Abstract
In Escherichia coli, the ferric uptake regulator (Fur) controls expression of the iron regulon in response to iron availability while the cyclic AMP receptor protein (Crp) regulates expression of the carbon regulon in response to carbon availability. We here identify genes subject to significant changes in expression level in response to the loss of both Fur and Crp. Many iron transport genes and several carbon metabolic genes are subject to dual control, being repressed by the loss of Crp and activated by the loss of Fur. However, the sodB gene, encoding superoxide dismutase, and the aceBAK operon, encoding the glyoxalate shunt enzymes, show the opposite responses, being activated by the loss of Crp and repressed by the loss of Fur. Several other genes including the sdhA-D, sucA-D, and fumA genes, encoding key constituents of the Krebs cycle, proved to be repressed by the loss of both transcription factors. Finally, the loss of both Crp and Fur activated a heterogeneous group of genes under sigmaS control encoding, for example, the cyclopropane fatty acid synthase, Cfa, the glycogen synthesis protein, GlgS, the 30S ribosomal protein, S22, and the mechanosensitive channel protein, YggB. Many genes appeared to be regulated by the two transcription factors in an apparently additive fashion, but apparent positive or negative cooperativity characterized several putative Crp/Fur interactions. Relevant published data were evaluated, putative Crp and Fur binding sites were identified, and representative results were confirmed by real-time PCR. Molecular explanations for some, but not all, of these effects are provided.
Highlights
Processes that alter the rates of transcriptional initiation, elongation and termination, mRNA degradation, and mRNA translation control gene expression in all living organisms
We show that the loss of cyclic AMP receptor protein (Crp) and ferric uptake regulator (Fur) regulates expression of the genes encoding the oxidative stress enzyme, superoxide dismutase, and the aceBAK operon encoding the glyoxalate shunt enzymes in directions opposite to those observed for the iron transport genes
The n-fold change was at least 4 times higher than the SDLR for the ALS of the gene when comparing wt and fur or wt and crp fur. (ii) A large signal was observed in at least one of the mutant strains. (iii) The ratio for crp fur/fur was Յ0.5 or Ն2 following growth in LB broth
Summary
Processes that alter the rates of transcriptional initiation, elongation and termination, mRNA degradation, and mRNA translation control gene expression in all living organisms. The global regulator, responsive to select cellular stimuli, binds to specific sites in the control regions of these operons Examples of such pleiotropic transcription factors in E. coli include Crp, a primary sensor of carbon availability [8, 15, 23, 65], NtrBC, a sensor of nitrogen availability [32, 63, 77], CysB, the sensor of sulfur availability [38, 39, 41, 42], and Fur, a dominant sensor of iron availability [30, 31, 50, 71]. This work serves to suggest a previously unrecognized transcriptional regulatory connection between iron and carbon metabolism
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