Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

• Published in: PLoS biology Vol. 7; no. 3; pp. e48 - e1000048
• Main Authors: Schrimpf, Sabine P, Weiss, Manuel, Reiter, Lukas, Ahrens, Christian H, Jovanovic, Marko, Malmström, Johan, Brunner, Erich, Mohanty, Sonali, Lercher, Martin J, Hunziker, Peter E, Aebersold, Ruedi, von Mering, Christian, Hengartner, Michael O
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.03.2009; Public Library of Science (PLoS)
• Subjects: Animals; Biochemistry; Biotechnology; Caenorhabditis elegans; Caenorhabditis elegans - genetics; Caenorhabditis elegans Proteins - genetics; Drosophila melanogaster; Drosophila melanogaster - genetics; Drosophila Proteins - genetics; Evolutionary Biology; Gene Duplication; Genetics; Genome; Genomics; Medical research; Metazoa; Nematoda; Nematodes; Operon; Proteins; Proteome; Proteomics - methods; Sequence Homology, Amino Acid; Gene Duplication; Sequence Homology, Amino Acid; Caenorhabditis elegans; Drosophila Proteins; Caenorhabditis elegans Proteins; Animals; Operon; Proteomics; Proteome; Genome; Drosophila melanogaster
• ISSN: 1545-7885; 1544-9173; 1545-7885
• DOI: 10.1371/journal.pbio.1000048

The nematode Caenorhabditis elegans is a popular model system in genetics, not least because a majority of human disease genes are conserved in C. elegans. To generate a comprehensive inventory of its expressed proteome, we performed extensive shotgun proteomics and identified more than half of all predicted C. elegans proteins. This allowed us to confirm and extend genome annotations, characterize the role of operons in C. elegans, and semiquantitatively infer abundance levels for thousands of proteins. Furthermore, for the first time to our knowledge, we were able to compare two animal proteomes (C. elegans and Drosophila melanogaster). We found that the abundances of orthologous proteins in metazoans correlate remarkably well, better than protein abundance versus transcript abundance within each organism or transcript abundances across organisms; this suggests that changes in transcript abundance may have been partially offset during evolution by opposing changes in protein abundance.