f08b0c5a877a2a6ebb926d2e970beb33 mbi_a2024m10v15n10pe02120-24.pdf a7dfda016fe2d7812623f783bf87e2b04b5fcf55 mbi_a2024m10v15n10pe02120-24.pdf b0f3c49b99288aa0a7ccc5104a76381f20baa3f283edde7e0068a982cdb2466e mbi_a2024m10v15n10pe02120-24.pdf Title: Reconceptualizing transcriptional slippage in plant RNA viruses Subject: mBio 2024.15:e02120-24 Keywords: RNA virus, RNA polymerases, evolution, Potyviridae, Ebola virus, plant viruses, polymerase slippage, transcriptional slippage, overlapping ORFs, RNA replication, viral replication Author: Adrian A. Valli, María Luisa Domingo-Calap, Alfonso González de Prádena, Juan Antonio García, Hongguang Cui, Cécile Desbiez, Juan José López-Moya Creator: Antenna House XSL Formatter V7.4 MR2 Linux : 7.4.3.63807 (2024-03-22T11:49+09) Producer: Antenna House PDF Output Library 7.4.1901; modified using iText 4.2.0 by 1T3XT CreationDate: Tue Oct 8 08:56:02 2024 CEST ModDate: Mon Sep 29 20:00:18 2025 CEST Custom Metadata: yes Metadata Stream: yes Tagged: yes UserProperties: no Suspects: no Form: none JavaScript: no Pages: 26 Encrypted: no Page size: 585 x 783 pts Page rot: 0 File size: 1192609 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- JHFDCY+MyriadPro-Regular Type 1C Custom yes yes yes 95 0 JHFDCY+MyriadPro-Semibold Type 1C Custom yes yes yes 96 0 JHFDCY+MyriadPro-Regular Type 1C Custom yes yes yes 97 0 JHFDCY+MyriadPro-It Type 1C Custom yes yes yes 98 0 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edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'fig-caption-kriyadocs-F5_0' cannot be found ID: PDF-HUL-122 Offset: 1187090 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'fig-caption-kriyadocs-F4_0' cannot be found ID: PDF-HUL-122 Offset: 1187090 MIMEtype: application/pdf Profile: Tagged PDF PDFMetadata: Objects: 0 FreeObjects: 2 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: true NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseNone Language: EN Outlines: Item: Title: Reconceptualizing transcriptional slippage in plant RNA viruses Children: Item: Title: RESULTS Children: Item: Title: An atypical TS in the ipomovirus CocMoV Item: Title: The atypical TS in CocMoV is not the consequence of nucleotides flanking slippage motifs Item: Title: The atypical TS in CocMoV can be attributed to particular features of CocMoV Item: Title: Wide distribution of diverse slippage motifs in the family Potyviridae Item: Title: A naturally occurring U8 motif promotes access to the pipo ORF Item: Title: Many slippage motifs in a single potyvirid Item: Title: Factors unrelated to the cognate virus shape TS rate Item: Title: Transcriptional slippage outside the Potyviridae family Item: Title: DISCUSSION Item: Title: MATERIALS AND METHODS Children: Item: Title: Plants, virus isolates, and bacteria strains Item: Title: Primers Item: Title: Plasmids Item: Title: Virus inoculation Item: Title: Transient expression of proteins Item: Title: RNA extraction, next-generation sequencing, and data analyses Item: Title: Fluorescence imaging and quantification Item: Title: Detection of proteins by Western blot Filters: FilterPipeline: 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application/pdfReconceptualizing transcriptional slippage in plant RNA virusesmBio02120-24Adrian A. ValliMaría Luisa Domingo-CalapAlfonso González de PrádenaJuan Antonio GarcíaHongguang CuiCécile DesbiezJuan José López-MoyaAmerican Society for MicrobiologyCopyright © 2024 Valli et al.This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.20242023RNA 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.Transcriptional 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.20240718202408192150-7511uuid:d50b2638-1792-4361-9a32-c3731aa63cefuuid:b4b76a64-1c1b-41cf-9c2c-4a887c86f23d Antenna House PDF Output Library 7.4.1901; modified using iText 4.2.0 by 1T3XT Antenna House XSL Formatter V7.4 MR2 Linux : 7.4.3.63807 (2024-03-22T11:49+09) 2024-10-08T06:56:02+00:00 2025-09-29T11:00:18-07:00 2025-09-29T11:00:18-07:00 d131477b-a02e-487c-86b8-ac90000e1700 1 Pages: Page: Sequence: 1 Annotations: Annotation: Subtype: Link Contents: CHECK_FOR_UPDATE_LOGO Rect: 505, 701, 544, 742 LastModified: D:20241008065602+00'00' Flags: Print Annotation: Subtype: Link Contents: 10.1128/mbio.02120-24 Rect: 462, 23, 534, 32 LastModified: D:20241008065602+00'00' Flags: Print Annotation: Subtype: Link Contents: Commons Attribution 4.0 International license Rect: 391, 47, 530, 65 LastModified: D:20241008065602+00'00' Flags: Print 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