Factor-Dependent Internal Ribosome Entry Site and -1 Programmed Frameshifting Signal in the Bemisia-Associated Dicistrovirus 2
department or school: Medicine, Faculty of
department or school: Non UBC
department or school: Biochemistry and Molecular Biology, Department of
data provider: DSpace
identifier citation: Viruses 16 (5): 695 (2024)
contributor: University of British Columbia. Life Sciences Institute
creator: Chen, Yihang
creator: Chapagain, Subash
creator: Chien, Jodi
creator: Pereira, Higor Sette
creator: Patel, Trushar R.
creator: Inoue-Nagata, Alice K.
creator: Jan, Eric
issued: 2024-05-27T21:52:41Z
issued: 2024-04-28
description: The dicistrovirus intergenic (IGR) IRES uses the most streamlined translation initiation mechanism: the IRES recruits ribosomes directly without using protein factors and initiates translation from a non-AUG codon. Several subtypes of dicistroviruses IRES have been identified; typically, the IRESs adopt two -to three overlapping pseudoknots with key stem-loop and unpaired regions that interact with specific domains of the ribosomal 40S and 60S subunits to direct translation. We previously predicted an atypical IGR IRES structure and a potential -1 programmed frameshift (-1 FS) signal within the genome of the whitefly Bemisia-associated dicistrovirus 2 (BaDV-2). Here, using bicistronic reporters, we demonstrate that the predicted BaDV-2 -1 FS signal can drive -1 frameshifting in vitro via a slippery sequence and a downstream stem-loop structure that would direct the translation of the viral RNA-dependent RNA polymerase. Moreover, the predicted BaDV-2 IGR can support IRES translation in vitro but does so through a mechanism that is not typical of known factorless dicistrovirus IGR IRES mechanisms. Using deletion and mutational analyses, the BaDV-2 IGR IRES is mapped within a 140-nucleotide element and initiates translation from an AUG codon. Moreover, the IRES does not bind directly to purified ribosomes and is sensitive to eIF2 and eIF4A inhibitors NSC1198983 and hippuristanol, respectively, indicating an IRES-mediated factor-dependent mechanism. Biophysical characterization suggests the BaDV-2 IGR IRES contains several stem-loops; however, mutational analysis suggests a model whereby the IRES is unstructured or adopts distinct conformations for translation initiation. In summary, we have provided evidence of the first -1 FS frameshifting signal and a novel factor-dependent IRES mechanism in this dicistrovirus family, thus highlighting the diversity of viral RNA-structure strategies to direct viral protein synthesis.
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/88380
note: Citation: Chen, Y.; Chapagain, S.;Chien, J.; Pereira, H.S.; Patel, T.R.;Inoue-Nagata, A.K.; Jan, E.Factor-Dependent Internal RibosomeEntry Site and -1 ProgrammedFrameshifting Signal in theBemisia-Associated Dicistrovirus 2.Viruses 2024, 16, 695. https://doi.org/10.3390/v16050695Academic Editor: Bo LiangReceived: 4 February 2024Revised: 25 April 2024Accepted: 26 April 2024Published: 28 April 2024Copyright: © 2024 by the authors.Licensee MDPI, Basel, Switzerland.This article is an open access articledistributed under the terms andconditions of the Creative CommonsAttribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).virusesArticleFactor-Dependent Internal Ribosome Entry Site and -1Programmed Frameshifting Signal in the Bemisia-AssociatedDicistrovirus 2Yihang Chen 1, Subash Chapagain 1, Jodi Chien 1, Higor Sette Pereira 2 , Trushar R. Patel 2 ,Alice K. Inoue-Nagata 3 and Eric Jan 1,*1 Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia,Vancouver, BC V6T 1Z3, Canada; yihangchen1013@gmail.com (Y.C.); chsubash@student.ubc.ca (S.C.);chienjodi@gmail.com (J.C.)2 Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University ofLethbridge, Lethbridge, AB T1K 3M4, Canada; higor.pereira@uleth.ca (H.S.P.); trushar.patel@uleth.ca (T.R.P.)3 Embrapa Vegetables, Brasília 70770-901, Brazil; alice.nagata@embrapa.br* Correspondence: ej@mail.ubc.caAbstract: The dicistrovirus intergenic (IGR) IRES uses the most streamlined translation initiationmechanism: the IRES recruits ribosomes directly without using protein factors and initiates translationfrom a non-AUG codon. Several subtypes of dicistroviruses IRES have been identified; typically,the IRESs adopt two -to three overlapping pseudoknots with key stem-loop and unpaired regionsthat interact with specific domains of the ribosomal 40S and 60S subunits to direct translation. Wepreviously predicted an atypical IGR IRES structure an…
has type: Article
is shown at: 10.14288/1.0443804
language: eng
peer review status: Reviewed
provider: Vancouver : University of British Columbia Library
publisher: Multidisciplinary Digital Publishing Institute
publisher DOI: 10.3390/v16050695
rights: CC BY 4.0
rights URI: https://creativecommons.org/licenses/by/4.0/
scholar level: Faculty
scholar level: Researcher
subject: virus
subject: frameshifting
subject: RNA
subject: IRES
type: Text
identifier URI: http://hdl.handle.net/2429/88380