ecotype Columbia) were grown hydroponically under non-sterile conditions as described in earlier papers (Gibeaut et al., 1997; Lejay et al., 1999). Briefly, A inch thick Styrofoam was fitted to an 8L container as a floating platform to support plant  l  growth. Each platform contained 30 holes (diameter 1.5 cm) covered with nylon mesh at the bottom surface and these holes were filled with clean sand. Seeds were imbibed in a cold room at 4 °C for 3-5 days, and sown directly on the moistened sand in the platform. The nutrient solution which was used to support plant growth contained: I m M KH2PO4, 0.5mM M g S 0 , 0.25mM C a S 0 , 2 0 u M Fe-EDTA, 2 5 u M 4  4  H3BO3, 2 u M  M n S 0 , 0.5uM C u S 0 , 0.5uM (NH ) Mo 02 , and 0.5mM N H N 0 . 4  4  4  6  7  4  4  3  ZnS0 , 2uM 4  For the induction  study, 5-week-old plants were transferred to - N solution for one week (other nutrients remained as before), then re-induced with 0.5mM Ca(NC>3)2 for from 0 to 72 hours. p H of  40  the nutrient solution was maintained with CaC03 around 6.2. The walk in environment chamber was maintained under the following conditions: light/dark=8/16 hrs, 25/20 °C; RH=70 %. Light was provided from fluorescent tubes (VITA-LITE, 150 jiiE m" sec~'). A l l 2  flux determinations and plant harvesting for R N A extraction were undertaken at 4 hours after the light period began, and all pretreatments were appropriately staggered to meet this requirement. A l l experiments were repeated at least twice. The means of those experiments were used as physiological data, and some data such as gel pictures were representatives of the experiments.  RNA isolation and relative quantitative RT-PCR R N A was isolated using TRIzol Reagent (Life Technology, Grand Island, N Y ) according to the manufacturer's method followed by additional chloroform isolation and sodium acetate precipitation steps. Total R N A concentrations were determined by U V spectrophotometry. RT-PCR was carried out using OneStep RT-PCR Kit (Qiagen Inc., Mississauga, ON) with QuantumRNA 18S Internal Standards (Ambion, Inc., Austin, T X ) under the following conditions: 50 °C for 30 min; 95 °C for 15 min; 19-37 cycles (Table 3-1) of 94 °C for 30 s, 65 °C for 30 s, 72 °C for 1 min; 72 °C for 10 min. Total R N A , 25 to 250 ng (Table 3-1), was added to the reaction mixture containing 400 u M dNTP, 0.6 uM of gene specific primers (Table 3-1), 0.4 u M of the QuantumRNA 18S primers, 0.2 jj.g of hexamers, as well as buffer and enzymes according to the manufacturer's protocol, and RNase-free water was added to make a final volume of 12.5 ul. The RT-PCR products were electrophoresed on 1.3 % agarose gels and stained with SYBRGold (Molecular Probes, Inc., Eugene, OR) for  41  CD  E C  o  >s  O  CN  CN  O CO  o  CO  CD CM  CD CN  CD CNl  co  o  LO  LO CM  LO CM  O LO CM  CM  c  <  o  coc  Z  LO CN  LO CM  o  o  O LO CM  O LO CM  LO CM  ca  CO CO  co  CO CO  CO CN  CN CO  CO CM  CM  CO CM  CM  CM  O LO CM  o  O LO CM  O LO CM  O LO CN  O LO CM  O LO CM  O LO CM  O LO CM  O LO CM  O LO CM  o  CO CO CO  o  CO  o  LO  CD  LO  CO CD  cn  LO  CM  CO  LO  CO  CM  CO  ei  ei cc  I-  I-  LO CM  LO CM  CM  CD  E 3 C  0  O  O  o o n CO  CC  CM  LO CM  CU N CO  o  CM LO  o  CO  o  00  o  CO  a: o  0_ ha:  co o c  'i3 c  o o  T3 c CO  J2 CD  E  1—  a. o 'o CD Q. CO  CD  E  CD c CD  o CO  .o  CO  CD  c  CD  O  I  I  ei i  i  1  2  i  1 1  CM CD  30 minutes. The signals of the targeted gene products on the stained gels were captured and densitometry analyzed with an Alphalmager™ 1200 (Alpha Innotech Corp., San Leandro, CA). For each gene, the optimization of RT-PCR was strictly carried out as follows: 1. Preliminary RT-PCR trials to determine the specificities of the gene specific primers and the presence of the gene expression (e.g. product size and its sequence, and approximate expression levels among the samples); 2. Determination of the P C R cycle number which gave linear range of gene amplification, choosing one sample in which the target gene was expected to be the most abundant. After the RT step, aliquots were taken every two cycles in the PCR step. Signal intensities were then plotted versus cycle numbers on a log scale. A cycle number in the linear range was chosen for the subsequent experiments (Table 3-1). 3. The amounts of the 18S rRNA internal standard primers were determined according to the manufacture's protocol in order to amplify both the target gene and the 18S at a similar level.  3.3 Results Expression of Two NRT families by Relative Quantitative RT-PCR A unique feature of the transport of nitrate, compared to other inorganic nutrients is that nitrate (NO3") is both a substrate for transport and also for the induction of nitrate transport systems at the gene and at the physiological levels (Glass and Siddiqi, 1995; Forde, 2000). Therefore, as the first step in characterizing members of the two NO3" transporter families, their responses to induction by NO3" were examined by means of time-course experiments.  43  Five-week-old  Arabidopsis  plants were nitrogen starved for 7 days, in order to de-induce  NO3" transport (Siddiqi et al., 1989). Preliminary experiments showed that NO3" was undetectable in roots by 4 days after removing exogenous NO3", while shoot NO3" was reduced by >70 % by 7 days. The starved plants were then transferred to nutrient solution supplemented with I m M N 0 " for up to 3 days. Gene expression in response to this 3  renewed NO3" provision was analyzed using relative quantitative RT-PCR method. Designing the gene specific primer is the first and perhaps the most important step of the entire RT-PCR method. Some online programs are helpful to seek ideal primer sets by using information such as G C contents, Tm value, primer length, size of the product, and location on the gene. The final decision, however, has to be based on the need to select unique sequences. Table 3-1 shows the gene specific primer sets used in the study. The primers were designed either to flank half of a primer lay in one exon and the second half in the next exon to eliminate genomic D N A amplification, or to flank a region that contains intron(s) to indicate genomic D N A contamination (i.e., genomic D N A would be amplified in larger product size than that of c D N A due to intron(s)). The product sizes of the gene specific primers were aimed to be more than 300 bp since the internal standard primer sets produced about 300 bp fragment (Table 3-1). The specificities were confirmed by the sizes and sequences of the products. P C R conditions including amount of R N A template and P C R cycle numbers were optimized after several trials. Figure 3-1 shows a relative expression level among the  AtNRT  family genes. The  values were calculated by the amount of R N A used for RT-PCR, and the P C R cycle numbers (Table 3-1). Although quantitative relative RT-PCR does not count absolute copy number of an R N A transcript, it still provides a simple estimation of the relative expression  44  High  Shoots  Roots  on level  NRT2.1  CO o X 0 0  NRT1.2 NRT1.3 NRT1.1 NRT1.3NRT1.4 NRT1.2 NRT2.5 NRT2.1  Rela  NRT2.6 NRT2.2  NRT2.7  NRT2.3  NRT1.4 NRT2.4  NRT2.5  NRT2.6  NRT1.1 NRT2.7  >  ">4—»  NRT2.2  NRT2.4  NRT2.3  Low  Figure 3-1. Estimated relative expression levels of AtNRT genes. Relative value = 1 / (ax2 ), where a is amount of R N A used in the RTPCR; n is PCR cycle number. Y-axis is expressed in logarithmic scale. n  level among the genes. Typically, expression levels of all genes, with the exceptions of AtNRTl.1,  AtNRTl.4  and AtNRT2.5, were higher in roots than shoots. Within root tissues,  the following four genes (listed in order of decreasing transcript abundances) were more highly expressed than in shoots, and more highly expressed than all other genes whether in roots or shoots: AtNRTl.1  > 2.2 > 1.2 = 1.3. On a relative scale, based upon the number of  PCR cycles required and quantities of template R N A used to obtain a similar signal, and assigning an arbitrary value of 100% for root expression levels of AtNRT2.1, AtNRT 2.2, AtNRTl.2  and AtNRTl.3,  their expression levels in shoots and expression levels of all other  genes in roots or shoots were ~5 to 10%. By contrast, within shoot tissues, all members of the AtNRTl family were expressed in greater abundance than AtNRT2 genes (Figure 3-1). Despite diverse levels of transcript abundances it was possible to detect expression patterns of all eleven NO3" transporter genes (Figures 3-2 to 3-6). From the responses to NO3" exposure, genes were categorized into three groups, namely, nitrate-inducible, nitraterepressible, and nitrate-constitutive. In all of the following, plants that had been grown for 5 weeks with ammonium nitrate were N-deprived for 1 week and then re-exposed to 0.5 m M Ca(N0 ) for up to 72h. 3  2  Nitrate-inducible Genes Three genes in this category, AtNRT2.1,  AtNRT2.2  and AtNRTl.1  showed very strong  induction (>3 to 5-fold increases) in root tissues following exposure to 1 m M NO3", while other genes showed only modest increases in roots or shoots under the same conditions. In  46  Shoot  Root  Duration of induction (hour)  A  0  AtNRT2.1 18S  #*• *  3  6  6N§ • • • .  -  •  12 24 48 72 *'•««• •  B  Duration of induction (hour)  0  3  6  12 24 48  72  4 ,  ,  ,  ,  »  s  200  AtNRT2.2 + 18S •  200 00  150  £j 100 I 50 0  I  I  *•.  •—•  — •  0  24  48  Time (hour)  72  24  48  72  Time (hour)  Figure 3-2. Expression patterns of nitrate-inducible AtNRTl genes. RT-PCR products were obtained from 6-week-old Arabidopsis plants, which were grown hydroponically for 5 weeks and supplied with 0.5 m M N H N 0 . Plants were N deprived for 1 week (Oh), and then re-supplied with 0.5 m M C a ( N 0 ) for 3-72h. Relative values were obtained by the ratio of the gene specific amplicon over the 18S amplicon. The values shown are means of three RT-PCR replicates. Bars indicate SE. AtNRTl.l in shoot (A), root (B), AtNRTl.l in shoot (C), root (D). 4  3  3  2  47  Shoot  Root  Duration of induction (hour) 3  6  12  24  48  Duration of induction (hour)  72  3  6  12  24  48  72  AtNRT2.4 18S 200 co  ^  150 h 100  X  or £  50  0  0  24  48  72  Time (hour)  AtNRT2.3+~ 18S+~  24  48  Time (hour)  Figure 3-2 (continued). AtNRT2.4  in shoot (E), root (F); AtNRT2.3  in shoot (G).  48  Shoot Duration of induction (hour) A  0  AtNRTl.l  —  3 mmm  6  12 24  48 72  *•*•» «•«"* mmm ~ m  18S  * ~  —  —  —  200  2  150  £ 100 I |  50 0  Root  B AtNRTl.l 18S 400  —i  i  i  24  48  72  Time (hour)  Figure 3-3. Expression patterns of nitrate-inducible AtNRTl genes. RT-PCR products were obtained from 6-week-old Arabidopsis plants, which were grown hydroponically for 5 weeks and supplied with 0.5 m M NH4NO3. Plants were N deprived for 1 week (Oh), and then re-supplied with 0.5 m M Ca(N03)2 for 3-72h. Relative values were obtained by the ratio of the gene specific amplicon over the 18S amplicon. The values shown are means of three RT-PCR replicates. Bars indicate SE. AtNRTl.l in shoot (A), root (B).  49  Shoot Duration of induction (hour) 0  3  6  12  24  48 72  AtNRTl.3 18S 250 co  200  CO  CO  D AtNRT1.4 18S  flHP  M  i  M  B  4Mfll  W  *  250 CO  200  1 24  48  Time (hour)  Figure 3-3 (continued). AtNRTl.3 in shoot (C); AtNRTl.4 in shoot ( D ) .  72  Shoot Duration of induction (hour) 0  3  6  12  24  48  72  CO CD  100  50 0  •  Root  B  AtNRT2.7 18S  WHV  *MW*  mmm 4HW  150 oo  oo  > 100 |  50  Root AtNRTl.3 18S  24  48  Time (hour) Figure 3-4. Expression patterns of nitrate-repressible AtNRT genes. RT-PCR products were obtained from 6-week-old Arabidopsis plants, which were grown hydroponically for 5 weeks and supplied with 0.5 m M NH4NO3. Plants were N deprived for 1 week (Oh), and then re-supplied with 0.5 m M Ca(N03)2 for 3-72h. Relative values were obtained by the ratio of the gene specific amplicon over the 18S amplicon. The values shown are means of three RT-PCR replicates. Bars indicate SE. AtNRT2.7 in shoot (A), root (B); AtNRTl.3 in root (C). 51  Root  Shoot Duration of induction (hour) 0  A AtNRT2.5 18S  3  Duration of induction (hour)  6 12 24 48 72 I  w  •  • *  .....  HUH  co 2 0 0  Ms*  4Mto4  IWWI  200  CO  \  150h  io  f t  • i  1  150  i  100 50  £ 1001  0 0  co 2 0 0 CO  \  150  CO  100 §  50 0  24  48  72  Time (hour) AtNRT2.3 18S  24  48  T i m e (hour) Figure 3-5. Expression patterns of nitrate-constitutive AtNRT2 genes. RT-PCR products were obtained from 6-week-old Arabidopsis plants, which were grown hydroponically for 5 weeks and supplied with 0.5 m M NH4NO3. Plants were N deprived for 1 week (Oh), and then re-supplied with 0.5 m M Ca(N03)2 for 3-72h. Relative values were obtained by the ratio of the gene specific amplicon over the 18S amplicon. The values shown are means of three RT-PCR replicates. Bars indicate SE. AtNRT2.5 in shoot (A), root (B); AtNRT2.6 in shoot (C), root (D); ArNRT2.3 in root (E). 52  Root  Shoot Duration of induction (hour) 0  3  6  12 24  B  48 72  AtNRTl.2 18S  Duration of induction (hour) 0  3  6  12  24  48 72  • 4 M B S M i *• • * - » i •i  •  V I M * mm  « M »  co 150 oo  CM  |  h  100  Hj—.  1  —i  50 0 0  24  48  72  Time (hour)  c  AtNRT1.4 18S CO oo  24  48  72  Time (hour)  Figure 3-6. Expression patterns of nitrate-constitutive A t N R T l genes. RT-PCR products were obtained from 6-week-old Arabidopsis plants, which were grown hydroponically for 5 weeks and supplied with 0.5 m M NH4NO3. Plants were N deprived for 1 week (Oh), and then re-supplied with 0.5 m M Ca(N03)2 for 3-72h. Relative values were obtained by the ratio of the gene specific amplicon over the 18S amplicon. The values shown are means of three RT-PCR replicates. Bars indicate SE. AtNRTl.2 in shoot (A), root (B); AtNRTl.4 in root (C). 53  the AtNRTl  family, AtNRTl.1  showed the strongest induction by NO3" in roots (Figure 3-  2B). By three hours of NO3" provision, the expression level had reached > 5 fold that of Oilplants. This peak was sustained for up to 24h, followed by a gradual reduction to about half of the peak level by 72h. In shoots, on the other hand, there was only a small enhancement in the expression of AtNRTl. 1 after 3h of exposure to NO3", followed by rapid downregulation after 6h, until by 24 h the level was lower than it had been at Oh. Transcript level in shoots was less than 1% of that observed in roots based on the fact that shoot P C R required 7 times the number of PCR cycles and 10 times more R N A template than root PCR (Figure 3-2A, Table 3-1). AtNRT 1.1 was also induced by N 0 " both in roots and 3  shoots. As was the case for AtNRTl.1,  this was more pronounced in roots where 4 fold  increases in transcript abundance were evident by 3h. However, after this peak, expression levels were quickly down-regulated and returned to a value that was close to the original level by 24h (Figures 3-2C and 3-2D). This rapid down-regulation was different from that observed for AtNRTl. 1, although the expression level of AtNRTl. 1 was initially similar to 1.1 as we described earlier. AtNRTl.1  in shoots as well as AtNRTl.4  in both in shoots and  roots showed similar expression patterns which were characterized by modest increases culminating in peaks at 3h followed by declines that stabilized by 24h (Figures 3-2C, 3-2E, and 3-2F). AtNRTl.1  also showed a strong induction by N C V i n roots. The induction peaked  rapidly, as early as the third hour of NO3" provision, and reached a maximum level that was 2.5 times that of the Oh. This high level of transcript was sustained from 12h to 48h (Figure 3-3B). The expression of AtNRTl.1  in shoots showed a similar pattern to that of AtNRTl. 4,  namely a small spike at 3 hours, followed by a return to a level that was as low as the  54  original level (Figure 3-3A). AtNRTl.1  Interestingly, unlike AtNRTl.I,  the expression level of  was equal to, or even higher in shoots than roots considering both the PCR cycle  numbers and R N A template provided (Table 3-1, Figures 3-3A, and 3-3B). There were three genes, AtNRTl.3  = 1.4 > 1.3, which were induced by nitrate only  in shoots (Figure 3-2G, 3-3C, and 3-3D). The expression patterns of those genes in the roots will be described later. AtNRTl.3  was induced slowly, reaching peak expression that  was 90% higher than at time 0 h, only after 48 h of NO3" provision (Figure 3-2G). AtNRTl.3  expression level in the shoots was much lower than that in the roots (based on a  requirement for 10 times as many PCR cycle numbers as in the roots) (Table 3-1). In fact, within shoot transcript abundance of this gene was among the lowest of all of the NRT family of genes. AtNRTl.3  expression level was also gradually induced, increasing to more  than 2 fold at 48h, although there was a slight decline during the first 6 hours. However, there was subsequently a significant down-regulation, which began at 48h, reducing transcript abundance to a level that was similar to that at 24 h (Figure 3-3C). Another NRT1 family member, AtNRTl.4  also had a slow induction pattern, reaching the plateau  after 48h, a level that was maintained for the next 48 hours (Figure 3-3D).  Nitrate-Repressible Genes In contrast to NO3"-inducible genes, there were some genes whose transcript abundances were actually reduced by nitrate provision. AtNRTl.7  conformed to this pattern, in both  roots and shoot, while this pattern was only observed in roots for AtNRTl.3.  Highest levels  55  of AtNRT2.7 were evident prior to the provision of nitrate (Oh). By 3-6 h after exposure to I m M NO3", transcript abundances had declined to 50% (shoots) and 25% (roots) of the Oh values (Figures 3-4A and 3-4B). Although both shoots and roots shared a similar response pattern, roots responded more rapidly than shoots. It is also notable that the transcript abundance in roots was more than 100 times higher than that of the shoots at Oh (Table 3-1, Figures 3-1). AtNRTl.3  also revealed a repressible pattern in the roots, although gene  expression was induced by NO3" in the shoots (Figures 3-3C and 3-4C). The initial response to nitrate provision was as rapid as that of AtNRT2.7 in the roots. However, after 6h, expression level decreased, reaching a value that was about 30 % of the initial (Oh) value by 48h (Figure 3-4C).  Nitrate-Constitutive Genes The third group of nitrate transporter genes is described as constitutively expressed. A characteristic pattern of this group is that substantial transcript abundance was already present even under NO3"-starved conditions (Oh), and the expression levels did not change substantially during 72 h of exposure to NO3". AtNRT2.5 and 2.6 in the NRT2 family, and AtNRTl.2  in the NRT1 family showed such a constitutive expression pattern both in shoots  and roots, wherein the fluctuations of expression levels were less than ± 50 % (Figures 3-5 and 3-6). Interestingly, the expression level of AtNRT2.5 in the shoot was higher than that in the roots (Figures 3-1, 3-5A, and 3-5B). This is unique in the AtNRT2 family because all other members had greater transcript abundance in roots (Figure 3-1). Although  AtNRTl.2  56  expression level in shoots was -10% of that in roots, this gene was among the most highly expressed of shoot-expressed genes. Given that the AtNRTl.2  is constitutively expressed,  overall, this is one of the most highly expressed nitrate transporter genes throughout the plant during all stages of our investigation. As mentioned earlier, AtNRT2.3 showed a nitrate-inducible pattern in the shoots, but its expression in roots was essentially constitutive, although a slight down-regulation was observed during the first 6 hours (Figure 3-5E). Besides differences in root/shoot expression patterns, expression levels were also significantly different (i.e., root levels were typically -10 times higher than those of the shoots) (Figure 3-1). The expression of AtNRTl.4  in the roots also showed a constitutive pattern (Figure 3-6C). This insensitivity to  NO3" did not match its shoot expression where the gene was induced by NO3" provision (Figure 3-3D). Similar to AtNRT2.5 and AtNRTl.l,  AtNRTl.4  was the third gene whose  expression levels were higher in shoots than in roots (Figure 3-1).  3.4 Discussion The present study using RT-PCR clearly showed that all 11 NO3" transporter genes were expressed in roots and shoots, whereas previous reports have claimed that expression levels of nitrate transporters in the shoots were either extremely low or undetectable. This applies specifically to AtNRT2.1 (Filleur and Daniel-Vedele, 1999; Zhuo et al., 1999), AtNRT2.2 (Zhuo et al., 1999), AtNRTl.l  (Tsay et al., 1993), and AtNRTl.2  (Huang et al., 1999). Our  successful demonstration of shoot expression of these genes, though in low abundance, is  57  probably due to the greater sensitivity of the RT-PCR method but might also result from differences in plant growth conditions among different laboratories. In previous reports plants were grown in sterilized systems where sucrose was added in the media (Tsay et al., 1993;  Huang et al., 1999; Zhuo et al., 1999). Sucrose additions to growth media have been  documented to produce significant effects at both the physiological and molecular levels. Hanisch and Breteler (1981) showed that exogenous sucrose application restored the decreased nitrate uptake rate and nitrate reductase activity to 83 % and 108 % of the level of the intact plants, respectively, in decapitated dwarf bean roots. This indicated that carbon metabolites normally provided through photosynthesis could be compensated for by sugar supplement via root tissues. In Arabidopsis 1 % sucrose in the media stimulated transcripts of A t N R T l . 1 and AtNRT2.1,  and nitrate influx during dark periods (Lejay et al., 1999). On  the other hand, photosynthetic genes were down-regulated by sugars in isolated maize mesophyll protoplasts (Sheen, 1990). Furthermore, Krapp and Stitt (1995) demonstrated that a cold-girdle treatment on spinach leaves led to an increase of sugar contents in the leaves, and inhibition of the rate of photosynthesis and expression of photosynthetic genes. In addition, when sucrose is provided via roots, any carbon limitation upon NO3" reduction and  assimilation is removed and in contrast to plants growing without sucrose, it is  reasonable to expect that there might be greater root than shoot assimilation of nitrate. Therefore, it is obvious that the presence of sucrose in the growth media has effects on N and C-metabolism, the localization (root versus shoot) of these activities, and its expression levels of genes involved in these processes at the gene and physiological levels, although the mechanisms of the interactions between sucrose and nitrate transporters are not clear (Coruzzi and Bush, 2001).  58  Although the patterns of, and extents of, expression levels of the genes were variable, we grouped all members into three categories in order to organize the information generated. Most of those genes investigated had similar expression patterns in roots and shoots. However, in specific cases, such as AtNRT2.3,  and 1.3, expression patterns were  quite different between roots and shoots (Figures 3-2 to 3-5). Another example of different expression patterns within the same plants was observed through a split-root experiment. The expression level of AtNRT2.1  in one portion of the roots under steady state condition  was up-regulated by N-depriving the other portion of the roots where NRT2.1  expression  was slowly down-regulated (Gansel et al., 2001). The result indicated that NRT2.1  was  controlled not only by local N-supply but also shoot-root signals of N demand (Gansel et al., 2001). Interestingly, the authors observed a different response with respect to A t A M T l . l expression which seemed to be controlled primarily by local conditions. In the present study, the N-pool size within the plant tissues changed during the period following re-provision of nitrate. These changes of nitrate concentration as well as amino acid pools are probably important in the regulation of some NRT genes, resulting in different expression patterns within the plant. To date, since little is known about the nitrate transporters and transport systems in shoots, we are not able to define the roles of specific NRT  genes in shoots, other than the stated importance of absorbing NO3" into leaf cells  from the leaf apoplasm. Yet, further proposed functions of the NRT nitrate transporters will be discussed in chapter 5. On the basis of correlations between physiological patterns of NO3" influx and corresponding patterns of gene expression, it has been suggested that the NRT2 proteins probably play a major role in inducible H A T S in A r a b i d o p s i s (Zhuo et al., 1999; Lejay et  59  al., 1999), N. p l u m b a g i n i f o l i a (Krapp et al., 1998), soybean (Amarasinghe et al., 1998), and barley (Glass et al., 2001). In this study A t N R T 2 . 1 , 2.2 and 2.4 showed nitrate-inducible patterns, suggesting that these genes might be involved in iHATS activity (Table 3-2). However, it is evident from the foregoing results, that not all members of the NRT2  family  of genes can be characterized as nitrate-inducible. The present findings demonstrate that "nitrate-inducible" is not a universal characteristic of the NRT  genes. Rather it appears that  two other characteristics, nitrate-constitutive, and nitrate-repressible must be included in the characteristics of these gene families. It is also apparent that Arabidopsis has substantial NO3" uptake capacity even prior to exposure to NO3" (Zhuo et al., 1999). Therefore, genes, which show nitrate-constitutive properties such as AtNRT2.3, in cHATS activity (Table 3-2). AtNRT2.4  2.5, and 2.6, might have roles  showed significant transcript abundance even in  un-induced plants, although this gene was considered to be nitrate-inducible because of its expression pattern (Figure 3-2F). According to physiological studies by Aslam et al. (1992) and Kronzucker et al. (1995), the constitutive flux of NO3" into roots of barley and white spruce was increased by exposure to NO3". Therefore a feature of the gene(s) encoding this NO3" flux would be (a) constitutive expression that is (b) increased by exposure to NO3". Thus, AtNRT2.4  might also be involved in the cHATS. Wang et al. (Wang and Crawford,  1996) isolated a mutant, which was impaired only in the cHATS transport in roots of A r a b i d o p s i s . It will be interesting to see i f this mutation is located in one of the aboveproposed candidates. In the same way, low-affinity nitrate transporter (AtNRTl) family members are predicted to have a role in i L A T S and cLATS, according to their nitrate-inducible, and nitrate-constitutive patterns, respectively (Table3-2). A Ml mutant study showed that  60  Table 3-2. AtNRT Genes and hypothesized nitrate transport systems Response to Nitrate (root)  Transport System  AtNRT2.1  Inducible  iHATS  AtNRT2.2  Inducible  iHATS  AtNRT2.3  Constitutive  cHATS  AtNRT2.4  Inducible  iHATS, c H A T S  AtNRT2.5  Constitutive  cHATS  AtNRT2.6  Constitutive  cHATS  AtNRT2.7  Repressible  ?  AtNRTl.l  Inducible  iLATS , HATS  AtNRTl.2  Constitutive  cLATS  AtNRTl.3  Inducible  iLATS  AtNRTl.4  Constitutive  cLATS  Gene  61  NH4NO3  grown mutant plants had about 75 % less nitrate influx, compared to WT in the  L A T S range (Touraine and Glass, 1997), and this defect was found even at cHATS and iHATS activities (Wang et al., 1998b; L i u et al., 1999). As a consequence it has been suggested that AtNRTl.l  may encode both high- and low-affinity transporters. In the  present study AtNRTl.l(CHLl)  and 1.3 in roots showed nitrate-inducible patterns.  Therefore, these genes are candidates for i L A T S activity (Table 3-2). AtNRTl.2  showed a  nitrate-constitutive expression partem and this is consistent with an earlier report, which demonstrated that transgenic plants expressing antisense AtNRTl.2  showed reduced levels  of low-affinity nitrate transport (Huang et al., 1999). Given that AtNRTl.4  also displayed a  similar expression pattern, these two genes are predicted to be involved in cLATS activity (Table 3-2). The third category of nitrate-repressible genes represents the most puzzling group. This response is largely unknown at the physiological level, except that it might be speculated that when NO3" is removed from the external medium there begins a net transfer of NO3" from vacuole to cytoplasm (Zhen et al., 1991; Glass and Siddiqi, 1995). Normally this transfer exhausts the vacuolar reserve within 3-4 d (van der Leij et al., 1998 and references therein; Okamoto, unpublished data). When NO3" is re-supplied, the [NO3"] of the vacuole restored. It is possible that genes encoding transporters involved in the transfer of NO3" from vacuole to cytoplasm are down-regulated when NO3" is re-supplied in order to restore vacuolar [NO3"] to its normal level. However, it is unclear from the molecular perspective whether members of the NRT2 family might function as tonoplast transporters since there is no indication of the appropriate signal peptide to direct expression of the transporter to the tonoplast (Chapter 2).  62  4 Tissue-Specific Expression Patterns of AtNRT Genes 4.1 Introduction It is reasonable to presume that nitrate absorption occurs mainly from the rhizosphere where most nutrients are available. In the present study, I have documented that six genes out of the seven NRT2  family members are expressed more dominantly in roots than shoot  (Chapter 3). The expression patterns of, and levels of expression genes of the NRT families were diverse. However, whole root and whole shoot analysis leave many questions unanswered. For example, how is the expression of NRT  genes localized within different  tissues? Is there any correlation between the expression patterns from total RNA analysis of roots or shoots and tissue-specific expression patterns? A t N R T l . 1(CHL1)  was the first gene among the NRT families of genes to be  investigated with respect to its tissue-specific expression by using in situ hybridization (Huang et al., 1996). A t N R T l . 1 mRNA accumulation was observed primarily in the epidermal tissues in young roots, while mainly in the cortex or endodermal cells in mature roots. Similar results were also obtained by GUS/GFP  fusion lines, where the 5' flanking  63  and partial coding regions of the AtNRTl.l  were fused in frame with either green  fluorescent protein (GFP) or ^-glucuronidase (GUS) reporter DNAs (Guo et al., 2001). The authors, furthermore, found that AtNRTl.l roots  and  shoots,  including flowers.  was expressed in nascent organs in both  The  findings  were  also  verified  with  immunolocalization using polyclonal antibodies raised against the A t N R T l . l protein (Guo et al., 2001). In contrast to AtNRTl.l, AtNRTl.2 was highly expressed in the epidermis and root hairs regardless of the stage of root development (Huang et al., 1999). These locations are consistent with the belief that NRT1 genes are involved in NO3" uptake. As well, it is possible that AtNRTl. 1(CHL1) has a role in early organ development (Guo et al., 2001). Among cloned NRT2 genes, NpNRT2.1 from Nicotiana plumbaginifolia was the only gene that has been analyzed for its tissue-specific expression pattern. The accumulated mRNA was localized in the epidermal and endodermal cells of the root tip, while lateral root primordia were the main targets in mature roots (Krapp et al., 1998). To date, no publication is available detailing the tissue localization of the NRT2 gene expression in Arabidopsis. Therefore, this work was particularly focused on the NRT2 family genes. To investigate NRT2 gene expression at the cellular level, transgenic plants were produced, which carry the promoter regions of AtNRT2 genes fused to GUS reporter genes. Four gene constructs (i.e., AtNRT2.1-GUS, 2.2-GUS, 2.4-GUS, and 2.6-GUS) showed GUS signals. Predominant expression was observed in roots as expected, but each gene had an unique expression pattern. AtNRT2.1 and AtNRT2.6 were also expressed in shoots. The significance of each expression pattern will be discussed.  64  4.2 Materials and Method Construction of NRT2-GUS Fusion Genes The NRT2.1  promoter region was obtained from a plasmid pCRN2.1pro which contained  1.2 kb upstream flanking sequences and the start codon of A t N R T 2 . 1 . To fuse the promoter region to the GUS reporter gene, a Hindlll-Ncol fragment from pCRN2.1pro was cloned into the corresponding sites of pBI320X. A Hindlll-SacI fragment from the pBI320X, consisting of the NRT2.1 promoter region, G U S , and NOS3', was then ligated into the corresponding sites of a binary vector pMOG402. The promoter regions from the rest of NRT2  gene family members were cloned by  PCR. Primers used to amplify each 5' franking region were: N2.2P5 (5'A A G C T T C A A C A G A G G G G A A C A C C G G C C A C G ) , andN2.2P3 (5'G G G C T C A T C A G T A G A A C C C A T G G A T T T T A A A G C ) for N R T 2 . 2 , N2.3P5 (5'-), and N2.3P3 (5' - A C A A A C A T T A A A A T C C A G T G G C A G C C A T G G T A A ) for N R T 2 . 3 , N2.4P5A (5' -TCT A A G C T T C C A G T T T A A A T T T C T A T A T A A T T G AG), andN2.4P3 (5'C A T C G G G C C A T G G T G T G A A T A T T T ) for NRT2.4,2.5P5-1  (5'-  A A G C T T T C C A T C C T C A C C C T G C A G A A G C A C ) , and2.5P3-l (5'G C A A A A C A A G A C A T G G T T A G T T T G T A T C C A A A A ) for NRT2.5,  N2.6P5 (5'-  A A G C T T T C T A A A A T A T G A G T T T A C G T T C C A A ) , andN2.6P3 (5'G T G A G C C A T G G A T C T T T A G T T C A A A G A ) for NRT2.6,  andN2.7P5 (5'-  A A G C T T C T G A T C C C C G A T C T C A A G T A T T G A C T ) , andN2.7P3 (5'C C A T G G T T G T G A T C T T T G T G A A G G T T C A G A G A A T T T T G ) for NRT2.7.  These primer  65  sets amplified the promoter regions of 1.2-2.0 kb. PCR was carried out using Expand High Fidelity PCR System (Roche, Laval, QC) under the following conditions: 94 °C for 2 min; 10 cycles of 94 °C for 15 s, 65 °C for 30 s, 72 °C for 2 min; 20 cycles of 94 °C for 15 s, 65 °C for 30 s, 72 °C for 2 min + cycle elongation of 5 s for each cycle; 72 °C for 7 min. The fragments were cloned into pCR2.1. A Ncol-Xhol fragment in the pCR2.1 was introduced to pBI320.X, and resulting fusion gene, NRT2.X-GUS-3 (NRT2.1,  2.2, and 2.4) or pMOG402 (NRT2.3,  'NOS, was cloned into pBIN+  2.5, 2.6, and 2.7).  Plant Transformation Binary vectors, which contained the fusion genes, were transformed into A g r o b a c t e r i u m tumefaciens  strain GV3102. Transformation into Arabidopsis plants was carried out  according to Clough and Bent (Clough and Bent, 1998). Overnight cultures of A g r o b a c t e r i u m ( I L LB) grown at room temperature ( O D 6 0 0 - 0.8-1.0) were harvested and re-suspended in 500mL of inoculation media, containing 5% sucrose and 0.005% Silwet lull (Lehle Seeds, Round Rock, TX). A r a b i d o p s i s plants (ecotype Columbia) were grown in soil (Redi-Earth Potting Soil, Grace-Sierra Horticultural Co., Lansing, MI) until flowering stage in a controlled-environment chamber with 24/18°C at 16/8h of light/dark cycle. Whole shoots of 4-5 week-old plants (flowering stage) were dipped in the inoculation media containing appropriate A g r o b a c t e r i u m strain for 60 sec twice. The whole plants were then covered with a plastic bag to maintain moisture for the next two days. Seeds ( T l generation) were harvested when sliques turned yellow to brown. T l seeds were selected on respective selection substrates (i.e., 25mg L" kanamycin for N R T 2 . 1 , 2.2, 2.4 on petri 1  66  plates; 25mg L" Basta with 0.02% Silwet L-77 for NRT2.3, 1  2.5, 2.6, 2.7 applied by spray  on soil grown plants). Basta selection was also performed on petri plates with lOmg L"  1  Basta. The selection media for plates contained Vi M S medium (Murashige and Skoog, 1962), 1% sucrose, 0.8% agar, 0.5g M E S in I L , pH 5.7. Subsequent GUS analysis was based on the T2 generation.  G U S Staining T2 seeds were germinated on selection plates after surface sterilization, and resistant plants were transferred onto growth plates (i.e., same as selection plates without kanamycin or Basta) for up to 2 weeks for vegetative stage or 3 weeks for flowering stage. The plants were then grown on a N-free plate (nutrient composition was the same as for the hydroponic solution in Chapter 3, omitting sucrose) for 1 week before plants were induced with l m M N 0 " . 3  Harvested plant materials were washed with water and placed in a 24-well plate or in small petri dishes. X-Gluc solution (0.5 m M 5-bromo-4-chloro-3-indolyl-P-Dglucoronide cyclohexylamine salt (Rose Scientific Ltd., Edmonton, AB), lOOmM sodium phosphate buffer p H 7, 0.1% Triton X-100, 2mM ferricyanide (K Fe(CN) ), 2mM 3  6  ferrocyanide (K4Fe(CNV3H20)) was added until whole plants were submerged. After vacuum infiltration, the solutions with plants were incubated at 37°C for 4-5 hours or overnight. The plants were "bleached" with a series of EtOH solutions (20% to 95%).  67  Cross-Sectioning and Histochemical Analysis GUS stained roots were investigated more thoroughly after sectioning in transverse and/or longitudinal planes. The root tissues fixed in 80% EtOH were dehydrated in a scintillation vial as follows: 30 min in 90% EtOH, 30 min in 95% EtOH, 3 times 30 min in 100% EtOH (molecular sieve-treated to get rid of traces of H2O). Subsequently, the tissues were embedded in Spurr's resin (J.B. E M Service Inc. Dorval, QE) prepared by following the manufacture's manual. The specimens were given an additional 100% EtOH change (1ml) before the embedding process. The concentration of resin was raised gradually as follows: one drop of resin was added into the vial and gently mixed for 5 min; two drops of resin were added and mixed for 5 min; the last step was repeated; two drops of resin were added and mixed for 45 min. One half of total volume of the resin/EtOH solution (=0.55 ml) was removed and replaced with the same volume of resin (mixing for 90 min). This was repeated once more and left on a rotary shaker overnight. On the subsequent day, the solution was replaced with 100% resin and mixed for 5h. Then the resin was refreshed once, and the solution was mixed overnight without cap, but with aluminum foil as a cap to let EtOH evaporate from the solution. After the incubation period, the solution was replaced with new resin. Finally, the tissues in the solution were transferred to an aluminumweighing dish with fresh resin, and arranged in the appropriate orientation under a dissecting microscope. The polymerization of resin was achieved in an oven at 60 ° C overnight. A trimmed polymerized block was sectioned in 2-4 urn thickness with a microtome (Reichert, Model OM-U3, Austria). Images of the samples were captured in digital formats with a SPOT system (Diagnostic Instruments Inc. Sterling Heights, MI).  68  4.3 Results Tissue-Specific Expression Patterns of NRT Genes To visualize the specific expression patterns of AtNRT2 genes within the tissue, the promoter regions of each member of the family were fused to GUS reporter gene. AtNRT2.3, 2.5 and 2.7 were unable to be used as subjects for further analysis either because no G U S activity was shown or an insufficient number of positive transformants were observed. Therefore only AtNRT2.1, 2.2, 2.4, and 2.6 were investigated in detail. A transgenic line which carried AtNRTl.1(CHL1)-GUS  (Guo et al., 2001), donated by the authors was also  analyzed for comparison. Since AtNRT2.1, 2.2, 2.4, and / . / are nitrate-inducible, the plants were first N-deprived for lweek, and then, re-induced by 0.5 m M Ca(N03)2 for 6 h (see detail in Materials and Method). More than eight lines of transformants from each construct were examined, and the studies that showed the reproducible results, were repeated at least three times. The pictures in the figures are representative of those experiments.  AtNRT2.1 In 3-week-old plants, blue GUS staining was found in entire roots, with stronger staining in the mature region of the root and in the root tip. By contrast, staining was minute or absent from the root cap and distal region close to the hypocotyls zone (Figures 4-1). The gradient of GUS activity is evident along the younger part of the root (Figure 4-1 A). From the meristematic to elongation zones GUS staining is lighter than in the mature region. In the  69  ire 4-1. Analysis of GUS activity in AtNRTl.1 plants.  promoter-GtTS'Arabidopsis  GUS histochemical staining in a root of an A t N R T l . 1 promoter-GcTS plant. Bar = 0.5 mm. Close up of root tip. Bar = 200 um. Basal region of a plant. Bar - 1 mm Close up of a lateral root near the basal region. Bar=0.5 mm.  70  Figure 4-1. (continued). (E) Longitudinal section close to a root tip. Low level of GUS expression in the outer most layer of the root cap. Bar = 50 um. (F) Cross-section of a root (5 mm from a root tip), c, cortical cells; e, epidermal cells; en, endodermal cells. Bar = 50 um. (G) Fully expanded leaf. GUS staining is seen in hydathodes indicated with arrows. (H) High magnificication near a leaf hydathode. Bar = 200 um.  more mature roots, developing lateral roots showed stronger GUS activity than the parental root (Figure 4-ID). To look at more detail of the localization, sectioning of the fixed samples was carried out (Figures 4-1 D and E). GUS activity was seen in epidermal cells, cortex, and endodermal cells, although the strongest signals were observed in the epidermal cells. In shoots GUS staining was especially evident in leaf hydathodes (Figures 4-1G and F).  AtNRT2.2  GUS expression in an AtNRT2.2  promoter-GUS plant is shown in Figure 4-2. GUS staining  was found in recently developed roots, but was absent in the tissue close to the root tip (Figure 4-2A). When lateral roots appeared, GUS activity was found in the newly developing root, whereas the parental root showed only faint GUS  staining (Figure 4-2B).  Once lateral roots developed to a certain stage where root hairs start appearing, the blue GUS  staining in the parental root completely disappeared (Figure 4-2C). However, the  intensity of GUS activity was not uniform. Figure 4-2D shows this irregular pattern along a root, and the GUS staining was primarily in epidermal cells and root hairs. There was no GUS activity in shoots including leaves, stems and flowers (data not shown).  AtNRT2.4  GUS  activity was primarily seen in developing or recently developed roots (Figure 4-3).  Similar to that of AtNRT2.2,  GUS staining in A t N R T 2 . 4 - G U S plants was absent in the  region of the primary root where lateral roots grew (Figure 4-3A). In a developing lateral root GUS staining was strong, although in the regions of the apical meristem and the root  72  Figure 4-2. Analysis of GUS activity in AtNRT2.2 plants. (A) Bar (B) (C) (D)  promoter-GcTS Arabidopsis  GUS histochemical staining in a root of an AtNRT2.2 promoter-GUS plant. = 0.5 mm. GUS staining in a lateral root. Bar = 100 um. GUS staining is localized in secondary roots. Bar = 1 mm. High magnification of GUS staining in the root hair zone. Bar =100 um.  73  Figure 4-3. Analysis of GUS activity in AtNRT2.4 promoter-Gc/S Arabidopsis plants. (A) GUS histochemical staining in roots of an AtNRT2.4 promoter-GC/S plant. Bar = 2 mm. (B) Lateral root. Bar = 200 um. (C) GUS staining in root close to a root tip. Bar = 100 pm. (D) Longitudinal section of root close to a root tip. Bar = 100 um. (E) and (F) No GUS activity in flowers (E), or leaves (F).  74  tip were not the targets for the expression (Figure 4-3B). Developed roots showed GUS activity in the root tip region, where the staining was placed in one to two layers of cells from the surface i.e., the root cap (Figures 4-3C and D). Shoot tissues showed no GUS activity (Figures 4-3E and F).  AtNRT2.6  GUS  activity in A t N R T 2 . 6 - G U S plants was seen both in roots and shoots (Figure 4-4). In  roots, the zone of maturation (including root hairs) showed the strongest GUS staining, although the expression was absent from the basal region, and from the root tip and zone of elongation (Figures 4-4A and B).  Cross-sections of the region close to the root tip showed  that GUS activity was primarily seen in the epidermis, endodermis, and pericycle (Figure 44C). In shoots, GUS  staining was specifically seen in the anthers of flower buds (Figures  4-4D). Under N-starvation the anthers of opened flowers also showed GUS activities, while N-fed plants seemed to have less or no GUS activity in the anthers (Figures 4-4E and F). Higher magnification and dissection analysis revealed that GUS  staining was localized in  pollen grains (Figures 4-4F and G).  AtNRTl. 1(CHL1)  A t N R T l . 1 promoter-Gt/5 plants obtained from Guo et al. (2001) were also induced by 1 mM NO3" for 6 h, and subjected to GUS root tips and leaves (Figure 4-5). GUS  staining. Strong GUS  activities were noticeable in  expression in a newly developed root was primarily  seen in outer layers (Figures 4-5A and B). The layers were verified as epidermal cells and  75  Figure 4-4. Analysis of GUS activity in AtNRT2.6 plants.  promoter-Arabidopsis  (A) GUS histochemical staining in a root of an AtNRTl. 6 promoter-GITS' plant. Bar = 0.5 mm. (B) Middle section of a root. GUS staining is fading out toward the basal (to the left in the picture) section. Bar = 100 um. (C) Cross section of a root 1 cm from the tip. c, cortical cells; e, epidermal cells; en, endodermal cells; p, pericycle. Bar = 50 um.  76  Figure 4-4. (continued). (D) GUS staining in a flower bud of an AtNRT2.6 promoter-GUS plant. G U S activity is seen in anthers. Bar = 200 um. (E) GUS staining in uninduced plants. Flower buds as well as opened flowers (indicated with arrows) show some GUS activities. (F) GUS expression in nitrate-induced plants. G U S staining is concentrated in developing flower buds, and diminished in opened flowers. (G) Higher magnification of an anther from a flower bud. G U S staining is seen in pollen grains. Bar = 100 um. (H) Higher magnification of pollen grains from a dissected anther. Bar = 50 um.  77  Figure 4-5. Analysis of GUS activity in AtNRTl.l plants.  promoter-Gc/S' Arabidopsis  (A) GUS histochemical staining in a root of an AtNRTl.l promoter-GCZS plant. Bar = 0.5 mm. (B) Strong GUS staining around a root tip. Bar = 200 um. (C) High magnification of mature section of a root. GUS staining is seen in the epidermal cells. Bar = 200 um.  78  ^^^^^^^^^^^^^^^^^^^  Figure 4-5. (continued). (D) GUS staining in leaves of an AtNRTl.l promoter-GiVS" plant. (E) Close up of a leaf. GUS staining is stronger along the vascular system. (F) Higher magnification of leaf surface. (G) GUS staining in a petiol. (H) GUS staining in a sepal. (I) Higher magnification of a sepal. Bars in (E), (G), and (H) = 200 urn, (F), and (I) - 50 urn.  79  cortex in previous studies (Huang et al., 1996; Guo et al., 2001). The GUS activities in these regions gradually disappeared toward the basal of the roots. Instead, the center region of the root took over the localization of GUS expression (Figures 4-5A and C). The region was claimed to correspond to endodermal cells by in situ hybridization (Huang et al., 1996). In shoots, GUS activity was seen in whole leaves, and stronger (dark staining) in the vascular system (Figures 4-5D and E). On the surface of a leaf, GUS activity was also observed in guard cells (Figure 4-5F). This characteristic was clearly visible in petioles and sepals (Figures 4-5G to I).  4.4 Discussion  Analysis of GUS activity controlled by AtNRT promoter genes revealed that each gene member of AtNRT families has a unique tissue-specific expression pattern. Every AtNRT gene, examined in the present GUS study showed GUS expression in roots. This evidence is consistent with the belief that NRT genes are involved in NO3" uptake. AtNRTl.l,  1.1,  and 1.4 showed high sequence similarity, and similar expression patterns as nitrateinducible genes as revealed by RT-PCR with total tissue R N A (Chapters 2 and 3). This highly homologous trio also displayed some similarities in the GUS expression patterns. For example, strong GUS activities were observed in epidermal cells and root hairs for all three genes. AtNRTl.l  and AtNRTl.l  had less or no G U S activity in meristematic and  elongation zones (Figures 4-1B and 4-3C), while AtNRTl.l  and AtNRTl.4 showed no GUS  expression in the older regions of roots where lateral roots emerged (Figures 4-2C and 4-  80  3A), and AtNRT2.1-GUS  expression was localized in both young and mature root regions  (Figure 4-1). This expression pattern perhaps explains why AtNRT2.1 expression level among the NRT2  showed the highest  gene family by RT-PCR in whole root studies (Chapter  3). No GUS staining was found in leaves of AtNRT2.2,  2.4, and 2.6, although RT-PCR  could show the expression patterns of the genes in the shoots (Chapter 3). These discrepancies could be due to their lower gene expression levels (Table 3-1, Figure 3-1), and GUS reporter system might not be sensitive enough to visualize the expression patterns. In N i c o t i a n a p l u m b a g i n i f o l i a , NpNRT2  using in situ hybridization, high-affinity nitrate transporter  was expressed in root tip, and epidermal and endodermal cells in developing roots,  while in older roots the transcript was primarily localized in the lateral root primordial, and there was little expression in the parental root (Krapp et al., 1998). This tissue-specific expression pattern is similar to that of AtNRT2.4, that NpNRT2  although Northern blot analysis showed  expression pattern was more similar to that of AtNRT2.1.  These results  therefore indicate that expression patterns revealed from total R N A and from tissue-specific methods may differ among species. Characterization of additional NRT2 plumbaginifolia  homologues in N.  or other species will solve this issue.  Plant roots experience biochemical gradients both in the longitudinal and the radial axes. Zhen et al. (1991) observed a longitudinal gradient of nitrate concentration in barley roots. The five-day-old roots were grown in 10 m M NO3" and divided into three regions i.e., from the tip, 0-2.5 cm, between 2.5 and 5.0 cm, and >5.0 cm. The middle section (2.5-5.0 cm) had 113.9 m M [NO3"], whereas the root tip and >5.0 cm regions possessed 90.9 and 93.3 m M , respectively. Siebrecht et al. (1995) also measured [NO3"], as well as, NO3" uptake and nitrate reductase (NR) activity along the barley root axis. Net NO3" uptake rates  81  by root tips of 7-day-old plants were half of those of the middle and basal zones. However, nitrate absorbed by root tips was translocated to older root zones, and induced NO3" uptake there. Furthermore, within 20 mm from the tip maximum NR. activity (on a weight basis) was seen at 1mm behind the apex (Siebrecht et al., 1995). These results indicate that nitrate absorption and metabolism in the root tip region may impact upon the rest of the root, although NO3" uptake per se was not high. Among low-affinity nitrate transporters A t N R T l . l was expressed in both mature and lateral root tips (Guo et al., 2001; this study), and A t N R T l . 2 was expressed in epidermal cells in the root tips (Huang et al., 1999). As well, among high-affinity transporters, AtNRT2.1  and 2.4 were expressed in the root tips (the present work). These multiple genes  expressed in the root tips might indicate the significance of this region for NO3" uptake or NO3" sensing. In the soil environment nutrient availability varies depending on mass flow, nutrient diffusion, and interception by root growth (Marschner, 1995), resulting in great soil heterogeneity in nutrient availability (Jackson and Caldwell, 1993; Wo It, 1994). The root tip region, as a "frontier", may have more chance to deal with higher nitrate concentrations in the media than mature regions of the roots, which create a gradient of the nutrient concentration surrounding the roots as a result of withdrawing NO3". In this case, the region close to the root tips might be well served by low-affinity nitrate transporter(s), while older regions of the roots are the zones where high-affinity transporter(s) becomes more important. High-affinity transporters AtNRT2.2  and 2.6 might be involved only in the latter  case, since both genes were specifically expressed in older regions of the roots (Figures 42A and 4-4A).  82  There are two pathways for nutrients to traverse the root in the radial direction. One is called the symplasmic pathway where nutrients enter root tissues through epidermal cells and move through plasmodesmata within the cytoplasm toward the stele. The other pathway is apoplasmic. The solutes enter the cell wall space and can travel through cell walls and intercellular spaces until reaching endodermal cells. Because a suberized Casparian strip is located in endodermal cell walls, solutes are blocked from entering the stele via the apoplasm. Therefore the nutrients need to be absorbed at endodermal cells. A l l of AtNRT  genes in the present study were expressed in the epidermal cells, and  AtNRT2.1,  2.6 and 1.1 (Huang et al., 1996) were also expressed in endodermal cells, indicating that all these genes are involved in symplasmic transport, and the latter group of genes may contribute in apoplasmic transport. Interesting findings involved the expression patterns of NRT genes in shoots. Quantitative relative RT-PCR using total tissue RNA family of genes and AtNRT2.5  extractions revealed that the  AtNRTl  had substantial levels of expressions in shoots (Chapter 3).  This was consistent with the results from transgenic lines which carry A t N R T l . 1 promoterGFP/GUS  genes. AtNRT  1.1(CHL1)  mutant analysis indicated that A t N R T l . 1 is not only  involved in NO3" uptake, but also in the growth of nascent organs both in roots and shoots (Guo  et al., 2001). However, the role of gene expression in the guard cells as revealed by  GUS  expression remains unsolved. It is well known that potassium ion fluxes in and out of  the guard cells to open/close the stomata by osmotic effects. Nitrate, an anion, may act as a counter ion when K moves into the guard cells in order to maintain electrical neutrality +  across the plasma membrane.  83  GUS 4-4D  staining in pollen grains of AtNRT2.6-GUS  plants was a novel finding (Figures  to H). Pollen is rich in nitrogen (N), ranging from 2.5 to 61 % of protein contents  (Roulston et al., 2000), and/or micro-molar concentrations of amino acids can be stored (Schwacke et al., 1999). In fact, flowers are an important diet for some animals because of the high protein content of pollen grains (van Tets and Hulbert, 1999). N-sources in pollen are most likely utilized for pollen development and for producing enzymes which are essential for pollen germination and pollen tube formation. In tomato pollen, proline is a dominant free amino acid (> 70 %), and a proline transporter L e P r o T l was observed to be expressed in mature and germinating pollens (Schwacke et al., 1999). On the other hand, GUS  activity in an A t N R T 2 . 6 - G U S plant was found primarily in pollen grains in flower  buds, suggesting that nitrate might be important for pollen development. One might argue that plants can grow and reproduce without nitrate as a N-source. However, nitrate can be stored at concentrations exceeding 100 m M in tissues (Glass and Siddiqi, 1995), whereas ammonium, another major N-source, may be toxic when accumulated to this level (Brito et al., 2001).  Therefore, given that pollen requires large amounts of N during its entry  developmental stage, it might be advantageous for plants to have nitrate transporter in pollen in order to gain high concentration of N when it is available. Further investigation needs to be done to address this hypothesis. In conclusion, the NRT genes investigated in this study and reported data of A t N R T l . 2 showed different tissue-specific expression patterns. In other words, the NRT gene family members are not genetically redundant. Rather, each nitrate transporter seems to be involved in a specific localized function. Of course some regions of roots are targets for more than a one gene (e.g., A t N R T l . l , 2.1, and 2.4 in the root tips; A t N R T 2 . 1 , 2.4, and  84  2.6 in epidermis and cortex cells in mature regions of roots). Each encoded transporter might have different K and Kmax values (as distinct from the differences between high- and m  low-affinity  transporters).  transporters, NrtA  Aspergillus  nidulans  contains  two  high-affinity nitrate  and N r t B , which show 61 % identity (Unkles et al., 1991, 2001). Mutant  analysis revealed that K values for the NrtA and NrtB transporters were 108 u M and 11 m  uM, respectively (Unkles et al., 2001). C h l a m y d o m o n a s r e i n h a r d t i i also has two highaffinity nitrate transporters, CrNRT2.1  and CrNRT2.2,  with K values of 1.6 and 11.0 u M , m  respectively (Galvan et al., 1996). The role of such closely related proteins (apparently) differing only in their kinetic properties is still unclear.  85  5 Functional Aspects of Nitrate Transporters 5.1 Introduction Nitrate transport systems fall into three groups, constitutive high-affinity transporter system (cHATS), inducible high-affinity transporter system (iHATS), and low-affinity transporter system (LATS). The cHATS and iHATS typically operate in the range of 10 to 250 u M NO3", while the L A T S only becomes evident above these concentrations. At such concentrations total uptake rates for NO3" are the sum of these three transporter activities (Siddiqi et al., 1990; Glass et al., 1992). The induction pattern of H A T S would vary depending on external NO3" concentration, growth condition, and species or even varieties (Siddiqi et al., 1989). A typical NO3" induction period to maximize NO3" influx is 6-12 hours in barley (Siddiqi et al., 1989; Vidmar et al., 2000). In spruce it took three days to induce maximum NO3" influx (Kronzucker et al., 1995). 3-week-old Arabidopsis plants (ecotype Columbia), grown on ammonium citrate, showed a peak of NO3" influx from 100 UM NO3" after 3 h induction by I m M NO3" (Zhuo et al., 1999), whereas 6-week-old  86  Arabidopsis (ecotype Wasselewskija) displayed a peak NO3" HATS influx after 12 h of induction with 4mM NO3" (Cerezo et al., 2001). The transcript abundances of A t N R T l . 1  and the patterns of high-affinity nitrate  influx showed high correlations, suggesting that A i N R T l . l is primarily responsible for iHATS activity (Zhuo et al., 1999; Lejay et al., 1999). This conclusion was substantiated by the recent finding that a T-DNA mutant, lacking AtNRT2.1  and a part of 2.2, lost about  70% of high-affinity NO3" uptake capacity compared to the WT plants, while L A T S transport was unaffected (Filleur et al., 2001). The green alga C h l a m y d o m o n a s  reinhardtii  has at least three genes that are involved in high-affinity nitrate transport, CrNRT2.2,  and NAR2,  CrNRT2.1,  located within the same gene cluster containing other nitrate-  regulated genes (Quesada et al., 1994; Galvan et al., 1996). CrNRT2.1  and CrNRT2.2  show  high homology with N r t A , a high-affinity nitrate transporter in A s p e r g i l l u s n i d u l a n s , while NAR2  is a much smaller gene sharing no sequence homology with the NRT2  families. A C h l a m y d o m o n a s  mutant lacking CrNRT2.1,  CrNRT2.2,  or NRT1  and NAR2  was  incapable of high-affinity NO3" transport. When this null mutant was transformed with various combinations of these three genes, it was reported that high-affinity NO3" transport was restored by combination of NAR2  together with either CrNRT2.1  appears to be obligatory for high-affinity transport by NRT2.1  or 2.2. Thus  and NRT2.2,  NAR2  although the  manner of the interaction between these two gene families is unknown. NO3" influx in the L A T S range increases linearly along with external [NO3"]. As well, L A T S was considered to be repressible but not inducible (Glass and Siddiqi, 1995). In Arabidopsis, however, L A T S appeared to have two components, namely a constitutive L A T S (cLATS) and an inducible L A T S (iLATS) (Huang et al., 1999). Recent observations  87  with chll mutants exhibiting defective L A T S , suggest that NOV uptake at concentrations typical of the HATS range (<250 uM) is also reduced, leading the authors to propose that the so-called L A T S transporters, formerly considered to be low-affinity, may function both as L A T S and H A T S (Huang et al., 1996; Wang et al., 1998). To characterize the functions of particular gene products, one common approach is the use of heterologous expression systems. NrtA Xenopus  from A . n i d u l a n s was expressed in  oocytes, and caused cell membrane depolarization when oocytes were subjected to  NO3" treatment, suggesting that NO3" was transported across the cell membrane (Zhou et al., 2000). However, plant NRT2  genes failed to cause membrane depolarization or nitrate  uptake when expressed in oocytes (Forde, 2000). As well, expressing A t N R T l . l  in A .  n i d u l a n s failed to complement a nitrate transport defective mutant (nrtA nrtB) (Okamoto et al., unpublished). These results suggest that the plant NRT2 nitrate transporters may not function by themselves. Similar experiments were undertaken to express CrNRT2.1, affinity NO3" transporter from C. r e i n h a r d t i i in Xenopus CrNRTl.l  a high-  oocytes (Zhou et al., 2000). When  mRNA was injected into oocytes, NO3" transport activity was not detected.  However, when C r N R T l . l was co-expressed with N A R 1 , the oocytes showed NO3" uptake. Interestingly, expressing NAR1  alone in oocytes resulted in increased mortality of oocytes  (Zhou et al., 2000b). These circumstantial lines of evidences suggest that some NRT2.1 transporter(s), but apparently not the A . n i d u l a n s transporter, require co-expression of NAR2-like proteins in order to be functional. Interestingly, A t N R T l . l injected Xenopus  or A t N R T l . 1 -  oocytes were able to show membrane depolarization and (presumably)  88  nitrate uptake activities by themselves (Tsay et al., 1993; Huang et al., 1999). This further emphasizes differences between these two families of nitrate transporters. The aim of this Chapter is to present physiological responses of Arabidopsis plants to nitrate induction treatments, and to confirm the presence of each physiologically defined nitrate transporter systems (i.e., iHATS, cHATS, iLATS, and cLATS) by  13  N 0 " tracer 3  experiments. Also, the occurrence and expression patterns of NAR2 homologues in A. thaliana were investigated. Finally an outlining hypothesis of a mechanism for NO3" transport depending upon co-regulation of NRT2 and N A R 2 proteins will be discussed.  5.2 Materials and Method  Plant growth condition  Same as for Chapter 3.  13  NC*3" influx experiments  Nitrate influx using NC»3" was measured as described before (Zhuo et al., 1999). The basic 13  components of the solution for pretreatment, influx, and washing were the same as those of the growth media. The plants were pretreated with solution containing either 100 u M or 5 mM  14  N 0 " for 5 min, then transferred for 10 min to the influx solution which had each 3  NO3" concentration labeled with N03 . After the influx period, plant roots were washed 13  _  with "cold" solution (same as pretreatment) for 3 min to remove NC>3" from the cell wall, 13  89  followed by counting  N contents with a y-counter ( M l N A X I y Auto-Gamma 5000 series,  Packard Instruments, Meriden, CT).  RNA isolation and RT-PCR RT-PCR was performed according to the method described in Chapter 3. Primers sets, NAR2./Forward:  5' A G G A C C A G G T G T T G T T T T G G A T G C C ,  NAR2.  /Reverse: 5'  A C T G A A A C A G A T G G A G G C A A T A T C T A G G G A , amplifying a product size of 421bp. The amount of total R N A used in the PCR was 250 ug in the total volume of 12.5 ul of the reaction mixture. PCR cycle numbers for AtNAR2.1  were 21 and 30 for roots and shoots,  respectively.  Bioinformatics Phylogenetic analysis: C L U S T A L W or X was used for an initial amino acid sequence alignment analysis (Thompson et al., 1994, 1997). The alignments were then finely adjusted and gaps were removed with Bioedit (Hall, 1999). Phylogenetic analysis was carried out with P A U P 4.0b5 (http://www.lms.si.edu/PAUP) with following condition: bootstrap method with heuristic search; otimality criterion = distance; starting tree(s) obtained via neighbor-joining; branchswapping algorithm = tree-bisection-reconnection (TBR). TreeView (http://taxonomy.zoology.gla.ac.uk/rod/rod.html) was employed to output the phylogenetic trees. Other methods:  90  Same as for Chapter 2.  5.3 Results and Discussion  N0 " Influx by H A T S and L A T S 3  Nitrate influx by Arabidopsis  roots was measured at low (100 uM) and high (5 mM)  external NO3"concentrations, representative of the high- and low-affinity NO3" transporter systems (HATS, and L A T S , respectively), using N 0 " , at intervals of time after the initial 13  3  exposure to I m M NO3". Prior to exposure to 1 m M N 0 " , there was already a substantial 3  H A T S influx of 2.5 umol g" FW h" at 100 u M NO3". This is considered to be due to the ]  1  constitutive HATS (cHATS) (Figure 5-1 A). After provision of 1 m M NO3" in the external media, influx via the HATS increased continuously for 6h, peaking at a value that was 2.5 times the constitutive value. After 12 hours, the flux steadily decreased down to 2 umol g"  1  F W h" by 72h, a value that was similar to the original (Oh) value (Figure 5-1). Figure 5-2A 1  shows that nitrate influx from media containing 5 m M external NO3" also increased initially and subsequently declined. Both HATS and L A T S are considered to contribute to NO3" influx at 5 m M (Glass et al., 1992; Lejay et al., 1999). To estimate LATS-mediated influx as distinct from the H A T S influx, flux values due to the HATS activity were subtracted from those measured at 5 m M , corresponding to both H A T S and L A T S influx, presuming that the root influx from 100 u M was close to the  for HATS influx, and that the HATS  contribution remained unchanged at the two external concentrations (Figure 5-2B). These  91  h  5  I  i ^  CO  8  o —«  •  •  0  24  48  1  l  -  72  Duration of induction (hour)  Figure 5-1. Time-course of NC»3" influx into Arabidopsis roots at high-affinity range. 13  High-affinity nitrate influx measured with 100 uM NO3". 6-week-old plants were N deprived for 7 days before being transferred to ImM NO3" solution for 0 to 72 hours. The values are the means of 8 replicates, and vertical bars indicate SE.  92  15 A  Duration of induction (hour)  Figure 5-2. Time-course of NC»3" influx into Arabidopsis roots at low-affinity range. 13  (A) Low-affinity nitrate influx measured with 5 m M NO3". 6-week-old plants were N deprived for 7 days before being transferred to ImM NO3" solution for 0 to 72 hours. (B) L A T S activity at 5 m M NO3". To estimate L A T S mediated nitrate influx, mean values at 100 u M (data from Figure 5-1) subtracted from those at 5mM. The values are the means of 8 replicates, and vertical bars indicate SE.  93  "corrected" values for L A T S influx were initially < 1 umol g F W h" (at 0 h) but showed !  1  a rapid induction after NO3" provision, reaching a peak of 8 umol g ~ FW h" , at 24 h. This !  1  was followed by a slow down-regulation (Figures 5-2A and 5-2B). In summary, the cHATS influx (Oh-plants) was higher than the constitutive L A T S (cLATS). Induction of both H A T S and L A T S by NO3" was rapid, but times of peak activity and flux values were different. Furthermore, down-regulation in HATS appeared earlier and faster than that in LATS.  AtNRT Families and High- and Low-affinity Nitrate Transport System iHATS Transport It is evident from the foregoing results, that not all members of the NRT2  family of genes  can be characterized as nitrate-inducible. On the basis of correlations between physiological patterns of NO3" influx arid corresponding patterns of gene expression, it has been suggested that the NRT2.1 protein probably plays a major role in inducible HATS in A r a b i d o p s i s (Zhuo et al., 1999; Lejay et al., 1999), N. p l u m b a g i n i f o l i a  (Krapp et al., 1998),  soybean (Amarasinghe et al., 1998), and barley (Glass et a l , 2001). Our present data also showed that AtNRT2.1  transcript abundance in roots corresponded closely with the  temporal patterns of N03 influx in the HATS range following provision of NO3" to N O 3 13  _  deprived plants (Figures 3-2B and 5-1). In fact, AtNRT2.1  was the only one which showed  statistically significant positive correlation among NRT genes (Table 5-1).  94  Table 5-1. Coefficients of determination (r ) for the relationships between AtNRT gene expression levels and two nitrate transport systems. 2  r' 2  HATS  LATS  AtNRT2.1  0.55**  0.62  AtNRT2.2  0.22  0.04  AtNRT2.3  0.62**  0.17  AtNRT2.4  0.01  0.26  AtNRT2.5  0.03  0.18  AtNRT2.6  0.22  0.19  AtNRT2.7  0.11  0.72**  AtNRTl.l  0.32  0.77**  AtNRTl.2  0.04  0.16  AtNRTl. 3  0.00  0.27  AtNRTl.4  0.06  0.06  Gene  * Regressions were based on measurements of seven intervals (HATS; data from Figure 5-1), or six intervals (LATS; data from Figure 5-2) during nitrate induction period of 72 h. Negative correlations were underlined. **P<0.05  95  Recently, atnrt2,  a T-DNA knockout mutant in which AtNRT2.1  and the 3' end of  A t N R T 2 . 2 were deleted, has been characterized (Filleur et al., 2001; Cerezo et al., 2001). NC>3" influx associated with iHATS activity of this Arabidopsis  15  mutant was reduced to ~  30 % of that of WT plants, while the L A T S activity was relatively intact (Filleur et al., 2001). Although the data presented did not allow the authors to categorically distinguish which of the two genes, AtNRT2.1  or A t N R T 2 . 2 , was the predominant contributor for  iHATS at this stage, they were, nevertheless, able to conclude that these genes represent the major players (Cerezo et al., 2001). Our findings support this conclusion and further, as shown in Figure 3-2B, suggest that the pattern of AtNRT2.1  expression most closely  corresponds with the pattern of iHATS influx. A t N R T 2 . 2 expression pattern did not match the iHATS profile except during the first 3 hours. After 3 hours of NO3" provision the expression of AtNRT2.2 Thus, AtNRT2.1  was rapidly reduced compared to AtNRT2.1  (Figures 3-2D and 5-1).  appears to be a more likely candidate for iHATS influx.  Despite the identification of two distinct families of genes, NRT1 and N R T 2 , encoding low- and high-affinity NO3" transporters, respectively, it has been suggested that A t N R T l . l (CHL1) should receive the status of a dual-affinity nitrate transporter (Crawford and Glass, 1998; L i u et al., 1999; Wang et al., 1998). This proposal is based on two observations: (1) Defective N0 " transport by both the HATS and L A T S in A t N R T l . l 3  mutants grown on NH4NO3 (but not on KNO3), and (2) Heterologous expression of A t N R T l . l in Xenopus  oocytes resulted in both HATS and L A T S activities (Touraine and  Glass, 1997; Wang et al., 1998; Liu et al., 1999). Since our observations were also based on NH4N03-grown plants, A t N R T l . l protein might also be involved in the measured iHATS activity (Figures 3-3B and 5-1).  96  cHATS Transport Figure 5-1 shows that A r a b i d o p s i s  plants have substantial cHATS activity in un-induced  plants (i.e., 2.5 umol g F W h" ), as was the case in soybean plants (Amarasinghe et al., _1  1  1998) and in Steptoe barley (King et al., 1993). On the other hand, other barley varieties and spruce tend to have relatively small cHATS capacities (Siddiqi et a l , 1990; Glass and Siddiqi, 1995; Kronzucker et al., 1995). Despite the disruption of AtNRT2.1 in the atnrt2  and  AtNRT2.2  mutant (Filleur et al., 2001), cHATS activity was almost the same as that of  the WT in uninduced plants, suggesting that AtNRT2.1  and AtNRT2.2  make no contribution  to cHATS activity. In N0 '-treated plants, this cHATS was even slightly increased by NO3" 3  treatment (Filleur et al., 2001; Cerezo et al., 2001), consistent with earlier reports in barley and white spruce (Aslam et al., 1992; Kronzucker et al., 1995). Surprisingly, when grown on 1 mM NH4NO3 for 5 weeks, and then on 1 mM N0 " 3  for 1 week, N 0 " influx in the 1 5  3  mutant was maximally reduced at -25 u M , while at lower (10 uM) and higher concentrations (100 uM) N03~ influx was not as strongly reduced. The authors interpreted 15  these observations to suggest that transporters other than AtNRT2.1  and  AtNRT2.2  contribute to influx at very low NO3" concentrations (Cerezo et al., 2001; Cerezo et al., 2001). CHATS candidates might be expected to satisfy two characteristics: (1) relatively high transcript abundance prior to exposure to NO3", and (2) modest up-regulation of this transcript following induction by NO3", the latter based on the documented increase of cHATS influx following this treatment (Aslam et al., 1992; Kronzucker et al., 1995).  97  Although several members of the NRT2 and NRT1 family, e.g. A t N R T l . 3 , 1 . 4 , 1 . 5 , 1 . 6  and  1.7 satisfy the first criterion, only A t N R T l . 4 also meets the second criterion, making it a viable candidate for the cHATS activity.  Wang et al. isolated a mutant, which was  impaired only in the cHATS transport in roots of Arabidopsis  (1998). It will be interesting  to see if this mutation is located in one of the above-proposed candidates.  LATS Transport Low-affinity transporter systems were originally thought to be either constitutive or repressible on the basis of flux analysis in barley (Glass and Siddiqi, 1995). However, the AtNRTl.l Arabidopsis,  (CHL1)  gene, considered to encode a low-affinity NO3" transporter in  was induced by nitrate (Tsay et al., 1993). These contradictory findings may  have been resolved by the demonstration that Arabidopsis  possessed both an inducible- and  a constitutively-expressed member of the NRT1 family (Huang et al., 1996; Lejay et al., 1999; L i u et al., 1999).  Our present findings confirm this, and also suggest that one  member of the NRT1 family is nitrate-repressible.  However, the function of a nitrate-  repressible NRT1 gene is unclear at present given that our physiological evidence demonstrates only cLATS and i L A T S (Figures 5-2A and 5-2B). As expected, A t N R T l . l showed a NO3"-inducible expression pattern in roots, and the pattern corresponded well with the observed L A T S activity (Figures 3-3B and 5-2B). A t N R T l . l also showed the highest correlation (r values 0.77) against the L A T S activity (Table 5-1). Other members 2  of the NRT1 family were either constitutively ( A t N R T l . l expressed (AtNRTl.3),  and 1.4), or repressively  indicating that these three transporters are unlikely to be major  contributors to the i L A T S . Rather A t N R T l . l and/or AtNRT  1.4 may encode the cLATS.  98  According to L i u and Tsay (personal communications) the A t N R T l . 1 (CHL1), a putative dual affinity transporter, switches between high and low-affinity through protein phosphorylation.  This surprising finding adds even greater complexity to the existing  situation vis a vis the 7 NRT2 nitrate transporters and the 4 NRT1 transporters. In the present study, although at the transcript level AtNRT2.1  and AtNRTl. 1 behaved similarly,  there were distinct differences between patterns of H A T S and L A T S influx: (1) the iHATS peaked at 18 hours earlier than the L A T S ; (2) the iHATS influx was reduced to the original influx value after 72 h of NO3" exposure, whereas L A T S remained considerably higher (5.1 umol g F W h" ) than its original value (<1 umol g ~ FW h" ) even after 72 h (Figures 5-1 _ 1  1  !  1  and 5-2B). Thus at the physiological and molecular levels, the two nitrate transport systems (Wang and Crawford, 1996) not only co-exist but they appear to be differently regulated. Nevertheless, both HATS and L A T S have constitutive and inducible systems.  Shoot and Root Differences and Similarities Roots are considered to be the main organ for nitrogen uptake by terrestrial plants, and have consequently been the focus of attention in studies of N 0 " transport. By contrast, only a 3  few studies have reported on ion transport by shoot tissue. Nitrate translocated to shoots is released from vascular tissue to the leaf apoplasm before being re-absorbed by leaf cells. In consideration of the thermodynamics of NO3" transport even when apoplasmic NO3" is in the high m M range (>20 mM) the NO3" re-absorption step in leaves would be active, requiring a source of free energy (presumably the proton motive force) and appropriate transporters (Glass and Siddiqi, 1995). Based upon typical analyses of apoplasmic [NO3"],  99  leaf re-absorption would most likely be mediated by low-affinity nitrate transporters. In fact, all members of AtNRTl family showed relatively high expression level in the shoots in our present study. Furthermore, a recent study of AtNRTl.l  showed high levels of gene  expression to be present in the developing organs of entire plants including leaves and flowers (Guo et al., 2001). These observations provide support for the rationale that nitrate uptake by shoot tissues is vitally important for the assimilation of NO3" by leaf tissues. Nevertheless, i f this is mediated by low-affinity transporters, the question remains: what is the relevance of the observed expression patterns of NRT2 transporters in shoots?  In  Limium and Bromus, the concentrations of leaf apoplastic nitrate varied from 0.11 m M to 2.38 m M in N-deficient and N-replete plants, respectively (J. Schjoerring, personal communication). This suggests the possibility that as apoplasmic NO3" declines from m M to u M concentrations, as for example under field conditions as external supplies of NO3" are depleted, high-affinity transport systems may be necessary to scavenge apoplasmic NO3" from the latter range of concentration. This argument suggests that both the NRT2 and NRT1 transporters may participate in the re-absorption of NO3" by leaf cells.  Gene Structures and Functions- C a n we predict functions from sequence homology? 13  Using the differential patterns of gene expression and documented patterns of NO3" influx, we have attempted to attribute known transport functions (cHATS, iHATS, cLATS, and iLATS) to particular nitrate transporter genes identified from A. thaliana.  Although we are  as yet unable to ascribe functional roles to all members of the NRT1 and NRT2 families of genes, in a limited number of cases e.g. NRT1.1 and NRT2.1 and NRT2.2 (Cerezo et al.,  100  2001) there is sufficient evidence to allow reasonable predictions concerning functions to be made. Genes with high sequence homology might be anticipated to perform similar functions. Figure 5-3 shows amino acid sequence comparisons among known NRT2 members from various organisms. In A r a b i d o p s i s  family  nitrate-inducible genes A t N R T l . I ,  2.2,  and 2.4 have high sequence similarity, and it is reasonable to assume that their functions might also share some similarities. Another homologous duo AtNRT2.3  and 2.6 also  showed some similarities in the expression patterns, although the functions are unknown (Figures 3-5D and 3-5E). Most of the cloned NRT2 from N. p l u m b a g i n i f o l i a ,  soybean, A r a b i d o p s i s ,  family members from higher plants (e.g. and tomato (Amarasinghe et al., 1998)  were nitrate inducible (Figure 5-3), and exhibited high sequence homology with AtNRT2.1 and 2.2 proteins. Thus these transporters may function as iHATS (Quesada et al., 1997; Trueman et al., 1996; Zhuo et al., 1999). Similarly, nitrate-inducible A t N R T l . I has high sequence similarity with  BnNRT1.2  that is also induced by nitrate (Muldin and Ingemarsson, 1995; Zhou et al., 1998). Likewise, A t N R T l . 2 from A . t h a l i a n a (Huang et al., 1999; this work), O s N R T l . l from Oryza  sativa  (Lin et al., 2000) and G m N R T l . 3 from Glycine  max (Yokoyama et al., 2001)  are constitutive genes and these three genes encode proteins that have closely related amino acid sequences (Figure 5-4). Therefore, these transporters may serve as cLATS. Clearly greater details of function will be necessary in order to develop useful predictions.  Gene Structures and Predicted Protein Sequences of AtNAR2 Genes NAR2  genes may be involved in nitrate transport system in higher plants as has been  demonstrated for the alga C. reinhardtii.  A homology search was performed using the  101  HvNRT2.1 * HvNRT2.3* HvNRT2.4* 72r-TaNRT2.1  61 100 100  74  -n-TaNRT2.2 1  100  — TaNRT2.3 HvNRT2.2 * OsNRT2  ioor-LeNRT2.1*  10  89  °P-LeNRT2.2*  —NpNRT2 * LeNRT2.3 ioo r~ G m N R T 2 * LJNRT2 54r-AtNRT2.1 * ioop-AtNRT2.2* —— — BnNRT2.1 AtNRT2.4 * r - AtNRT2.3 AtNRT2.6 AtNRT2.7 AtNRT2.5Chlorella CrNRT2.1 * j - CfNATI * CfNAT2 * 1001— NrtA(crnA)* AnNRTB* N.crassa Hebeloma YNT1* E.coli narK* 1  69  |  95  100  65  1  1  ioo  L  1001 95  ioo  L  100  Figure 5-3. Sequence relationships of NRT2 family. Amino acid sequences were aligned with C L U S T A L X and BIOEDIT, the neighborjoining trees were generated with PAUP 4.0b8. Bootstrap values are shown in branching positions. Nitrate-inducible and nitrate-constitutive genes are indicated with asterisks and (-), respectively. Sequence sources: Arabidopsis thaliana (accession numbers: see Table 1); Aspergillus nidulans, NrtA(crnA)(M61125), NrtB(AF453778); Brassica napus, BnNRT2(CAC05338); Chlamydomonas reinhardtii, CrNRT2.1(Z25438); Chlorella  sorokiniana (AY026523); Cylindrothecafusiformis, CfNATl(AF135038), CfNAT2(AF135039); Escherichia coli, nark(X15996); Glycine max, GmNRT2(AF047718); Hebeloma cylindrosporum (AJ238664); Hordeum vulgare,  HvNRT2.1(U34198), HvNRT2.2(U34290), HvNRT2.3(AF091115), HvNRT2.4(AF091116); Lotus japonicus, LjNRT2(AJ292342); Lycopersicon  esculentum, LeNRT2.1(AF092655), LeNRT2.2(AF092654), LeNRT2.3(AY038800); Nicotiana plumbaginifolia, NpNRT2(Y08210); Neurospora crawa(b8gl2_170 in the  MIPS N.crassa database; http://mips.gsf.de/); Oriza sativa, OsNRT2(AB008519); Pichia angusta, YNT1(T43154); Triticum aestivum, TaNRT2.1(AF288688),  TaNRT2.2(AF332214),TaNRT2.3(AY053452). 102  NpNRTH  100  LeNRT1.1 -  100  NpNRT1.2  90  LeNRT1.2*  61  92  BnNRT1.2*  100  • AtNRTl. 1 *  89 I  OsNRT1.2 100  A t N R T l .4 A t N R T l .3  100  OsNRTI.1-  60  AtNRTl .2-  100  — GmNRT1.3— OsNRT1.3 i—GmNRT1.1  1001 100  GmNRT1.2* GmNRT1.5 GmNRT1.4  Figure 5-4. Sequence relationships of N R T 1 family. Amino acid sequences were aligned with C L U S T A L X and BIOEDIT, the neighbor-joining trees were generated with PAUP 4.0b8. Bootstrap values are shown in branching positions. Nitrate-inducible and nitrate-constitutive genes are indicated with asterisks and (-), respectively. Sequence sources: Arabidopsis thaliana (accession numbers: see Table 1); Brassica hapus, BnNRT1.2(U 17987); Glycine max, GmNRTl.l(BAB19756), GmNRT1.2(BAB19757), GmNRT1.3(AB052786), GmNRT1.4(BAB 19759), GmNRT1.5(BAB19760); Lycopersicon esculentum, LeNRTl.l(X92853), LeNRT1.2(X92852); Nicotiana plumbaginifolia, NpNRTl.l(CAC00544), NpNRTl:2(AJ277085); Oriza sativa, O s N R T l . l ( A F 140606), OsNRT1.2(AC037426), OsNRT1.3(AP003263).  103  sequence of the CrNAR2 protein against the Arabidopsis gene database, and two homologues were found, namely AtNAR2.1  and A t N A R 2 . 2 (Figures 5-5 and 5-6).  AtNAR2.1  is located on chromosome 5. It is interrupted by one intron (291 bp), and encodes 210 amino acids with M W of 23.4 kD. In the promoter regions there are two nitrate-dependent transcriptional motifs at -78 and -325, a putative T A T A box, and several G A T S boxes. AtNAR2.2  also consists of one intron (298 bp) and two exons (142, 485 bp), coding  polypeptides of 209 amino acids (23.3 kD) on chromosome 4. The nitrate-dependent transcriptional motif was only observed far upstream (-1322) of the NAR2.2  gene. This may  not be functioning because of the location (i.e., typically -140 to -250 bp upstream in Arabidopsis; Hwang et al., 1997).  SignalP (Nielsen et al., 1999) predicted that both  N A R 2 proteins possess signal peptides, cleaving between amino acid 22 and 23. These predictions were also supported by PSORT program (Nakai and Kanehisa, 1992). One transmembrane region was predicted at the C-termini, leaving a long hydrophilic N terminal end that is exoplasmic (Figure 5-7). NAR2.1 and 2.2 proteins share 61 % of identity and 76 % of similarity. In N-terminus TonB-dependent receptor protein signatures "TonB-Box",  [DENF]-[ST]-[LIVMF]-[LIVSTEQ]-V-x-[AGP]-STANEQPK],  were  observed in NAR2.2 in high degree, and in NAR2.1 with less conservation (Figure 5-7). The function of TonB, a periplasmic protein in Gram-negative bacteria, has been suggested in following way. TonB, dimerizing at C-termini interacts with outer membrane receptor proteins providing energy, and the receptor proteins execute high-affinity binding and transport of substrates through the plasma membranes into the periplasmic space (Chang et al., 2001). The substrates include iron, colicin, and vitamin B12 (Bassford et al., 1976;  104  1500 CAGAGAAGAGGTACGAGTAAAAGAAACAAAAGTGACTTAGGAAACGCCATTGTTGGAGACTGCTCACTGGAAGATAGAGAGT 1418 CGTGAGAGACAGTGATAAAGCGTATCAAGTCATATAGAGGGTCTTCTTATCTTTTTCTTTAACATGTGAGGGTTGAGTTAAT 1336 TATGCGGGCTGATTATAGAGTTTTTAAATTGAATTTACGATTGTTTTTTTCTTACATATAAATGCAATCTATATTTGTGTTC 1254 GGAATAACCCATCTAATATTACTCCATGTATTAAACTAAAATATTTTGCATGTTTTGGTAGATCAACTTTTTGAATGATCAC 1172 AGACCTACAAACATCAACCCTCTAATTATCCAATTTTACCATAATCCACGAGCTCTTAAAATTCATTTTTAATATATATAAT 1090 TAAAATAGTTCAAACAGTTTAAACTTTGTGACCAAGTTAAAATATTTAAAATAGTTTGACTTTGTGATCAACATATTTAAAT 1008 ATAATCAATATTTTCATTTTTAAGCCGGAAAATCACGTCTTACAAATATATTTCTGATAGACACACCTATAATTCCAAAATT -9 2 6 TTGACTTTTAAAACAAACAAAAAAAAATCTCATTAATACCACTACATACGTTTTTACAAAAATACCATTAAAAGATATTTTT -844 TCAAATACTAAAAAAAACTAAAACTAAACTTTAAACCTATAAAACACTAAATCCTATAAAGTTTATATTCGAGTATAAACCT -762 TAAAAGTTCAACCCTAAATCCTGAAAGCAAGACCCTAAACCCAAACTCAAACTTTTAAATTATAAATCCTTAAACAAAATCA -680 TTTTTAGTCTTTATGGTATTTTTAGAGTTAACAGTTTGTAGTTGTATTTTTGAAAAAAAAACACTAGTGATAGGTTTTTAGA - 598 ATAAAAACTTAATTTAGTGGTATTGAGGATATTTCTCTAATAAAAATTATTCACAAAAAATATGTATTAAAGCAAAGTGCTA -516 TGCTTATTCCATGCAATCTTTTTTGAAAAAAAAAATATTTTCTAACCGATTAGTATATCTTCTAGAGGATTCATAGAAAAAG -4 3 4 AGGATACAATTACAATATGTAGAGTATCTTATAGGTGACGTAACCATGAAATATAGAATTCTTTGGAATCTGAAACTGAATT -352 ATTCAGTTGATAAATGATAAAACAAATACTCATATCTCATCCTTTGGCATGTTTAGGAGCCATCTCTCAGCTGGACGGAGAC -27 0 AACACAGACACTTGTGCCAGAGAGGGAACACAATCTTCCCAAGTCTTCGAAAGGGTAATCTCAGACCAAACCGTTGACTTTG -18 8 TTCTCATTAATTGTTTATGCTAAACCACAAGATATTTGGATCAAAAGTATTACCATAAATCACTATATAAAGACATAAATGT -10 6 GCACCCCACTTTTCTTATCAATCATAAAAGTCAGCAAAACACAAGGCATATTCCTCTTCTCTTCCTCAGCCTTATTTTTCTG -2 4 ATATTCAGTTTCAAGGATATATCCATGGCGATCCAGAAGATCCTCTTTGCTTCACTTCTCATATGCTCACTGATCCAATCCA M A I Q K I L F A S L L I C S L I Q S I 2 0 59 TCCACGGGGCGGAAAAAGTAAGACTCTTCAAAGAGCTGGACAAAGGTGCACTTGATGTCACCACTAAACCCAGCCGAGAAGG H G A E K V R L F K E L D K G A L D V T T K P S R E G 47 141 ACCAGGTGTTGgtatgtataattctcttcaaaacatctatcatttgctacttcattagccatgcottataaatgtgcgattt P  223 305  G  V  V  51  tgctctaataccatgttagattttaaagctttatgaatgttaagacaaatttttatgagtgttggaaacattagttctcttt intron I agtcgtttattacaacatcattagatcttatcctattaattagaattacttagaattaagtgatatgaatgatagtatgatc  387  taatatcaatttacaagaataagttggaattaatattttgaatgtttggtctttagTTTTGGATGCCGGCAAGGATACGTTG L D A G K D T L 469 AACATTACATGGACGCTAAGCTCGATTGGGTCTAAAAGAGAGGCTGAATTTAAGATCATCAAAGTTAAGCTATGCTACGCTC N I T W T L S S I G S K R E A E F K I I K V K L C Y A P 8 551 CACCTAGCCAAGTTGACCGACCATGGCGCAAAACCCATGACGAGCTCTTCAAAGACAAGACCTGCCCACACAAGATCATAGC P S Q V D R P W R K T H D E L F K D K T C P H K I I A 633 CAAGCCTTATGACAAAACACTTCAATCAACTACTTGGACTCTTGAGCGTGACATCCCCACCGGAACCTACTTCGTTCGTGCC K P Y D K T L Q S T T W T L E R D I P T G T Y F V R A 715 TACGCGGTTGATGCCATTGGCCATGAAGTTGCCTATGGACAGAGCACCGACGATGCCAAGAAAACCAATCTCTTCAGCGTTC Y A V D A I G H E V A Y G Q S T D D A K K T N L F S V Q 797 AGGCTATCAGTGGCCGCCACGCGTCCCTAGATATTGCCTCCATCTGTTTCAGTGTCTTCTCCGTCGTGGCTCTTGTCGTCTT A I S G R H A S L D I A S I C F S V F S V V A L V V F 879 CTTTGTCAATGAGAAGAGGAAGGCCAAGATAGAGCAAAGCAAATGAGTCGTTTACTTTGCGTATTTGTGACGTTGAACCCAA F V N E K R K A K I E Q S K * 961 AAAAAGTTGACTTTGAACTTTCTTGTTTACCAATTCCTTTTGTCTTGTTGCACACTTCTTCTTTCTTATATGCTTTTATTTA 1043 TGTGTTTGTACAATTAAGCCATTGATATGGAACAAAACTAATCCTACGGTGGTGATGCGTTTGTGTGCTTTATATATTTTTT 1125 ATACACCTTTTGATATATTCTTACACACTTTTTTCACAAAGATTGATATTTGCATAATTTGTGGTAATCATTCTCAAAATAC 1207 GGTATATATACTTCACCTCTTACTTTCAAAGAGAAATCATAAGTATAACTAAGCAATAATTCTATATATAGGGAATTATGAT 1289 ATAAAATTTATCCAAATTTTCAAAATATTAAACAAA  Figure 5-5. D N A and deduced amino acid sequence of the AtNAR2.1  59 7 114 141 169 196 210  gene.  The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. G A T A boxes are underlined. T A T A box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined.  105  1336 TTGCACTATGAGATAGTCATCAACTATCAGAGAGAAGACTCTTCCTCCAACAGACATTTTTTTGATGAGAAGCTGAATTGGT 1254 GATGTGGGCAGTAGCTCCTGTGTCTGGAAGACTGACTTTGATCTGACACCCTCATAGCAGCCAGAGCATTATGTAGATTTTC 1172 AGGCTGGTAGTCATGTTTTAAACCTGTTGTGACACTTGAATGCAGAGTGCCCATATCTACCACATATCTGACTTGTAGGTTT 1090 TTGTCCAGATCCAGAACCTGTGCTTGAACCTGATCCAAACTGTTGCTGGAAACCTCTACCACGGGAATCATTATAGCCTCCA 1008 CGAGTATAGTATGCTTTCTCAATGTGATATGCCATGTGAGGAGTGACTTCAGAGGGAGAATTAGCATAGGCTATTAACTTAT -92 6 AATCAAAGGCTGTGAGTTTATGCACCACATCATCAAAACAAGGACCAGGATAGAGATTTAGATAGTGCTCTATCACAGTTGC -844 CACAGACTCATGTTCCGTGCCTAATCCGTTTAGAACCCCATAAAAATTCTCTTGTACTTGTTCTCTTGATAAAACCTTCTGT -762 CGGAGGAAGAGTCTTCCCTCTGATATCAACAAGGCTTATGAGTTCGATTGCAAAGCAAATACTGTAGCCCGTTTTATGTAGC -680 AATTACTAATTTGATTCCAAATTTAGTAATTCCCTAGGAAGTAAGGAAAGTGTAACTGTCTTGCTGAATCCTTTTGGTGAGT -598 CTACACTTCACAGAAGTTCGGGGTTGAATCGAAGCAGTTGCAATCCTGTTTGTAATATTCACTAATAATTCACAAGTGCGTG -516 ATTCAAAAATGCTGCATAAGCCAACATCATAAAGAGAATTTATTGGGAGACTGCTTTAGCTAGCAAACTTAGTGCATACTTG -4 3 4 TTCTAGAGATATTTAAACTAGCACATAATTTTTTTTGATGGACCAACAATCAATCTCAGCAAAAGAAACTCAAAACCGGATT -352 TCCTGAATTAGATGTCTTCCTGAATGATCAATTATTAGATTTCCGGATTGGGATCTAAGTAAGTCCAATTGGTATGATGAGG -2 7 0 AGTTTTTTTTTTTTTTTTTTTTTTTTTCATTCTTGGGCATTGTTTTTCGTGACTGAACATTATTCGATAGATCAACTATGTT -18 8 CGTGTCGACTACCGAGTAATGGCGCCCGAAAATTCCCTTAAATTCTTCGCACTAAATGATCGCCGGTTCAAATATTGGCGTC -10 6 TAGTGGCGTTTATGTATTTAAAGATGGGCATTCTATAAATATGAGACACATGTGTGACACACATTTAGTCGTCCTCCCTTAC -24 CAAGATCACATTCTCATTCGGATCATGGCCATCCACACTCTCCTCTTCGTATCACTTCTCATATTCTCACTCATCGAGTCGA M A I H T L L F V S L L I F S L I E S S 2 0 GTAGTGGAGGAAAGAAAGATAGACTCTTCACCGATCTCCAAAACTCAATTGAGGTCACCGCTAAACCCGTTAAAGATAGCGG S G G K K D R L F T D L Q N S I E V T A K P V K D S G 47 141 A G g t t t g t g a a c c g t c t t a c c t t c t t t a t a a t t c a a a g a t t t t g t a c c t t a t c t a t t a t c t t t t c a a a t c c g c g a c t a a a g t V 48 223 gtgtattcataagtagtgaagttgcccactaggctctaactgtaggttaagtataaagatatattacctattttaatacgga intron I 59  305  aaaaatagttattttcgtttatacatctctagactctttttttggaatatacatgatttatgattcatctccatacttgtat  387  tattattatttttataaatctatatactcaaatttgcacatggatgatctttagTTTTAGAGGCTGGAAAAGATATGGTGAC  469  AATTACATGGAAGCTAAAGTCGTCGTCAGCCAAGGTCGACACGGATACTGCCTTCAAGACAATCCAAGTCAAGCTTTGTTAT I T W K L K S S S A K V D T D T A F K T I Q V K L C Y GCACCGATCAGCCAAGTTGATAGACCGTGGCGTAAGACTGATAACAAGCTCTTCAAGGACAGAAGTTGCCCTCATGAGATTG A P I S Q V D R P W R K T D N K L F K D R S C P H E I V TGTCCAAGGCATACGACAAGACCCCCCAATCACTCGATTGGACAATCGGACTTGATATCCCCACTGGAACCTACTTCGTACG S K A Y D K T P Q S L D W T I G L D I P T G T Y F V R TGCCTATGGAATCGATGGAGATGGCCACGAAGTTGCATACGGACAGAGCACGGATGAGGGAAGGACGACAAATCTCTTCAGT A Y G I D G D G H E V A Y G Q S T D E G R T T N L F S GTTCATGCCATAAGTGGTCATCACGTGGGGCTAGACATAGCATCCACATTTTTCAGCGTCTTCTCCGTTGTTTCTCTGTTTG V H A I S G H H V G L D I A S T F F S V F S V V S L F V TCTTCTTTGTCATGGAGAAGAGGAAGGCCAAGTTAGAGCAAAGGGAGTGAGTTGGATTAACTATGAGGTCTTTTGTTAAGTC F F V M E K R K A K L E Q R E * GAATAAAAAAGCGTTTACGTCATAATTGTTCGTGTTTGTCGTTGTGAAGAAAATATATCCTTTCACTTTCCCAAAATCAATG TTAAAATGCAATAATCCTCCATATACATCTCATATAAACTAAATCTTACTTATAGAAAACCTTTTCACATAAACAAAAAGTG AAAAGATATGATATTCAAAACAGTACTAAGTTCTCCTACGTTTTGTCACACTTT  L  551 633 715 797 879 961 1043 112 5  E  A  G  K  D  Figure 5-6. DNA and deduced amino acid sequence of the AtNAR2.2  M  V  T  57  84 112 139 166 194 209  gene.  The number on the left starts at the proposed start codon, and the numbers on the right refer to amino acid residues. Intron sequences are shown in lower cases. GATA boxes are underlined. TATA box is indicated with thick underline. Nitrate-dependent transcription motifs are double underlined.  106  AtNar2.1 AtNar2.2  43 42 TonB Box  AtNar2.1 AtNar2.2  AtNar2.1 AtNar2.2  SREGPl VKDS-  gTLNmgTJIs|lGS|SREAE- - g g l g l -BEg  llMVTfflEKiKis S ASJVDTDT A@ST|C  fetsp QVDRPWRK QVDRPWRKT i  QSHWT  AtNar2.1 AtNar2.2  AtNar2.1 AtNar2.2  84 83  127 126  170 169  L D I A S IC L.DIAS TF  SSSFg  Figure 5-7. Amino acid sequence alignment of AtNar2.1 and AtNar2.2. Arrow indicates predicted cleavage sites. Transmembrane regions predicted by T M H M M (Sonnhammer et al., 1998) are boxed. Potential protein kinase C and casein kinase 2 phosphorylation, and N-glycosylation sites, specified in bold letters with (*), ( • ) , and ( A ) , respectively, were searched with the ProSite database (http://www.expasy.ch/prosite/). The serine-70 of AtNar2.1 is a recognition site for both P K C and C K 2 . Accession number: AtNar2.1 (BAB09391), AtNar2.2(T05562). TonB-dependent receptor signature (TonB Box) is underlined.  107  Lundrigan and Kadner, 1986; Schramm et al., 1987). The receptors fail to uptake substrates in the absence of TonB (Raynolds et al., 1980).  Expression Patterns of  AtNAR2.1  To examine the expression patterns of the AtNAR2  genes, relative quantitative RT-PCR was  carried out. The expression patterns were revealed when PCR cycles reached at 21 and 30 in root and shoots, respectively in A t N A R 2 . 1 . For unknown reasons, AtNAR2.2  was  undetectable even when cycle numbers were raised to 40 in the roots (data not shown). In roots the time-course expression patterns of AtNAR2.1  was similar to that of  AtNRT2.1  (Figure 5-8). Linear regression analysis showed a strong correlation between the two gene expression patterns (r =0.86) (Figure 5-9). AtNAR2.1 displayed a similarity with that of AtNRT2.1  expression patterns in shoots also  (Figure 5-10).  It is possible that NRT2.1 and perhaps other members of the NRT2 family are unable to function independently i.e., in the absence of N A R 2 . Rather, they may require other gene product(s) which may act as a receptor, or a part of a signal transduction system in order to activate NRT2.1. The expression of AtNAR2.1, a candidate for this function, is highly correlated with AtNRT2.1 at the transcriptional level. Although many genes are regulated by nitrate (Wang et al., 2000a), and their expression patterns might correlate with that of N R T 2 . 1 , the evidence from C. r e i n h a r d t i i strongly support this hypothesis. Nevertheless, the function of N A R 2 is still unknown. From the predicted 2-D structure, AtNAR2 possesses a single transmembrane domain at the C-terminus. Similarly, other proteins with single transmembrane domains are involved in membrane transport activities directly or indirectly. For instance, G m S A T l ,  108  Duration of induction (hour) 0  0  '—'  0  3  6  12  24  48  72  '  1  1  24  48  7;  Time (hour)  Figure 5-8. Expression patterns of AtNAR2.1  gene in roots.  RT-PCR products were obtained from 6-week-old Arabidopsis plants, which were grown hydroponically for 5 weeks and supplied with 0.5 m M NH4NO3. Plants were N deprived for 1 week (Oh), and then re-supplied with 0.5 m M Ca(NC>3)2 for 3-72h. Relative values were obtained by the ratio of the gene specific amplicon for the 18S amplicon. The values shown are means of three RT-PCR replicates. Bars indicate SE.  109  250  Q  I  0  I  100  I  I  I  I  I  200  300  400  500  600  AtNRT2.1/18S  Figure 5-9. Correlation between AtNRT2.1 and AtNAR2.1 expression levels in roots. Regression was based on 7 intervals during the time-course experiment (data of AtNRT2.1 from Figure 3-2B, AtNAR2.1 from Figure 5-8). Linear regression gives r value 0.86 (PO.01).  110  Duration of induction (hour) 0  AtNAR2.1 18S  3  6  mma#  12 (MM  24  48  72  * I  200 CO co  g  100  24 48 Time (h) B  72  200 co CO  CM  cc  I 200 AtNRT2.1/18S  Figure 5-10. Expression patterns of AtNAR2.1 gene and their correlation with AtNRT2.1 in shoots. (A) RT-PCR products were obtained from 6-week-old Arabidopsis plants, which were grown hydroponically for 5 weeks and supplied with 0.5 m M NH4NO3. Plants were N deprived for 1 week (Oh), and then re-supplied with 0.5 m M Ca(N03)2 for 3-72h. Relative values were obtained by the ratio of the gene specific amplicon for the 18S amplicon. The values shown are means of three RT-PCR replicates. Bars indicate SE. (B) Correlation between AtNRT2.1 and AtNAR2.1 expression levels in shoots. Regression was based on 7 intervals during the time-course experiment (data of AtNRT2.1 from Figure 3-2A, AtNAR2.1 from (A)). Linear regression gives r value 0.58 (PO.05). Ill  soybean nodule ammonium transporter, has been proposed as a N H / transporter, although it has only single transmembrane region (Kaiser et al., 1998). The receptor-activitymodifying proteins (RAMPs), which have a single transmembrane domain, regulate the transport and ligand specificity of the calcitonin-receptor-like-receptor (CRLR) (McLatchie et al., 1998). AtNAR2 might perform these kinds of functions (i.e., it may transport substrates by itself, or modify and/or traffic other proteins) (Zhou et al., 2000). Furthermore, AtNAR2 also displays TonB-dependent receptor proteins signatures, suggesting that the gene products might also be involved in other protein-protein interactions at the outer surface of the plasma membrane. In other words, the function of the NRT2 nitrate transporters may require more complicated interaction with other proteins, rather than being independently functional membrane proteins. In any event, the function of the NRT2 nitrate transporters is still unclear, and needs to be explored further.  112  6 Conclusion and Future Prospective  The present study has demonstrated that all putative nitrate transporters of the AtNRT2 and A t N R T l families, revealed by the A . t h a l i a n a genome project, could be detected in roots and shoots of this species by relative quantitative RT-PCR. In addition the use of GUS technology has proved information concerning the tissue-specific localization of a limited number of these genes. It was originally considered that NRT2  high-affinity nitrate transporter genes are  nitrate-inducible (Crawford and Glass, 1998; Forde, 2000). However, it is evident from the forgoing results that not all members of the NRT2 nitrate-inducible. Rather, two genes (AtNRT2.5  family of genes can be characterized as and AtNRT2.6)  showed constitutive  expression, and there was one gene even suppressed by nitrate provision  (AtNRT2.7).  113  Including classic nitrate-inducible genes (AtNRT2.1,  2.2, and 2.4), the NRT2  family  members are perhaps components of the high-affinity nitrate transport systems. Similarly, low-affinity nitrate transporter AtNRTl  family of genes showed three expression patterns in  response to NO3" provision. Unlike barley or spruce, Arabidopsis possesses inducible L A T S . This unique system showed correspondence with a nitrate-inducible low-affinity transporter AtNRT  1.1(CHL1).  Tissue-specific expression patterns of four NRT2 study AtNRT2.1,  genes were revealed in the present  2.2, and 2.4, a highly homologous trio, and also categorized as nitrate-  inducible genes, showed some similarities in their tissue-specific localization (Chapter 4). Adding A t N R T l . 2  by Huang et al (Huang et al., 1999), localizations of six nitrate  transporter genes have been confirmed, showing that those genes were expressed at least in the roots. This could support the belief that NRT genes are involved in NO3" uptake, although it may be too early to conclude their functions only from these localization patterns. In the GUS reporter gene analysis, AtNRT2.3,  2.5, and 2.7 failed to show  expression patterns. The explanations for this might include: 1. The expression levels are too low to detect with current protocols. 2. The promoter regions chosen did not contain sufficient information to initiate transcriptions (Sieburth and Meyerowitz, 1997).  3.  Technical difficulties. If the problem were caused by GUS reporter gene system itself, other systems such as green fluorescent protein (GFP) reporter D N A , in situ hybridization, in situ RT-PCR (Koltai and Bird, 2000), or immunolocalization analysis could be useful. In any cases, the localization of the rest of members of NRT genes probably will certainly be explored soon.  114  The current study showed both similarities and uniqueness among members of the NRT  gene families. Surprisingly, genes showed identical expression patterns. Nevertheless,  it may not be so simple to conclude that highly homologous multi-gene families are genetically redundant. Rather, each NRT gene may have unique functions such as specific localization, specific K and m  A t N R T l . 1(CHL1)  values, or some roles other than NO3" uptake as shown in  (Guo et al., 2001).  Screening mutants or generating mutant phenotypes is a well-established way to characterize the function of each nitrate transporter. Despite 11 nitrate transporters, only two mutants are identified (i.e., chll;  Tsay et al., 1993; and atnrt2:  Cerezo et al., 2000;  Filleur et al., 2001). Protocols for mutant screening are improving steadily. The techniques include well established T-DNA insertion mutagenesis, or gene silencing by over expression of R N A i . In addition to large populations of T-DNA lines, a recent method using degenerate primers enhances the screening efficiency dramatically, and this method is suitable for multi-gene families such like AtNRT  (Young et al., 2001). Advanced technique  of anti-sense recently emerged, in which the transforming gene contains sense and antisense c D N A fused with introns under an ectopic promoter, such as the cauliflower mosaic virus 35S promoter. The transgenic lines produced with this technique silence mRNA more efficiently than ordinal anti-sense lines (Chuang and Meyerowitz, 2000; Smith et al., 2000). The  function of the NRT genes might also be investigated by heterologous  expression system. This was most effectively employed in the original study by Tsay et al., (1993) to investigate A t N R T l . 1(CHL1) function. Since expressing A t N R T l . 1 alone failed to restore nitrate transport in a double mutant of A s p e r g i l l u s n i d u l a n s incapable of nitrate  115  uptake, a co-expression study with A t N a r 2 . 1 has been undertaken. It will be interesting to see whether Nar2  is required in Arabidopsis nitrate transport.  The A r a b i d o p s i s genome project unveiled 25,000 genes encoding proteins from 11,000 gene families, including 600 membrane transporters  (The Arabidopsis genome  initiative, 2000). Although microarray technique allows us to identify thousands of genes at once and to provide us with rudimentary ideas of gene regulation, follow up analysis is still necessary to arrive at more detail conclusions. It is encouraging that relative quantitative RT-PCR could identify and show the differential expression patterns of highly homologous gene copies as described in this study. It is also notable that the same primer sets, used in the quantitative RT-PCR analysis, are applicable for use in in situ RT-PCR for tissuespecific gene expression studies (Koltai and Bird, 2000). In summary, thanks to the A r a b i d o p s i s genome project, we now know the absolute number of gene copies in the NRT families, and I was able to characterize the gene expression patterns of all members. The results allowed to predict the physiological roles of the N R T transporters. Proving these hypothetical functions could be challenging. However, it may be feasible if we combine functional genomics and physiology.  116  References Amarasinghe, B.H.R.R., de Bruxelles, G.L., Braddon, M., Onyeocha, I., Forde, B.G., and Udvardi, M.K. (1998). Regulation of G m N r t 2 expression and nitrate transport activity in roots of soybean ( G l y c i n e max). Planta 206, 44-52. Aslam, M., Travis, R.L., and Huffaker, R.C. (1992). Comparative kinetics and reciprocal inhibition of nitrate and nitrite uptake in roots of uninduced and induced barley (Hordeum vulgare L.) seedlings. Plant Physiol. 99, 1124-1133. Cerezo, M., Tillard, P., Filleur, S., Munos, S., Daniel-Vedele, F., and Gojon, A. (2001). Major alterations of the regulation of root NO3" uptake are associated with the mutation of Nrt2.1 and Nrt2.2 genes in Arabidopsis. Plant Physiol. 127,262-271. Chang, C , Mooser, A., Pluckthun, A., and Wlodawer, A. (2001). Crystal structure of the dimeric C-terminal domain of TonB reveals a novel fold. J. Biol. Chem. 276,2753527540. Chuang, C.F., Meyerowitz, E.M. (2000). Specific and heritable genetic interference by double-stranded RNA in A r a b i d o p s i s t h a l i a n a . Proc. Natl. Acad. Sci. USA 97,49854990. Claros, M.G. and Von Heijne, G. (1994). TopPred II: A n improved software for membrane protein structure predictions. CABIOS 10, 685-686. Clough, S.J. and Bent, A.F. (1998). Floral dip: a simplified method for A g r o b a c t e r i u m mediated transformation of A r a b i d o p s i s t h a l i a n a . Plant J. 16, 735-743. Coruzzi, G. and Bush, D.R. (200,1). Nitrogen and carbon nutrient and metabolite signaling in plants. Plant Physiol. 125, 61-64. Crawford, N.M. and Glass, A.D.M. (1998). Molecular and physiological aspects of nitrate uptake in plants. Trends Plant Sci. 3, 389-395. Filleur, S. and Daniel-Vedele, F. (1999). Expression analysis of a high-affinity nitrate transporter isolated from A r a b i d o p s i s t h a l i a n a by differential display. Planta 207,461469. Filleur, S., Dorbe, M.F., Cerezo, M., Orsel, M., Granier, F., Gojon, A., and DanielVedele, F. (2001). An A r a b i d o p s i s T-DNA mutant affected in Nrt2 genes is impaired in nitrate uptake. FEBS Lett. 489, 220-224. Forde, B.G. (2000). Nitrate transporters in plants: structure, function and regulation. Biochim. Biophys. Acta 1465, 219-235.  117  Galvan, A., Quesada, A., and Fernandez, E. (1996). Nitrate and nitrite are transported by different specific transport systems and by a bispecific transporter in C h l a m y d o m o n a s reinhardtii. J. Biol. Chem. 271, 2088-2092. Gansel, X., Munos, S., Tillard, P., and Gojon, A. (2001). Differential regulation of the NO3" andNFf/ transporter genes A t N r t 2 . 1 and A t A m t l . l in A r a b i d o p s i s : relation with long-distance and local controls by N status of the plant. Plant J. 26, 143-155. Gibeaut, D.M., Hulett, J., Cramer, G.R., and Seem an n, J.R. (1997). Maximal biomass of A r a b i d o p s i s t h a l i a n a using a simple, low-maintenance hydroponic method and favorable environmental conditions. Plant Physiol. 115, 317-319. Glass, A.D.M., Brito, D.T., Kaiser, B.N., Kronzucker, H.J., Kumar, A., Okamoto, M., Rawat, S.R., Siddiqi, M.Y., Silim, S.M., Vidmar, J.J., and Zhuo, D. (2001). Nitrogen transport in plants, with an emphasis on the regulation of fluxes to match plant demand. J. Plant Nutr. Soil Sci. 164, 199-207. Glass, A . D . M . , Shaff, J.E., and Kochian, L., V. (1992). Studies of the uptake of nitrate in barley IV. Electrophysiology. Plant Physiol. 99, 456-463. Glass, A . D. M. and Siddiqi, M. Y. (1995) Nitrogen absorption by plant roots. Srivastava, H. S. and Singh, R. P. In Nitrogen nutrition in higher plants. 21-56. New Delhi, India, Associated Publishing Co. Guo, F.Q., Wang, R., Chen, M., and Crawford, N.M. (2001). The Arabidopsis dualaffinity nitrate transporter gene A t N R T l . l (CHL1) is activated and functions in nascent organ development during vegetative and reproductive growth. Plant Cell 13, 1761-1777. Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41, 95-98. Hanisch ten Cate, C H . and Breteler, H. (1981). Role of sugars in nitrate utilization by roots of dwarf bean. Physiol. Plant. 52, 129-135. Hatzfeld, Y. and Saito, K. (1999). Identification of two putative nitrate transporters highly homologous to CHL1 from A r a b i d o p s i s t h a l i a n a (Accession Nos. AJ011604 and AJ131464) (PGR99-018). Plant Physiol. 119, 805. Hildebrand, M. and Dahlin, K. (2000). Nitrate transporter genes from the diatom C y l i n d r o t h e c a fusiformis (Bacillariophyceae): mRNA levels controlled by nitrogen source and by the cell cycle. J. Phycol. 36, 702-713. Hirokawa, T., Boonchieng, S., and Mitaku, S. (1998). SOSUI - classification and secondary structure prediction system for membrane proteins. Bioinformatics 14, 378379.  118  Hofmann, K. and Stoffel, W. (1992). PROFILEGRAPH: an interactive graphical tool for protein sequence analysis. CABIOS 8, 331-337. Huang, N.C., Chiang, C.S., Crawford, N.M., and Tsay, Y.F. (1996). CHL1 encodes a component of the low-affinity nitrate uptake system in Arabidopsis and shows cell typespecific expression in roots. Plant Cell 8,2183-2191. Huang, N.C., Liu, K.H., Lo, H.J., and Tsay, Y.F. (1999). Cloning and functional characterization of an Arabidopsis nitrate transporter gene that encodes a constitutive component of low-affinity uptake. Plant Cell 11, 1381-1392. Hwang, C.F., Lin, Y., Dsouza, T., and Cheng, C L . (1997). Sequences necessary for nitrate-dependent transcription of arabidopsis nitrate reductase genes. Plant Physiol. 113, 853-862. Jones, D.T., Taylor, W.R., and Thornton, J.M. (1994). A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33, 3038-3049. Kaiser, B.N., Finnegan, P.M., Tyerman, S.D., Whitehead, L.F., Bergersen, F.J., Day, D.A., and Udvardi, M.K. (1998). Characterization of an ammonium transport protein from the peribacteroid membrane of soybean nodules. Science 281, 1202-1206. Keller, E.B. and Noon, W.A. (1984). Intron splicing: A conserved internal signal in introns of aminal pre-mRNAs. Proc. Natl. Acad. Sci. U S A 81, 7417-7420. King, B.J., Siddiqi, M.Y., Ruth, T.J., Warner, R.L., and Glass, A.D.M. (1993). Feedback regulation of nitrate influx in barley roots by nitrate, nitrite, and ammonium. Plant Physiol. 102,1279-1286. Koltai, H. and Bird, D.M. (2000). High throughput cellular localization of specific plant mRNAs by liquid-phase in situ reverse transcription-polymerase chain reaction of tissue sections. Plant Physiol. 123, 1203-1212. Krapp, A . , Fraisier, V., Scheible, W.R., Quesada, A . , Gojon, A . , Stitt, M., Caboche, M., and Daniel-Vedele, F. (1998). Expression studies of N r t 2 : l N p , a putative high-affinity nitrate transporter: evidence for its role in nitrate uptake. Plant J. 14, 723-731. Krapp, A . and Stitt, M . (1995). An evaluation of direct and indirect mechanisms for the "sink-regulation" of photosynthesis in spinach: changes in gas exchange, carbohydrates, metabolites, enzyme activities and steady-state transcript levels after cold-girdling source leaves. Planta 195, 313-323. Kronzucker, H., Glass, A.D.M., and Siddiqi, M . (1995). Nitrate induction in spruce: an approach using compartmental analysis. Planta 196, 683-690.  119  Lauter, F.R., Ninnemann, O., Bucher, M., Riesmeier, J.W., and Frommer, W.B. (1996). Preferential expression of an ammonium transporter and of two putative nitrate transporters in root hairs of tomato. Proc. Natl. Acad. Sci. U S A 93, 8139-8144. Lejay, L., Tillard, P., Lepetit, M., Olive, F.D., Filleur, S., Daniel-Vedele, F., and Gojon, A. (1999). Molecular and functional regulation of two NO3" uptake systems by N - and C-status of A r a b i d o p s i s plants. Plant J. 18, 509-519. Lin, C M . , Koh, S., Stacey, G., Yu, S.M., Lin, T.Y., and Tsay, Y.F. (2000). Cloning and functional characterization of a constitutively expressed nitrate transporter gene, O s N R T l , from rice. Plant Physiol. 122, 379-388. Liu, K.H., Huang, C.Y., and Tsay, Y.F. (1999). CHL1 is a dual-affinity nitrate transporter of Arabidopsis involved in multiple phases of nitrate uptake. Plant Cell 11, 865-874. Marschner, H. Mineral nutrition of higher plants. 2nd ed. (1995). London: Academic Press Inc. McLatchie, L . M . , Fraser, N.J., Main, M.J., Wise, A., Brown, J., Thompson, N., Solari, R., Lee, M.G., and Foord, S.M. (1998). RAMPs regulate the transport and ligand specificity of the calcitonin-receptor-like receptor. Nature 393, 333-339. Moller, S., Croning, M.D.R., and Apweiler, R. (2001). Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17, 646-653. Muldin, I. and Ingemarsson, B. (1995). A c D N A from B r a s s i c a napus L. encoding a putative nitrate transporter (GenBank U17987). Plant Physiol. 108, 1341. Murashige, T. and Skoog, F. (1962). A revised medium for rapid growth and bioassay with tobacco tissue cultures . Physiol. Plant. 15, 473-497. Nakai, K. and Kanehisa, M . (1992). A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14, 897-911. Nicholas, K.B. and Nicholas, H.B.Jr. (1997). GeneDoc: a tool for editing and annotating multiple sequence alignments. Distributed by the author. Nielsen, H., Brunak, S., and von Heijne, G. (1999). Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng. 12, 3-9. Ono, F., Frommer, W.B., and von Wiren, N. (2000). Coordinated diurnal regulation of low- and high-affinity nitrate transporters in tomato. Plant Biol. 2, 17-23. Padgett, R.A., Grabowski, P.J., Konarska, M.M., Seiler, S., and Sharp, P.A. (1986). splicing of messenger rna precursors. Ann. Rev. Biochem. 55,1119-1150.  120  Pao, S.S., Paulsen, I.T., and Saier, M.H. (1998). Major facilitator superfamily. Microbiol. Mol. Biol. Rev. 62, 1-34. Perez, M.D., Gonzalez, C., Avila, J., Brito, N., and Siverio, J.M. (1997). The YNT1 gene encoding the nitrate transporter in the yeast H a n s e n u l a polymorpha is clustered with genes YNI1 and YNR1 encoding nitrite reductase and nitrate reductase, and its disruption causes inability to grow in nitrate. Biochem. J. 321, 397-403. Persson, B. and Argos, P. (1994). Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J. Mol. Biol. 237, 182-192. Quesada, A., Hidalgo, J., and Fernandez, E. (1998). Three Nrt2 genes are differentially regulated in C h l a m y d o m o n a s reinhardtii. Mol. Genet. Genomics. 258, 373-377. Quesada, A., Krapp, A., Trueman, L.J., Daniel-Vedele, F., Fernandez, E., Forde, B.G., and Caboche, M. (1997). PCR-identification of a N i c o t i a n a p l u m b a g i n i f o l i a c D N A homologous to the high-affinity nitrate transporters of the c r n A family. Plant Mol. Biol. 34, 265-274. Quesada, A., Galvan, A., and Fernandez, E . (1994). Identification of nitrate transporter genes in C h l a m y d o m o n a s reinhardtii. Plant J. 5,407-419. Raun, W.R. and Johnson, G.V. (1999). Improving nitrogen use efficiency for cereal production. Agronomy J. 91, 357-363. Roulston, T . \ , Cane, J.H., and Buchmann, S.L. (2000). What governs protein content of pollen: Pollinator preferences, pollen-pistil interactions, or phylogeny? Ecological Monographs 70, 617-643. Rowe, J.J., Ubbink-Kok, T., Molenaar, D., Konings, W.N., and Driessen, A.J. (1994). NarK is a nitrite-extrusion system involved in anaerobic nitrate respiration by E s c h e r i c h i a coli. Mol. Microbiol. 12, 579-586. Schwacke, R., Grallath, S., Breitkreuz, K.E., Stransky, E., Stransky, H., Frommer, W.B., and Rentsch, D. (1999). LeProTl, a transporter for proline, glycine betaine, and gamma-amino butyric acid in tomato pollen. Plant Cell 11, 377-391. Sheen, J . (1990). Metabolic repression of transcription in higher plants. Plant Cell 2, 10271038. Siddiqi, M.Y., Glass, A.D.M., Ruth, T.J., and Fernando, M. (1989). Studies of the regulation of nitrate influx by barley seedings using N03~. Plant Physiol. 90, 806-813. 13  Siddiqi, M.Y., Glass, A.D.M., Ruth, T.J., and Rufty, T.W., Jr. (1990). Studies of the uptake of nitrate in barley I. Kinetics of N Q " influx. Plant Physiol. 93, 1426-1432. 13  3  121  Siebrecht, S., Maeck, G., and Tischner, R. (1995). Function and contribution of the root tip in the induction of N0 "uptake along the barley root axis. J. Exp. Bot. 46, 1669-1676. 3  Sieburth, L.E. and Meyerowitz, E.M. (1997). Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. Plant Cell 9, 355-365. Smith, N.A., Singh, S.P., Wang, M.B., Stoutjesdijk, P.A., Green, A.G., and Waterhouse, P.M. (2000). Total silencing by intron-spliced hairpin RNAs. Nature 407, 319-320. Sonnhammer, E.L.L., von Heijne, G., and Krogh, A. (1998). A hidden Markov model for predicting transmembrane helices in protein sequences. Int. Conf. Intell. Syst. Mol. Biol. 176-182. The Arabidopsis Genome Initiative. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994). C L U S T A L W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 46734680. Touraine, B. and Glass, A.D.M. (1997). N 0 " and C10 ~ fluxes in the chll-5 mutant of Arabidopsis thaliana. Does the CHL1-5 gene encode a low-affinity N 0 " transporter? Plant Physiol. 114, 137-144. 3  3  3  Trueman, L.J., Richardson, A., and Forde, B.G. (1996). Molecular cloning of higher plant homologues of the high-affinity nitrate transporters of Chlamydomonas reinhardtii and Aspergillus nidulans. Gene 175, 223-231. Tsay, Y.F., Schroeder, J., I, Feldmann, K.A., and Crawford, N . M . (1993). The herbicide sensitivity gene CHL1 of arabidopsis encodes a nitrate-inducible nitrate transporter. Cell 72, 705-713. Tusnady, G.E. and Simon, I. (1998). Principles governing amino acid composition of integral membrane proteins - application to topology prediction. J. Mol. Biol. 283,489506. Unkles, S.E., Hawker, K.L., Grieve, C , Campbell, E., I, Montague, P., and Kinghorn, J.R. (1991). crnA encodes a nitrate transporter in Aspergillus nidulans. Proc. Natl. Acad. Sci. U S A 88, 204-208. Unkles, S.E., Zhou, D., Siddiqi, M.Y., Kinghorn, J.R., and Glass, A.D.M. (2001). Apparent genetic redundancy facilitates ecological plasticity for nitrate transport. E M B O J. 20, 6246-6255.  122  van der Leij, M., Smith, S.J., and Miller, A.J. (1998). Remobilisation of vacuolar stored nitrate in barley root cells. Planta 205, 64-72. Vidmar, J.J., Zhuo, D.G., Siddiqi, M.Y., and Glass, A.D.M. (2000). Isolation and  characterization of HvNRT2.3 and H v N R T 2 . 4 , cDNAs encoding high-affinity nitrate transporters from roots of barley. Plant Physiol. 122, 783-792. Wang, R. and Crawford, N.M. (1996). Genetic identification of a gene involved in constitutive, high-affinity nitrate transport in higher plants. Proc. Natl. Acad. Sci. USA 93, 9297-9301. Wang, R., Liu, D., and Crawford, N.M. (1998). The Arabidopsis CHL1 protein plays a major role in high-affinity nitrate uptake. Proc. Natl. Acad. Sci. USA 95,15134-15139. Wang, R., Guegler, K., LaBrie, S.T., and Crawford, N.M.  (2000). Genomic analysis of a  nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell 12, 1491-1509. Yokoyama, T., Kodama, N., Aoshima, H., Izu, H., Matsushita, K., and Yamada, M .  (2001). Cloning of a cDNA for a constitutive NRT1 transporter from soybean and comparison of gene expression of soybean N R T l transporters. Biochim. Biophys. Acta 1518, 79-86. Young, J . C , Krysan, P.J., and Sussman, M.R. (2001). Efficient screening of arabidopsis T-DNA insertion lines using degenerate primers. Plant Physiol. 125, 513-518. Zhen, R.G., Koyro, H.W., Leigh, R.A., Tomos, A.D., and Miller, A.J. (1991).  Compartmental nitrate concentrations in barley root cells measured with nitrate-selective microelectrodes and by single-cell sap sampling. Planta 185, 356-361. Zhou, J.J., Theodoulou, F.L., Muldin, I., Ingemarsson, B., and Miller, A.J. (1998).  Cloning and functional characterization of a B r a s s i c a napus transporter that is able to transport nitrate and histidine. J. Biol. Chem. 273, 12017-12023. Zhou, J.J., Fernandez, E., Galvan, A., and Miller, A.J. (2000). A high affinity nitrate transport system from Chlamydomonas requires two gene products. FEBS Lett. 466, 225-227. Zhou, J.J., Trueman, L.J., Boorer, K.J., Theodoulou, F.L., Forde, B.G., and Miller,  A.J. (2000). A high affinity fungal nitrate carrier with two transport mechanisms. J. Biol. Chem. 275, 39894-39899. Zhuo, D.G., Okamoto, M., Vidmar, J.J., and Glass, A.D.M. (1999). Regulation of a  putative high-affinity nitrate transporter (Nrt2;lAf) Plant J. 17, 563-568.  in roots of Arabidopsis  thaliana.  123  

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