title: Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes.
abstract: 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.
authors.affiliation: Institute of Molecular Biology, University of Zurich, Zurich, Switzerland. sabine.schrimpf@molbio.uzh.ch
authors.forename: Sabine P
authors.initials: SP
authors.lastname: Schrimpf
authors.forename: Manuel
authors.initials: M
authors.lastname: Weiss
authors.forename: Lukas
authors.initials: L
authors.lastname: Reiter
authors.forename: Christian H
authors.initials: CH
authors.lastname: Ahrens
authors.forename: Marko
authors.initials: M
authors.lastname: Jovanovic
authors.forename: Johan
authors.initials: J
authors.lastname: Malmström
authors.forename: Erich
authors.initials: E
authors.lastname: Brunner
authors.forename: Sonali
authors.initials: S
authors.lastname: Mohanty
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Lercher
authors.forename: Peter E
authors.initials: PE
authors.lastname: Hunziker
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.forename: Michael O
authors.initials: MO
authors.lastname: Hengartner
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics*; D020440:Gene Duplication; D016678:Genome; D009876:Operon; D020543:Proteome; D040901:Proteomics / Q000379:methods; D017386:Sequence Homology, Amino Acid
chemical_list: D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D020543:Proteome