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Bioinformatic and physical characterizations of genome-scale ordered RNA structure in mammalian RNA viruses

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Davis, M. (Matthew), Sagan, Selena M., Pezacki, John P., Evans, D. J. (David J.) and Simmonds, Peter. (2008) Bioinformatic and physical characterizations of genome-scale ordered RNA structure in mammalian RNA viruses. Journal of Virology, Vol.82 (No.23). pp. 11824-11836. ISSN 0022-538X

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Official URL: http://dx.doi.org/10.1128/JVI.01078-08

Abstract

By the analysis of thermodynamic RNA secondary structure predictions, we previously obtained evidence for evolutionarily conserved large-scale ordering of RNA virus genomes (P. Simmonds, A. Tuplin, and D.J. Evans, RNA 10: 1337-1351, 2004). Genome-scale ordered RNA structure (GORS) was widely distributed in many animal and plant viruses, much greater in extent than RNA structures required for viral translation or replication, but in mammalian viruses was associated with host persistence. To substantiate the existence of large-scale RNA structure differences between viruses, a large set of alignments of mammalian RNA viruses and rRNA sequences as controls were examined by thermodynamic methods (to calculate minimum free energy differences) and by algorithmically independent RNAz and Pfold methods. These methods produced generally concordant results and identified substantial differences in the degrees of evolutionarily conserved, sequence order-dependent RNA secondary structure between virus genera and groups. A probe hybridization accessibility assay was used to investigate the physical nature of GORS. Transcripts of hepatitis C virus (HCV), hepatitis G virus/GB virus-C (HGV/GBV-C), and murine norovirus, which are predicted to be structured, were largely inaccessible to hybridization in solution, in contrast to the almost universal binding of probes to a range of unstructured virus transcripts irrespective of G + C content. Using atomic force microscopy, HCV and HGV/GBV-C RNA was visualized as tightly compacted prolate spheroids, while under the same experimental conditions the predicted unstructured poliovirus and rubella virus RNA were pleomorphic and had extensively single-stranded RNA on deposition. Bioinformatic and physical characterization methods both identified fundamental differences in the configurations of viral genomic RNA that may modify their interactions with host cell defenses and their ability to persist.

Item Type:

Journal Article

Subjects:

Q Science > QP Physiology
Q Science > QR Microbiology > QR355 Virology

Divisions:

Faculty of Science > Life Sciences (2010- ) > Biological Sciences ( -2010)

Library of Congress Subject Headings (LCSH):

RNA -- Structure, RNA viruses, Genomics, Bioinformatics

Journal or Publication Title:

Journal of Virology

Publisher:

American Society for Microbiology

ISSN:

0022-538X

Official Date:

December 2008

Dates:

Date	Event
December 2008	Published

Volume:

Vol.82

Number:

No.23

Number of Pages:

Page Range:

pp. 11824-11836

Identification Number:

10.1128/JVI.01078-08

Status:

Peer Reviewed

Publication Status:

Published

Access rights to Published version:

Restricted or Subscription Access

Funder:

Wellcome Trust (London, England)

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