Phylogenetic prediction of cis-acting elements: a <it>cre</it>-like sequence in Norovirus genome?

• Main Authors: Leite José P, Miagostovich Marize, Colina Rodney, Victoria Matías, Cristina Juan
• Format: Article
• Language: English
• Published: BMC 2009-09-01
• Series: BMC Research Notes
• Online Access: http://www.biomedcentral.com/1756-0500/2/176

<p>Abstract</p> <p>Background</p> <p>Discrete RNA structures such as <it>cis</it>-acting replication elements (<it>cre</it>) in the coding region of RNA virus genomes create characteristic suppression of synonymous site variability (SSSV). Different phylogenetic methods have been developed to predict secondary structures in RNA viruses, for high-resolution thermodynamic scanning and for detecting SSSV. These approaches have been successfully in predicting cis-acting signals in different members of the family <it>Picornaviridae </it>and <it>Caliciviridae</it>. In order to gain insight into the identification of <it>cis</it>-acting signals in viruses whose mechanisms of replication are currently unknown, we performed a phylogenetic analysis of complete genome sequences from 49 Human Norovirus (NoV) strains.</p> <p>Findings</p> <p>The complete coding sequences of NoV ORF1 were obtained from the DDBJ database and aligned. Shannon entropy calculations and RNAalifold consensus RNA structure prediction identified a discrete, conserved, invariant sequence region with a characteristic AAACG <it>cre </it>motif at positions 240 through 291 of the RNA dependant RNA polymerase (RdRp) sequence (relative to strain [EMBL:<ext-link ext-link-id="EU794713" ext-link-type="embl">EU794713</ext-link>]). This sequence region has a high probability to conform a stem-loop.</p> <p>Conclusion</p> <p>A new predicted stem-loop has been identified near the 5' end of the RdRp of Human NoV genome. This is the same location recently reported for <it>Hepatovirus cre </it>stem-loop.</p>