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Quantitative Analysis of RNA Polymerase Slippages for Production of P3N-PIPO Trans-frame Fusion Proteins in Potyvirids

  • Systems and Synthetic Microbiology and Bioinformatics
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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 GAAAAAA (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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Data availability

We used only publicly available data, and the accession numbers are presented in the text or tables.

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Acknowledgements

This work was supported by the National Research Foundation of Korea (NRF) Grants funded by the Government of Korea (Grant numbers: 2018R1A5A1025077 and RS-2023-00208564).

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  1. Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea

    Dongjin Choi & Yoonsoo Hahn

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  1. Dongjin Choi
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Correspondence to Yoonsoo Hahn.

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Choi, D., Hahn, Y. Quantitative Analysis of RNA Polymerase Slippages for Production of P3N-PIPO Trans-frame Fusion Proteins in Potyvirids. J Microbiol. 61, 917–927 (2023). https://doi.org/10.1007/s12275-023-00083-z

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