Reconceptualizing transcriptional slippage in plant RNA viruses
Valli, Adrian A. (Centro Nacional de Biotecnología)
Domingo Calap, María Luisa (Centre de Recerca en Agrigenòmica)
González de Prádena, Alfonso (Centro Nacional de Biotecnología)
García, Juan Antonio (Centro Nacional de Biotecnología)
Cui, Hongguang (Hainan University)
Desbiez, Cécile (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement)
Lopez-Moya, Juan Jose (Centre de Recerca en Agrigenòmica)

Data:	2024
Resum:	RNA viruses have evolved sophisticated strategies to exploit the limited encoded information within their typically compact genomes. One of them, named transcriptional slippage (TS), is characterized by the appearance of indels in nascent viral RNAs, leading to changes in the open reading frame (ORF). Although members of unrelated viral families express key proteins via TS, the available information about this phenomenon is still limited. In potyvirids (members of the Potyviridae family), TS has been defined by the insertion of an additional A at An motifs (n ≥ 6) in newly synthesized transcripts at a low frequency, modulated by nucleotides flanking the A-rich motif. Here, by using diverse experimental approaches and a collection of plant/virus combinations, we discover cases not following this definition. In summary, we observe (i) a high rate of single-nucleotide deletions at slippage motifs, (ii) overlapping ORFs acceded by slippage at an U8 stretch, and (iii) changes in slippage rates induced by factors not related to cognate viruses. Moreover, a survey of whole-genome sequences from potyvirids shows a widespread occurrence of species-specific An/Un (n ≥ 6) motifs. Even though many of them, but not all, lead to the production of truncated proteins rather than access to overlapping ORFs, these results suggest that slippage motifs appear more frequently than expected and play relevant roles during virus evolution. Considering the potential of this phenomenon to expand the viral proteome by acceding to overlapping ORFs and/or producing truncated proteins, a re-evaluation of TS significance during infections of RNA viruses is required.
Ajuts:	Ministerio de Economía y Competitividad BIO2015-73900-JIN Agencia Estatal de Investigación PID2019-110979RB-I00 Agencia Estatal de Investigación PID2019-105692RB-I00 Agencia Estatal de Investigación PID2022-139314OB-I00 Agencia Estatal de Investigación PID2022-139376OB-C33 Agencia Estatal de Investigación PID2022-138530OB-I00 Ministerio de Economía y Competitividad SEV-2015-0533 Agencia Estatal de Investigación CEX2019-000902-S Ministerio de Economía y Competitividad BES-2014-068970
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	RNA virus ; RNA polymerases ; Evolution ; Potyviridae ; Ebola virus ; Plant viruses ; Polymerase slippage ; Transcriptional slippage ; Overlapping ORFs ; RNA replication ; Viral replication
Publicat a:	mBio, Vol. 15, Issue 10 (October 2024) , art. e02120-24, ISSN 2150-7511

DOI: 10.1128/mbio.02120-24
PMID: 39287447

26 p, 1.1 MB

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