Title |
Quantitative Analysis of RNA Polymerase Slippages for Production of P3N‑PIPO Trans‑frame Fusion Proteins in Potyvirids |
Author |
Dongjin Choi, and Yoonsoo Hahn* |
Address |
Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea |
Bibliography |
Journal of Microbiology, 61(10),917-927, 2023,
|
DOI |
10.1007/s12275-023-00083-z
|
Key Words |
P3N-PIPO · Pretty interesting potyviridae ORF · Potyviridae · RNA polymerase slippage |
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. |