A Survey of Putative Secreted and Transmembrane Proteins Encoded in the C. elegans Genome

Background: Almost half of the Caenorhabditis elegans genome encodes proteins with either a signal peptide or atransmembrane domain. Therefore a substantial fraction of the proteins are localized to membranes, reside in thesecretory pathway or are secreted. While these proteins are of interest to a variety of different researchers rangingfrom developmental biologists to immunologists, most of secreted proteins have not been functionallycharacterized so far.Results: We grouped proteins containing a signal peptide or a transmembrane domain using various criteriaincluding evolutionary origin, common domain organization and functional categories. We found that putativesecreted proteins are enriched for small proteins and nematode-specific proteins. Many secreted proteins arepredominantly expressed in specific life stages or in one of the two sexes suggesting stage- or sex-specificfunctions. 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 thetransmembrane proteins can be grouped into broad functional categories based on sequence similarity to proteinswith known function. By far the largest groups are channels and transporters, various classes of enzymes andputative receptors with signaling function.Conclusion: Our 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 geneticapproaches.