This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Yang, Y.
Right arrow Articles by Lemon, S. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yang, Y.
Right arrow Articles by Lemon, S. M.

 Previous Article  |  Next Article 

Journal of Virology, October 2008, p. 10118-10128, Vol. 82, No. 20
0022-538X/08/$08.00+0     doi:10.1128/JVI.00787-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Identification of a Conserved RNA Replication Element (cre) within the 3Dpol-Coding Sequence of Hepatoviruses{triangledown}

Yan Yang ,1,{dagger},{ddagger} MinKyung Yi,1,{ddagger} David J. Evans,2 Peter Simmonds,3 and Stanley M. Lemon1*

Center for Hepatitis Research, Institute for Human Infections and Immunity, and the Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555-1073,1 Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom,2 Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom3

Received 12 April 2008/ Accepted 29 July 2008

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 3Dpol-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 3Dpol, 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.

* Corresponding author. Mailing address: Center for Hepatitis Research, 4.104 Blocker Medical Research Bldg., University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1073. Phone: (409) 747-7048. Fax: (409) 747-7030. E-mail: smlemon{at}utmb.edu

{triangledown} Published ahead of print on 6 August 2008.

{dagger} Present address: University of Texas M. D. Anderson Cancer Center, Houston, TX.

{ddagger} These authors contributed equally to this work.

Journal of Virology, October 2008, p. 10118-10128, Vol. 82, No. 20
0022-538X/08/$08.00+0     doi:10.1128/JVI.00787-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Chen, T.-C., Chang, H.-Y., Lin, P.-F., Chern, J.-H., Hsu, J. T.-A., Chang, C.-Y., Shih, S.-R. (2009). Novel Antiviral Agent DTriP-22 Targets RNA-Dependent RNA Polymerase of Enterovirus 71. Antimicrob. Agents Chemother. 53: 2740-2747 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»