Reconceptualizing transcriptional slippage in plant RNA viruses

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.IMPORTANCETranscriptional slippage (TS) is used by RNA viruses as another strategy to maximize the coding information in their genomes. This phenomenon is based on a peculiar feature of viral replicases: they may produce indels in a small fraction of newly synthesized viral RNAs when transcribing certain motifs and then produce alternative proteins due to a change of the reading frame or truncated products by premature termination. Here, using plant-infecting RNA viruses as models, we discover cases expanding on previously established features of plant virus TS, prompting us to reconsider and redefine this expression strategy. An interesting conclusion from our study is that TS might be more relevant during RNA virus evolution and infection processes than previously assumed.

This work was supported by grants BIO2015-73900-JIN (to AAV) funded by AEI-FEDER, PID2019-110979RB-I00 (to AAV), and PID2019-105692RB-100 (to JJLM) funded by MICIU/AEI/10.13039/501100011033, as well as PID2022-139314OB-I00 (to AAV), PID2022-139376OB-C33 (to JJLM), and PID2022-138530OB-I00 (supporting the work of JAG) funded by MICIU/AEI/10.13039/501100011033 and by FEDER, UE. The Center for Research in Agricultural Genomics (CRAG) was also supported by grants SEV‐2015‐0533 and CEX2019-000902-S funded by MCIN/AEI/10.13039/501100011033, and by the CERCA Program, Generalitat de Catalunya. MLD was supported during her work at CRAG and at INRA-Avignon by FPI contract BES-2014–068970 from MICIN and FEDER. Funders had no role in study design, data collection, and interpretation.

With funding from the Spanish goverment through the "Severo Ochoa Centre of Excellence" accreditation (SEV-2015-0533 and CEX2019-000902-S)

Peer reviewed