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- Quantitative Analysis of RNA Polymerase Slippages for Production of P3N‑PIPO Trans‑frame Fusion Proteins in Potyvirids
- Dongjin Choi , Yoonsoo Hahn
- J. Microbiol. 2023;61(10):917-927. Published online October 16, 2023
- DOI: https://doi.org/10.1007/s12275-023-00083-z
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- 3 Web of Science
- 3 Crossref
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Abstract
- Potyvirids, members of the family Potyviridae, produce the P3N-PIPO protein, which is crucial for the cell-to-cell transport of viral genomic RNAs. The production of P3N-PIPO requires an adenine (A) insertion caused by RNA polymerase slippage at a conserved GAA AAA A ( GA6) sequence preceding the PIPO open reading frame. Presently, the slippage rate of RNA polymerase has been estimated in only a few potyvirids, ranging from 0.8 to 2.1%. In this study, we analyzed publicly available plant RNA-seq data and identified 19 genome contigs from 13 distinct potyvirids. We further investigated the RNA polymerase slippage rates at the GA6 motif. Our analysis revealed that the frequency of the A insertion variant ranges from 0.53 to 4.07% in 11 potyviruses (genus Potyvirus). For the two macluraviruses (genus Macluravirus), the frequency of the A insertion variant was found to be 0.72% and 10.96% respectively. Notably, the estimated RNA polymerase slippage rates for 12 out of the 13 investigated potyvirids were reported for the first time in this study. Our findings underscore the value of plant RNA-seq data for quantitative analysis of potyvirid genome variants, specifically at the GA6 slippage site, and contribute to a more comprehensive understanding of the RNA polymerase slippage phenomenon in potyvirids.
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Citations
Citations to this article as recorded by
- Discovery of novel tepovirus genomes with a nucleic acid-binding protein homolog by systematic analysis of plant transcriptome data
Dongjin Choi, Hyerin Park, Seungwoo Baek, Myeung Seok Choi, Sylvain Legay, Gea Guerriero, Jean-François Hausman, Yoonsoo Hahn
Acta Virologica.2025;[Epub] CrossRef - Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins
Veronika Hýsková, Kateřina Bělonožníková, Josef Chmelík, Hana Hoffmeisterová, Noemi Čeřovská, Tomáš Moravec, Helena Ryšlavá
Plants.2024; 13(9): 1236. CrossRef - Reconceptualizing transcriptional slippage in plant RNA viruses
Adrian A. Valli, María Luisa Domingo-Calap, Alfonso González de Prádena, Juan Antonio García, Hongguang Cui, Cécile Desbiez, Juan José López-Moya, Shou-Wei Ding, Andrew Firth
mBio.2024;[Epub] CrossRef
- Discovery of novel tepovirus genomes with a nucleic acid-binding protein homolog by systematic analysis of plant transcriptome data
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