A survey of putative secreted and transmembrane proteins encoded in the <it>C. elegans</it> genome
<p>Abstract</p> <p>Background</p> <p>Almost half of the <it>Caenorhabditis elegans</it> 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...
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| Format: | Article |
| Language: | English |
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BMC
2012-07-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/333 |
| _version_ | 1811283610051805184 |
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| author | Suh Jinkyo Hutter Harald |
| author_facet | Suh Jinkyo Hutter Harald |
| author_sort | Suh Jinkyo |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Almost half of the <it>Caenorhabditis elegans</it> 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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>Our analysis provides an overview of all putative secreted and transmembrane proteins in <it>C. elegans</it>. This can serve as a basis for selecting groups of proteins for large-scale functional analysis using reverse genetic approaches.</p> |
| first_indexed | 2024-04-13T02:15:40Z |
| format | Article |
| id | doaj.art-3a430769b0bd40ab943760ad29b4a159 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T02:15:40Z |
| publishDate | 2012-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-3a430769b0bd40ab943760ad29b4a1592022-12-22T03:07:10ZengBMCBMC Genomics1471-21642012-07-0113133310.1186/1471-2164-13-333A survey of putative secreted and transmembrane proteins encoded in the <it>C. elegans</it> genomeSuh JinkyoHutter Harald<p>Abstract</p> <p>Background</p> <p>Almost half of the <it>Caenorhabditis elegans</it> 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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>Our analysis provides an overview of all putative secreted and transmembrane proteins in <it>C. elegans</it>. This can serve as a basis for selecting groups of proteins for large-scale functional analysis using reverse genetic approaches.</p>http://www.biomedcentral.com/1471-2164/13/333<it>Caenorhabditis elegans</it>Secretome, Transmembrane proteinsGenomeProtein domainSignal peptide |
| spellingShingle | Suh Jinkyo Hutter Harald A survey of putative secreted and transmembrane proteins encoded in the <it>C. elegans</it> genome BMC Genomics <it>Caenorhabditis elegans</it> Secretome, Transmembrane proteins Genome Protein domain Signal peptide |
| title | A survey of putative secreted and transmembrane proteins encoded in the <it>C. elegans</it> genome |
| title_full | A survey of putative secreted and transmembrane proteins encoded in the <it>C. elegans</it> genome |
| title_fullStr | A survey of putative secreted and transmembrane proteins encoded in the <it>C. elegans</it> genome |
| title_full_unstemmed | A survey of putative secreted and transmembrane proteins encoded in the <it>C. elegans</it> genome |
| title_short | A survey of putative secreted and transmembrane proteins encoded in the <it>C. elegans</it> genome |
| title_sort | survey of putative secreted and transmembrane proteins encoded in the it c elegans it genome |
| topic | <it>Caenorhabditis elegans</it> Secretome, Transmembrane proteins Genome Protein domain Signal peptide |
| url | http://www.biomedcentral.com/1471-2164/13/333 |
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