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Titel:
Conserved RNA Secondary Structures in Flaviviridae Genomes
Author(s):
Caroline Thurner,
Christina Witwer,
Ivo L. Hofacker,
Peter F. Stadler,
Abstract:
We report here on 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, Hepacivirus and the group of
Hepatitis G Viruses 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 that exhibit translation control by means of a Internal
Ribosomal Entry Site (IRES) in the 5'UTR and a much shorter less structured
3'UTR. The main findings of our survey are: strong evidence for the
possibility of genome cyclization in Hepatitis C and G viruses 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.
Keywords:
Flaviviridae, RNA secondary structure,
Internal Ribosomal Entry Site (IRES), Genome Cyclization.
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Last modified: 2004-02-11 13:15:31 ivo