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Sequence comparison and secondary structure analysis of the 3′ noncoding region of flavivirus genomes reveals multiple pseudoknots

Published online by Cambridge University Press:  11 January 2002

RENÉ C.L. OLSTHOORN  and
JOHN F. BOL
RENÉ C.L. OLSTHOORN
Affiliation:
Institute of Molecular Plant Sciences, Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, The Netherlands
JOHN F. BOL
Affiliation:
Institute of Molecular Plant Sciences, Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, The Netherlands
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Abstract

Sequences of 191 flavivirus RNAs belonging to four sero-groups were used to predict the secondary structure of the 3′ noncoding region (3′ NCR) directly upstream of the conserved terminal hairpin. In mosquito-borne flavivirus RNAs (n = 164) a characteristic structure element was identified that includes a phylogenetically well-supported pseudoknot. This element is repeated in the dengue and Japanese encephalitis RNAs and centers around the conserved sequences CS2 and RCS2. In yellow fever virus RNAs that contain one CS2 motif, only one copy of this pseudoknotted structure was found. The conserved pseudoknotted element is absent from the 3′ NCR of tick-borne virus RNAs, which altogether adopt a secondary structure that is very different from that of mosquito-borne virus RNAs. The strong conservation of the pseudoknot in mosquito-borne flavivirus RNAs implies a stronger relationship between these viruses than concluded from previous secondary structure analyses. The role of the (tandem) pseudoknots in flavivirus replication is discussed.

Keywords

dengue virusJapanese encephalitis virusmosquito-borne flavivirusphylogenetic comparisonRNA secondary structuretick-borne encephalitisyellow fever virus
Type
REPORTS
Information
RNA , Volume 7 , Issue 10 , October 2001 , pp. 1370 - 1377
Copyright
2001 RNA Society

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