Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli

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 S 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.Processes that alter the rates of transcriptional initiation, elongation and termination, mRNA degradation, and mRNA translation control gene expression in all living organisms. Of these, regulation of transcriptional initiation is of greatest physiological importance in bacteria (34). About one-fourth of all Escherichia coli proteins interact functionally with nucleic acids, and about one-fourth of these are pleiotropic transcriptional regulators that control expression of multioperon regulons, primarily by influencing the transcriptional initiation step (57, 72). In fact, each regulon is defined by the activity of a transcription factor that coordinately controls expression of the operons included within that regulon (28). 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). Crp when complexed with cyclic AMP (cAMP) binds to a consensus sequence in the DNA and activates transcription of many genes while repressing transcription of a few others. Some genes are subject to both positive and negative regulation by the cAMP-Crp complex due to th...

A Comparative Analysis of Perturbations Caused by a Gene Knock-out, a Dominant Negative Allele, and a Set of Peptide Aptamers

“…5A), thus confirming the identity of the samples, the proper expression of the transgenes, and the strong Fur basal activity under our experimental conditions. 75 of the 196 selected genes have already been identified in previous transcriptome studies as Fur-and/or iron-regulated genes in E. coli (17,42), Helicobacter pylori (38,(43)(44)(45), Neisseria meningitidis (46,47), Pseudomonas aeruginosa (48,49), Campylobacter jejuni (50), Shewanella oneidensis (51,52), and Pasteurella multicoda (53). Conversely we unveiled 121 genes that have not been reported by previous studies.…”

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in StarvingEscherichia coli

“…H-NS is also required for MBR (Figure 1, A and B) apparently via its transcriptional repression of sodB (Niederhoffer et al 1990;Dubrac and Touati 2002;Zhang et al 2005), which encodes a superoxide dismutase that detoxifies ROS. Deletion of sodB completely and specifically alleviated the need for H-NS in MBR ( Figure 5F), presumably by allowing the accumulation of ROS.…”

“…The following data indicate that the known H-NS role in transcriptional repression of sodB (Niederhoffer et al 1990;Dubrac and Touati 2002;Zhang et al 2005), a superoxide dismutase that detoxifies ROS, can explain H-NS function in MBR. We found that deletion of sodB, which increases superoxide levels (Liochev and Fridovich 1997), completely substituted for H-NS in MBR ( Figure 5F).…”

Iron and Fur Regulation in Vibrio cholerae and the Role of Fur in Virulence

“…In view of this, we must consider that other Fur-regulated genes, namely those with complex regulation involving additional factors, may not have been identified in these studies. Reports for other organisms have described a number of regulatory circuits that respond to changes in iron levels, including the stringent control pathways (72) and those involving Crp (83) or the manganese regulator MntR (38,40). These networks could potentially influence the iron-dependent Fur regulon in V. cholerae.…”