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.
Highlights
The rapid lifecycle, small size, reproducible development, and ease of cultivation in the laboratory have made Caenorhabditis elegans an important experimental system for biological studies
We used mass spectrometry to extensively characterize the proteins of a popular model organism, the nematode Caenorhabditis elegans
Because many C. elegans and D. melanogaster proteins have counterparts in humans, our results suggest that similar rules may apply to our own proteins
Summary
The rapid lifecycle, small size, reproducible development, and ease of cultivation in the laboratory have made Caenorhabditis elegans an important experimental system for biological studies. Sequencing and annotation of its genome has revealed more than 19,000 genes [2] coding for more than 22,000 proteins, including splice variants. Extensive systematic studies of gene function have been performed. To completely understand complex biological processes such as development, aging, or disease, the analysis of the proteome—i.e., the entire set of the expressed proteins—is becoming increasingly important. Knowledge of the complete sequence of a genome is a necessary prerequisite for proteomics, but the DNA sequence itself does not reveal which proteins are expressed when, where, and to what level. The analysis of the proteome is a key method to provide systems-level information about protein function in time and space, and to obtain a concise view of biological processes. In the case of C. elegans, previous analyses of the proteome were either limited in scope and coverage [6,7], or largely focused on improving genome annotation [8], with the biggest C. elegans proteome dataset published so far encompassing 6,779 proteins [8]
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