Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157
Date
2011-11-21
Authors
Little, Nicole S.
Quon, Taylor
Upton, Christopher
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: Although the crocodilepox virus (CRV) is currently unclassified, phylogenetic analyses suggest that its
closest known relatives are molluscum contagiosum virus (MCV) and the avipox viruses. The CRV genome is
approximately 190 kb and contains a large number of unique genes in addition to the set of conserved
Chordopoxvirus genes found in all such viruses. Upon sequencing the viral genome, others noted that this virus
was also unusual because of the lack of a series of common immuno-suppressive genes. However, the genome
contains multiple genes of unknown function that are likely to function in reducing the anti-viral response of the
host.
Results: By using sensitive database searches for similarity, we observed that gene 157 of CRV-strain Zimbabwe
(CRV-ZWE) encodes a protein with a domain that is predicted to bind dsRNA. Domain characterization supported
this prediction, therefore, we tested the ability of the Robetta protein structure prediction server to model the
amino acid sequence of this protein on a well-characterized RNA binding domain. The model generated by
Robetta suggests that CRV-ZWE-157 does indeed contain an RNA binding domain; the model could be overlaid on
the template protein structure with high confidence.
Conclusion: We hypothesize that CRV-ZWE-157 encodes a novel poxvirus RNA binding protein and suggest that as
a non-core gene it may play a role in host-range determination or function to dampen host anti-viral responses.
Potential targets for this CRV protein include the host interferon response and miRNA pathways.
Description
BioMed Central
Keywords
Crocodilepox, vaccinia, poxvirus, dsRNA-binding protein, HHpred, virus, interferon, Robetta
Citation
Little et al.: Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157. Microbial Informatics and Experimentation 2011 1:12.