Lopez-Moya, J. J. | Search bioRxiv

bioRxiv2025

Nucleotide sequence analysis reveals the presence of PVY-Tam isolates affecting tamarillo in Colombia

1.Tamarillo or tree tomato (Solanum betaceum Cav.) is a fruit tree species of Andean origin with cultural and economic relevance in Colombia. However, the high incidence of complex viral diseases termed "virosis" in all tamarillo-growing regions of the country leads to huge production losses and seriously threatens its cultivation. The lack of effective treatments implies eradication as the only alternative in severe cases. In this work, we characterized the virome of eight tamarillo-growing locations across the Department of Narino (Colombia). By in-depth sequence analysis of RNA libraries, we confirmed the presence of up to four different virus species belonging to the genera Torradovirus, Potyvirus and Polerovirus in symptomatic tamarillo plants. These results represent the first report of torradovirus infection in tamarillo. Additionally, we identified a novel isolate of potato virus Y-Tamarillo (PVY-Tam) in Narino that could have originated in South America by a recent divergence of the PVYN lineage. We propose that length variability in the P3N-PIPO protein, which in the case of PVY-Tam contains two premature stop codons not identified in other PVY isolates, might be involved with host-specific adaptations. Our findings broaden the knowledge of tamarillo virosis in the Andean region, and overall, worldwide, thus offering new possibilities for developing effective diagnostic and control strategies.

plant biology↗

bioRxiv2024

Reconceptualizing programmed transcriptional slippage in RNA viruses

RNA viruses have evolved sophisticated strategies to exploit the limited encoded information within their typically compact genomes. One of such, named programmed transcriptional slippage (PTS), is defined by the insertion of an additional A at An motifs (n [≥] 6) of newly synthetized viral transcripts to get access to overlapping open reading frames (ORFs). Although key proteins from Ebolavirus and potyvirids (members of the Potyviridae family) are expressed via PTS, available information about this phenomenon is very scarce. Here, by using diverse experimental approaches and a collection of plant/virus combinations, we discover cases in which PTS does not fit with its current definition. In summary, we observe (i) high rate of single nucleotide deletions at slippage motifs, (ii) overlapping ORFs acceded by slippage at an U8 stretch, and (iii) significant changes in slippage rates induced by factors not related to cognate viruses. Moreover, a survey of full-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. In conclusion, our data prompt to broaden PTS definition in RNA viruses. Considering the potential of this phenomenon to expand the viral proteome by acceding to overlapping ORFs and/or producing truncated proteins, a revaluation of PTS significance during infections of RNA viruses is required. IMPORTANCEProgrammed transcriptional slippage (PTS) is used by RNA viruses as another strategy to maximise the coding information in their genomes. This phenomenon is based on a peculiar feature of viral replicases: they insert an untemplated A in An motifs (n [≥] 6) in a small fraction of newly synthesised viral RNAs. As a consequence, ribosomes can get access to overlapping open reading frames (ORFs) when translating those particular transcripts. Here, using plant-infecting RNA viruses as models, we discover cases challenging the previously stablished definition of viral PTS, prompting us to reconsider and redefine this expression strategy. An interesting conclusion from our study is that PTS might be more relevant during RNA virus evolution and infection processes than previously assumed.

molecular biology↗