Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157

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dc.contributor.authorLittle, Nicole S.
dc.contributor.authorQuon, Taylor
dc.contributor.authorUpton, Christopher
dc.date.accessioned2014-02-24T22:15:58Z
dc.date.available2014-02-24T22:15:58Z
dc.date.copyright2011en_US
dc.date.issued2011-11-21
dc.descriptionBioMed Centralen_US
dc.description.abstractBackground: 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.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.description.sponsorshipThis work was funded by a Canadian NSERC Discovery grant. We would like to thank all the University of Victoria Co-op students that have contributed to the http://Virology.ca Bioinformatics Resourceen_US
dc.identifier.citationLittle et al.: Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157. Microbial Informatics and Experimentation 2011 1:12.en_US
dc.identifier.urihttp://www.microbialinformaticsj.com/content/1/1/12
dc.identifier.urihttp://dx.doi.org/10.1186/2042-5783-1-12
dc.identifier.urihttp://hdl.handle.net/1828/5189
dc.language.isoenen_US
dc.publisherBioMed Centralen_US
dc.subjectCrocodilepox
dc.subjectvaccinia
dc.subjectpoxvirus
dc.subjectdsRNA-binding protein
dc.subjectHHpred
dc.subjectvirus
dc.subjectinterferon
dc.subjectRobetta
dc.subject.departmentDepartment of Biochemistry and Microbiology
dc.titlePrediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157en_US
dc.typeArticleen_US

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