Reconceptualizing transcriptional slippage in plant RNA viruses
2024
Valli, Adrian | Domingo-Calap, María Luisa | González de Prádena, Alfonso | García, Juan Antonio | Cui, Hongguang | Desbiez, Cecile | López-Moya, Juan José | Centro Nacional de Biotecnología [Madrid] (CNB-CSIC) ; Consejo Superior de Investigaciones Cientificas [España] = Spanish National Research Council [Spain] (CSIC) | Centre for Research in Agricultural Genomics (CRAG) | Evolving Therapeutics SL | Hainan University | Unité de Pathologie Végétale (PV) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | AEI-FEDER : BIO2015-73900-JIN | MICIU/AEI/10.13039/501100011033 : PID2019-110979RB-I00; PID2019-105692RB-100; PID2022-139314OB-I00, PID2022-139376OB-C33; PID2022-138530OB-I00 | Feder, UE : PID2022-139314OB-I00; PID2022-139376OB-C33; PID2022-138530OB-I00 | MCIN/AEI/10.13039/501100011033 and the CERCA Program, Generalitat de Catalunya : grants SEV‐2015‐0533; CEX2019-000902-S | MICIN and FEDER : FPI contract BES-2014–068970
International audience
Mostrar más [+] Menos [-]Inglés. 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.
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