The transcriptional regulation of protein complexes; a cross-species perspective.
The extent of co-expression of the components of a comprehensive set of 244 multi-subunit protein complexes over large DNA microarray data sets was investigated in S. cerevisiae, A. thaliana, C. elegans, D. melanogaster and H. sapiens. Co-expression amongst the components of protein complexes is substantial and occurs in all the species studied, reflecting the importance of regulation at the level of the transcript. Complexes that are conserved in all species, and tend to be associated with very fundamental biological processes, are significantly more likely to have co-expressed components, indicating the fundamental and ancient evolutionary nature of transcriptional regulation. Less conserved complexes are more likely to have evolved alternative regulatory mechanisms. Within the conserved complexes there is evidence that regulatory mechanisms (transcriptional or other) are evolutionarily conserved, but there are exceptions. The fact that complexes that share subunits are more likely to share co-expression is further evidence of evolutionary conservation of regulatory mechanisms. This extensive study contributes to the fundamental biological understanding of important protein complexes by enabling evolutionary insights into their regulation through a new multi-genome perspective. In addition, it is relevant to developers and users of gene function prediction methods that use gene co-expression to indicate potential functional linkage.
Webb
Elizabeth C
EC
Institute of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK. bgy7ecw@leeds.ac.uk
Westhead
David R
DR
D000818:Animals; D029681:Arabidopsis Proteins / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics*; D018844:Cyclin-Dependent Kinases / Q000235:genetics; D016213:Cyclins / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D029721:Drosophila Proteins / Q000235:genetics*; D004579:Electron Transport / Q000235:genetics; D005786:Gene Expression Regulation; D018506:Gene Expression Regulation, Plant; D006801:Humans; D046912:Multiprotein Complexes / Q000235:genetics*; D046988:Proteasome Endopeptidase Complex / Q000235:genetics; D011499:Protein Processing, Post-Translational; D016601:RNA-Binding Proteins / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D013045:Species Specificity; D014158:Transcription, Genetic; D025262:Vacuolar Proton-Translocating ATPases / Q000235:genetics
D029681:Arabidopsis Proteins; D029742:Caenorhabditis elegans Proteins; D016213:Cyclins; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D046912:Multiprotein Complexes; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; D029701:Saccharomyces cerevisiae Proteins; D018844:Cyclin-Dependent Kinases; D046988:Proteasome Endopeptidase Complex; D025262:Vacuolar Proton-Translocating ATPases