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 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.

FIG. 1.

The aceBAK upstream regulatory region showing all known binding sites for protein transcription factors known to influence operon expression as well as the putative Crp and Fur binding sites. The relative positions and lengths of all binding sites are drawn to scale. See the text for discussion of the regulators.

FIG. 2.

Effect of glucose on growth of E. coli strains used in this study. Cells were grown in LB medium (A) or in LB medium plus 0.4% glucose (B) at 37°C with shaking (250 rpm) in 25 ml of medium in 250-ml Erlenmeyer flasks. These conditions are identical to those used for the transcriptome and real-time PCR experiments. Strains were as follows: triangles, wild type (BW25113); diamonds, crp mutant; squares, fur mutant; circles, crp fur double mutant.