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Journal of Virology, July 2008, p. 7047-7058, Vol. 82, No. 14
0022-538X/08/$08.00+0     doi:10.1128/JVI.00654-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Genetic Interactions among the West Nile Virus Methyltransferase, the RNA-Dependent RNA Polymerase, and the 5' Stem-Loop of Genomic RNA

Bo Zhang,¹ Hongping Dong,¹ Yangsheng Zhou,² and Pei-Yong Shi^1,2*

Wadsworth Center, New York State Department of Health,¹ Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York 12201²

Received 24 March 2008/ Accepted 21 April 2008

Flavivirus methyltransferase catalyzes both guanine N7 and ribose 2'-OH methylations of the viral RNA cap (GpppA-RNAm⁷GpppAm-RNA). The methyltransferase is physically linked to an RNA-dependent RNA polymerase (RdRp) in the flaviviral NS5 protein. Here, we report genetic interactions of West Nile virus (WNV) methyltransferase with the RdRp and the 5'-terminal stem-loop of viral genomic RNA. Genome-length RNAs, containing amino acid substitutions of D146 (a residue essential for both cap methylations) in the methyltransferase, were transfected into BHK-21 cells. Among the four mutant RNAs (D146L, D146P, D146R, and D146S), only D146S RNA generated viruses in transfected cells. Sequencing of the recovered viruses revealed that, besides the D146S change in the methyltransferase, two classes of compensatory mutations had reproducibly emerged. Class 1 mutations were located in the 5'-terminal stem-loop of the genomic RNA (a G35U substitution or U38 insertion). Class 2 mutations resided in NS5 (K61Q in methyltransferase and W751R in RdRp). Mutagenesis analysis, using a genome-length RNA and a replicon of WNV, demonstrated that the D146S substitution alone was lethal for viral replication; however, the compensatory mutations rescued replication, with the highest rescuing efficiency occurring when both classes of mutations were present. Biochemical analysis showed that a low level of N7 methylation of the D146S methyltransferase is essential for the recovery of adaptive viruses. The methyltransferase K61Q mutation facilitates viral replication through improved N7 methylation activity. The RdRp W751R mutation improves viral replication through an enhanced polymerase activity. Our results have clearly established genetic interactions among flaviviral methyltransferase, RdRp, and the 5' stem-loop of the genomic RNA.

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* Corresponding author. Mailing address: Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208. Phone: (518) 473-7487. Fax: (518) 473-1326. E-mail: ship{at}wadsworth.org

Published ahead of print on 30 April 2008.

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Journal of Virology, July 2008, p. 7047-7058, Vol. 82, No. 14
0022-538X/08/$08.00+0     doi:10.1128/JVI.00654-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

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