A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome - PubMed (original) (raw)

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

Jinkyo Suh et al. BMC Genomics. 2012.

Abstract

Background: Almost 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.

Results: We 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.

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 genetic approaches.

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Figures

Figure 1

Figure 1

The general characteristics of secreted and transmembrane proteins. (A) Distribution of transmembrane proteins according to number of TM domains. (B) Size distribution of secreted and transmembrane proteins. “all” refers to all secreted or transmembrane proteins. “secreted” refers to putative secreted proteins. “secreted, no domain” refers to putative secreted proteins without additional domains. “TM” refers to transmembrane proteins. “TM non sr” refers to all transmembrane proteins except serpentine-type GPCRs.

Figure 2

Figure 2

Evolutionary origin of secreted and transmembrane domain proteins. Proteins in the ‘nematode’ group have no homologs outside the nematodes. The ‘metazoan’ group consists of proteins with homologs in invertebrate and vertebrates, but not in plants or fungi. The ‘eukaryotic’ group contains proteins with homologs in all the above groups. The ‘unclassified” group contain proteins that could not be grouped (see Materials and Methods for details).

Figure 3

Figure 3

Complex and repetitive secreted proteins. (A) Complex secreted proteins with four or more different domains. (B) Repetitive secreted proteins containing multiple copies of one or two different domains. See the domain help page in GExplore (

http://genome.sfu.ca/gexplore

) for a description of the domains.

Figure 4

Figure 4

Grouping of transmembrane proteins. Three major groups of transmembrane proteins are proteins without any additional predicted domains, proteins with additional domains, and serpentine-type GPCR (putative chemoreceptors). Proteins with additional domains are further divided into broad functional categories (see main text for a detailed description of the categories).

Figure 5

Figure 5

Proteins upregulated in certain stages, in males or after infection. A) Genes more than 5-fold upregulated in a particular stage based on RNA-seq data from [14]. B) Genes more than 5-fold upregulated in L4 stage males compared to L4 stage hermaphrodites based on RNA-seq data from [14]. C) Genes upregulated in at least one of the five infection scenarios used by [28]. D) Overall fraction of proteins belonging to the various groups defined in this study.

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