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

Microbial Informatics and Experimentation

Chris Upton¹  Taylor Quon¹  Nicole S Little¹ 

[1] Biochemistry and Microbiology, University of Victoria, 213 Petch Building, Ring Road, Victoria, B.C., V8W 3P6, Canada

关键词: Robetta;    interferon;    virus;    HHpred;    dsRNA-binding protein;    poxvirus;    vaccinia;    Crocodilepox;   

Others  :  803845
DOI  :  10.1186/2042-5783-1-12

 received in 2011-05-18, accepted in 2011-11-21,  发布年份 2011

【 摘 要 】

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.

【 授权许可】

   
2011 Little et al; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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