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Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Coria, Aaztli 
Wienecke, Anastacia 
Knight, Michael L 
Desirò, Daniel 

Abstract

Due to genome segmentation, rotaviruses must co-package eleven distinct genomic RNAs. The packaging is mediated by virus-encoded RNA chaperones, such as the rotavirus NSP2 protein. While the activities of distinct RNA chaperones are well studied on smaller RNAs, little is known about their global effect on the entire viral transcriptome. Here, we used Selective 2'-hydroxyl Acylation Analyzed by Primer Extension and Mutational Profiling (SHAPE-MaP) to examine the secondary structure of the rotavirus transcriptome in the presence of increasing amounts of NSP2. SHAPE-MaP data reveals that despite the well-documented helix-unwinding activity of NSP2 in vitro, its incubation with cognate rotavirus transcripts does not induce a significant change in the SHAPE reactivities. However, a quantitative analysis of mutation rates measured by mutational profiling reveals a global 5-fold rate increase in the presence of NSP2. We demonstrate that the normalization procedure used in deriving SHAPE reactivities from mutation rates can mask an important global effect of an RNA chaperone. Analysis of the mutation rates reveals a larger effect on stems rather than loops. Together, these data provide the first experimentally derived secondary structure model of the rotavirus transcriptome and reveal that NSP2 acts by globally increasing RNA backbone flexibility in a concentration-dependent manner.

Description

Funder: National Institute of General Medical Sciences


Funder: NIGMS NIH HHS

Keywords

Molecular Chaperones, Protein Structure, Secondary, RNA, Viral, Rotavirus, Transcriptome, Viral Nonstructural Proteins

Journal Title

Nucleic Acids Res

Conference Name

Journal ISSN

0305-1048
1362-4962

Volume Title

50

Publisher

Oxford University Press (OUP)
Sponsorship
National Institutes of Health (R01 HL111527, R35 GM140844)
NIH HHS (R35 GM140844)
Wellcome Trust (213437/Z/18/Z, 103068/Z/13/Z)