Yang, Y. (Yan), Yi, MinKyung, Evans, D. J. (David J.), Simmonds, Peter and Lemon, Stanley M.. (2008) Identification of a Conserved RNA Replication Element (cre) within the 3D(pol)-Coding Sequence of Hepatoviruses. Journal of Virology, Volume 82 (Number 20). pp. 10118-10128. ISSN 0022-538X

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Abstract

Internally located, cis-acting RNA replication elements (cre) have been identified within the genomes of viruses representing each of the major picornavirus genera (Enterovirus, Rhinovirus, Aphthovirus, and Cardiovirus) except Hepatovirus. Previous efforts to identify a stem-loop structure with cre function in hepatitis A virus (HAV),the type species of this genus, by phylogenetic analyses or thermodynamic predictions have not succeeded. However, a region of markedly suppressed synonymous codon variability was identified in alignments of HAV sequences near the 5' end of the 3D(pol)-coding sequence of HAV, consistent with noncoding constraints imposed by an underlying RNA secondary structure. Subsequent MFOLD predictions identified a 110-nucleotide (nt) complex stem-loop in this region with a typical AAACA/G cre motif in its top loop. A potentially homologous RNA structure was identified in this region of the avian encephalitis virus genome, despite little nucleotide sequence relatedness between it and HAV. Mutations that disrupted secondary RNA structure or the AAACA/G motif, without altering the amino acid sequence of 3D(pol), ablated replication of a subgenomic HAV replicon in transfected human hepatoma cells. Replication competence could be rescued by reinsertion of the native 110-nt stem-loop structure (but not an abbreviated 45-nt stem-loop) upstream of the HAV coding sequence in the replicon. These results suggest that this stem-loop is functionally similar to cre elements of other picornaviruses and likely involved in templating VPg uridylylation as in other picornaviruses, despite its significantly larger size and lower free folding energy.

Item Type:	Journal Article
Subjects:	Q Science > QR Microbiology > QR355 Virology
Divisions:	Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	RNA viruses -- Reproduction, Viral genomes, Hepatitis A virus, Picornaviruses
Journal or Publication Title:	Journal of Virology
Publisher:	American Society for Microbiology
ISSN:	0022-538X
Date:	October 2008
Volume:	Volume 82
Number:	Number 20
Number of Pages:	11
Page Range:	pp. 10118-10128
Identification Number:	10.1128/JVI.00787-08
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	National Institutes of Health (U.S.) (NIH), McLaughlin Postdoctoral Fellowship
Grant number:	U19-AI40035 (NIH)
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URI:	http://wrap.warwick.ac.uk/id/eprint/29176

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