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J Gen Virol 85 (2004), 1113-1124; DOI 10.1099/vir.0.19462-0

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© 2004 Society for General Microbiology

Conserved RNA secondary structures in Flaviviridae genomes

Caroline Thurner1, Christina Witwer1, Ivo L. Hofacker1 and Peter F. Stadler1,2,3

1 Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria
2 Bioinformatik, Institut für Informatik, Universität Leipzig, Kreuzstraße 7b, D-04103 Leipzig, Germany
3 The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA

Correspondence
Ivo L. Hofacker
ivo{at}tbi.univie.ac.at

Presented here is a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae. This virus family consists of the three genera Flavivirus, Pestivirus and Hepacivirus and the group of GB virus C/hepatitis G virus with a currently uncertain taxonomic classification. Based on the control of replication and translation, two subgroups were considered separately: the genus Flavivirus, with its type I cap structure at the 5' untranslated region (UTR) and a highly structured 3' UTR, and the remaining three groups, which exhibit translation control by means of an internal ribosomal entry site (IRES) in the 5' UTR and a much shorter less-structured 3' UTR. The main findings of this survey are strong hints for the possibility of genome cyclization in hepatitis C virus and GB virus C/hepatitis G virus in addition to the flaviviruses; a surprisingly large number of conserved RNA motifs in the coding regions; and a lower level of detailed structural conservation in the IRES and 3' UTR motifs than reported in the literature. An electronic atlas organizes the information on the more than 150 conserved, and therefore putatively functional, RNA secondary structure elements.

Supplementary figures are supplied in JGV Online.




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