title: Non-canonical CRP sites control competence regulons in Escherichia coli and many other gamma-proteobacteria.
abstract: Escherichia coli's cAMP receptor protein (CRP), the archetypal bacterial transcription factor, regulates over a hundred promoters by binding 22 bp symmetrical sites with the consensus core half-site TGTGA. However, Haemophilus influenzae has two types of CRP sites, one like E.coli's and one with the core sequence TGCGA that regulates genes required for DNA uptake (natural competence). Only the latter 'CRP-S' sites require both CRP and the coregulator Sxy for activation. To our knowledge, the TGTGA and TGCGA motifs are the first example of one transcription factor having two distinct binding-site motifs. Here we show that CRP-S promoters are widespread in the gamma-proteobacteria and demonstrate their Sxy-dependence in E.coli. Orthologs of most H.influenzae CRP-S-regulated genes are ubiquitous in the five best-studied gamma-proteobacteria families, Enterobacteriaceae, Pasteurellaceae, Pseudomonadaceae, Vibrionaceae and Xanthomonadaceae. Phylogenetic footprinting identified CRP-S sites in the promoter regions of the Enterobacteriaceae, Pasteurellaceae and Vibrionaceae orthologs, and canonical CRP sites in orthologs of genes known to be Sxy-independent in H.influenzae. Bandshift experiments confirmed that E.coli CRP-S sequences are low affinity binding sites for CRP, and mRNA analysis showed that they require CRP, cAMP (CRP's allosteric effector) and Sxy for gene induction. This work suggests not only that the gamma-proteobacteria share a common DNA uptake mechanism, but also that, in the three best studied families, their competence regulons share both CRP-S specificity and Sxy dependence.
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Andrew D S
authors.initials: AD
authors.lastname: Cameron
authors.forename: Rosemary J
authors.initials: RJ
authors.lastname: Redfield
mesh_terms: D001426:Bacterial Proteins / Q000145:classification / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D002373:Cyclic AMP Receptor Protein; D004269:DNA, Bacterial / Q000737:chemistry; D004755:Enterobacteriaceae / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000145:classification / Q000378:metabolism*; D019143:Evolution, Molecular; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D006193:Haemophilus influenzae / Q000235:genetics; D015661:Pasteurellaceae / Q000235:genetics; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D011548:Pseudomonadaceae / Q000235:genetics; D011956:Receptors, Cell Surface / Q000145:classification / Q000378:metabolism*; D018085:Regulon; D015534:Trans-Activators / Q000145:classification / Q000378:metabolism; D014157:Transcription Factors / Q000145:classification / Q000378:metabolism*; D015533:Transcriptional Activation; D014737:Vibrionaceae / Q000235:genetics; D044166:Xanthomonadaceae / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D002373:Cyclic AMP Receptor Protein; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D011956:Receptors, Cell Surface; C093149:Tfox protein, Haemophilus influenzae; D015534:Trans-Activators; D014157:Transcription Factors; C481662:crp protein, E coli