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

Sequences of 191 flavivirus RNAs belonging to four sero-groups were used to predict the secondary structure of the 3' noncoding region (3' NCR) direct ly upstream of the conserved terminal hairpin. In mosquito-borne flavivirus RNAs (n = 164) a characteristic structure element was identified that incl udes a phylogenetically well-supported pseudoknot. This element is repeated in the dengue and Japanese encephalitis RNAs and centers around the conser ved!, sequences CS2 and RCS2. In yellow fever virus RNAs that contain one C S2 motif, only one copy of this pseudoknotted: structure was found. The con served pseudoknotted element is absent from the 3' NCR of tick-borne virus RNAs, which altogether adopt a secondary structure that is very different f rom that of mosquito-borne virus RNAs. The strong conservation of the pseud oknot in mosquito-borne flavivirus RNAs implies a stronger relationship bet ween these viruses than concluded! from! previous secondary structure analy ses. The role of the (tandem) pseudoknots in flavivirus replication is disc ussed.