title: The loose evolutionary relationships between transcription factors and other gene products across prokaryotes.
abstract: BACKGROUND
  Tests for the evolutionary conservation of associations between genes coding for transcription factors (TFs) and other genes have been limited to a few model organisms due to the lack of experimental information of functional associations in other organisms. We aimed at surmounting this limitation by using the most co-occurring gene pairs as proxies for the most conserved functional interactions available for each gene in a genome. We then used genes predicted to code for TFs to compare their most conserved interactions against the most conserved interactions for the rest of the genes within each prokaryotic genome available.
  
  
  RESULTS
  We plotted profiles of phylogenetic profiles, p-cubic, to compare the maximally scoring interactions of TFs against those of other genes. In most prokaryotes, genes coding for TFs showed lower co-occurrences when compared to other genes. We also show that genes coding for TFs tend to have lower Codon Adaptation Indexes compared to other genes.
  
  
  CONCLUSIONS
  The co-occurrence tests suggest that transcriptional regulation evolves quickly in most, if not all, prokaryotes. The Codon Adaptation Index analyses suggest quick gene exchange and rewiring of transcriptional regulation across prokaryotes.
authors.forename: Marc
authors.initials: M
authors.lastname: del Grande
authors.affiliation: Department of Biology, Wilfrid Laurier University, 75 University Ave, W,, N2L 3C5 Waterloo, Ontario, Canada. gmoreno@wlu.ca.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Moreno-Hagelsieb
mesh_terms: D001412:Bacillus subtilis / Q000145:classification / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D005075:Biological Evolution; D003062:Codon; D004926:Escherichia coli / Q000145:classification / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D016680:Genome, Bacterial; D010802:Phylogeny; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D014157:Transcription Factors