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This article is part of the supplement: Tenth International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Computational Biology

Open Access Proceedings

Functional characterization of protein domains common to animal viruses and mouse

Akira R Kinjo1*, Yutaro Kumagai2, Huy Dinh3, Osamu Takeuchi2 and Daron M Standley3*

Author Affiliations

1 Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan

2 Laboratory of Host Defense, WPI Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan

3 Laboratory of Systems Immunology, WPI Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan

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BMC Genomics 2011, 12(Suppl 3):S21  doi:10.1186/1471-2164-12-S3-S21

Published: 30 November 2011

Abstract

Background

Many viruses contain genes that originate from their hosts. Some of these acquired genes give viruses the ability to interfere with host immune responses by various mechanisms. Genes of host origin that appear commonly in viruses code for proteins that span a wide range of functions, from kinases and phosphotases, to cytokines and their receptors, to ubiquitin ligases and proteases. While many important cases of such lateral gene transfer in viruses have been documented, there has yet to be a genome-wide survey of viral-encoded genes acquired from animal hosts.

Results

Here we carry out such a survey in order to gain insight into the host immune system. We made the results available in the form of a web-based tool that allows viral-centered or host-centered queries to be performed (http://imm.ifrec.osaka-u.ac.jp/musvirus/ webcite). We examine the relationship between acquired genes and immune function, and compare host-virus homology with gene expression data in stimulated dendritic cells and T-cells. We found that genes whose expression changes significantly during the innate antiviral immune response had more homologs in animal virus than genes whose expression did not change or genes involved in the adaptive immune response.

Conclusions

Statistics gathered from the MusVirus database support earlier reports of gene transfer from host to virus and indicate that viruses are more likely to acquire genes involved in innate antiviral immune responses than those involved in acquired immune responses.