A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation

Nucleic Acids Research
Chaminda D GunawardeneK Andrew White

Abstract

Plus-strand RNA viruses can accumulate viral RNA degradation products during infections. Some of these decay intermediates are generated by the cytosolic 5'-to-3' exoribonuclease Xrn1 (mammals and yeast) or Xrn4 (plants) and are formed when the enzyme stalls on substrate RNAs upon encountering inhibitory RNA structures. Many Xrn-generated RNAs correspond to 3'-terminal segments within the 3'-UTR of viral genomes and perform important functions during infections. Here we have investigated a 3'-terminal small viral RNA (svRNA) generated by Xrn during infections with Tobacco necrosis virus-D (family Tombusviridae). Our results indicate that (i) unlike known stalling RNA structures that are compact and modular, the TNV-D structure encompasses the entire 212 nt of the svRNA and is not functionally transposable, (ii) at least two tertiary interactions within the RNA structure are required for effective Xrn blocking and (iii) most of the svRNA generated in infections is derived from viral polymerase-generated subgenomic mRNA1. In vitro and in vivo analyses allowed for inferences on roles for the svRNA. Our findings provide a new and distinct addition to the growing list of Xrn-resistant viral RNAs and stalling structures found associa...Continue Reading

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Citations

Aug 13, 2020·Viruses·Laura R NewburnK Andrew White
Feb 19, 2021·Journal of Virology·Muhammad IlyasAnne E Simon
May 1, 2021·International Journal of Molecular Sciences·Sara Ramos-LorenteAlfredo Berzal-Herranz
Jun 24, 2021·Journal of Virology·Shaoyan ZhangFeng Qu
Jul 14, 2021·Nature Chemical Biology·Meng Zhao, Michael T Woodside
Aug 5, 2021·Journal of Virology·Chaminda D GunawardeneK Andrew White

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Datasets Mentioned

BETA
D00942.1

Methods Mentioned

BETA
in vitro transcription
electrophoresis
Infection

Software Mentioned

TNV
QuantityOne

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