A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome

BMC Genomics

Research Article

Jinkyo Suh¹  Harald Hutter¹ 

[1] Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada;

关键词: Caenorhabditis elegans;    Secretome, Transmembrane proteins;    Genome;    Protein domain;    Signal peptide;   

DOI  :  10.1186/1471-2164-13-333

 received in 2012-01-19, accepted in 2012-05-25,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundAlmost half of the Caenorhabditis elegans genome encodes proteins with either a signal peptide or a transmembrane domain. Therefore a substantial fraction of the proteins are localized to membranes, reside in the secretory pathway or are secreted. While these proteins are of interest to a variety of different researchers ranging from developmental biologists to immunologists, most of secreted proteins have not been functionally characterized so far.ResultsWe grouped proteins containing a signal peptide or a transmembrane domain using various criteria including evolutionary origin, common domain organization and functional categories. We found that putative secreted proteins are enriched for small proteins and nematode-specific proteins. Many secreted proteins are predominantly expressed in specific life stages or in one of the two sexes suggesting stage- or sex-specific functions. More than a third of the putative secreted proteins are upregulated upon exposure to pathogens, indicating that a substantial fraction may have a role in immune response. Slightly more than half of the transmembrane proteins can be grouped into broad functional categories based on sequence similarity to proteins with known function. By far the largest groups are channels and transporters, various classes of enzymes and putative receptors with signaling function.ConclusionOur analysis provides an overview of all putative secreted and transmembrane proteins in C. elegans. This can serve as a basis for selecting groups of proteins for large-scale functional analysis using reverse genetic approaches.

【 授权许可】

CC BY   
© Suh and Hutter; licensee BioMed Central Ltd. 2012