Bacteria use their genetic material with great effectiveness to make the right products in the correct amounts at the appropriate time. Studying bacterial transcription initiation in Escherichia coli has served as a model for understanding transcriptional control throughout all kingdoms of life. Every step in the pathway between gene and function is exploited to exercise this control, but for reasons of economy, it is plain that the key step to regulate is the initiation of RNA-transcript formation.

Gene expression in bacteria relies on promoter recognition by the DNA-dependent RNA polymerase and subsequent transcription initiation. Bacterial cells are able to tune their transcriptional programmes to changing environments, through numerous mechanisms that regulate the activity of RNA polymerase, or change the set of promoters to which the RNA polymerase can bind. In this Review, we outline our current understanding of the different factors that direct the regulation of transcription initiation in bacteria, whether by interacting with promoters, with RNA polymerase or with both, and we discuss the diverse molecular mechanisms that are used by these factors to regulate gene expression.

Bacteria co-ordinate expression of virulence determinants in response to localised microenvironments in their hosts. Here we show that Shigella flexneri, which causes dysentery, encounters varying oxygen concentrations in the gastrointestinal (GI) tract, which govern activity of its type three secretion system (T3SS); the T3SS is essential for cell invasion and virulence 1 . In anaerobic environments (e.g. the GI tract lumen), Shigella expresses extended T3SS needles while reducing Ipa (Invasion plasmid antigen) effector secretion. This is mediated by FNR, a regulator of anaerobic metabolism that represses transcription of spa32 and spa33, virulence genes that the switch in secretion through the T3SS. We demonstrate there is a zone of relative oxygenation adjacent to the GI tract mucosa, caused by diffusing from the capillary network at the tips of villi. This would reverse the anaerobic block of Ipa secretion, allowing T3SS activation at its precise site of action, enhancing invasion and virulence.Shigella virulence depends on its ability to enter epithelial cells by delivering Ipa effectors via its T3SS into the host cell cytoplasm 1 . Secretion through T3SSs is highly regulated.Initially, T3SS needle components are secreted until it reaches a pre-defined length 23 . In inducing conditions, a switch then occurs allowing Ipa secretion through needles, mediating bacterial entry 4 .

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Cells of Escherichia coli growing on sugars that result in catabolite repression or amino acids that feed into glycolysis undergo a metabolic switch associated with the production and utilization of acetate. As they divide exponentially, these cells excrete acetate via the phosphotransacetylase-acetate kinase pathway. As they begin the transition to stationary phase, they instead resorb acetate, activate it to acetyl coenzyme A (acetyl-CoA) by means of the enzyme acetyl-CoA synthetase (Acs) and utilize it to generate energy and biosynthetic components via the tricarboxylic acid cycle and the glyoxylate shunt, respectively. Here, we present evidence that this switch occurs primarily through the induction of acs and that the timing and magnitude of this induction depend, in part, on the direct action of the carbon regulator cyclic AMP receptor protein (CRP) and the oxygen regulator FNR. It also depends, probably indirectly, upon the glyoxylate shunt repressor IclR, its activator FadR, and many enzymes involved in acetate metabolism. On the basis of these results, we propose that cells induce acs, and thus their ability to assimilate acetate, in response to rising cyclic AMP levels, falling oxygen partial pressure, and the flux of carbon through acetate-associated pathways.

Successful pathogens must be able to protect themselves against reactive nitrogen species generated either as part of host defense mechanisms or as products of their own metabolism. The regulatory protein NsrR (a member of the Rrf2 family of transcription factors) plays key roles in this stress response. Microarray analysis revealed that NsrR represses nine operons encoding 20 genes in Escherichia coli MG1655, including the hmpA, ytfE, and ygbA genes that were previously shown to be regulated by NsrR. Novel NsrR targets revealed by this study include hcp-hcr (which were predicted in a recent bioinformatic study to be NsrR regulated) and the well-studied nrfA promoter that directs the expression of the periplasmic respiratory nitrite reductase. Conversely, transcription from the ydbC promoter is strongly activated by NsrR. Regulation of the nrf operon by NsrR is consistent with the ability of the periplasmic nitrite reductase to reduce nitric oxide and hence protect against reactive nitrogen species. Gel retardation assays were used to show that both FNR and NarL bind to the hcp promoter. The expression of hcp and the contiguous gene hcr is not induced by hydroxylamine. As hmpA and ytfE encode a nitric oxide reductase and a mechanism to repair iron-sulfur centers damaged by nitric oxide, the demonstration that hcp-hcr, hmpA, and ytfE are the three transcripts most tightly regulated by NsrR highlights the possibility that the hybrid cluster protein, HCP, might also be part of a defense mechanism against reactive nitrogen stress.

Using chromatin immunoprecipitation (ChIP) and high-density microarrays, we have measured the distribution of the global transcription regulator protein, FNR, across the entire Escherichia coli chromosome in exponentially growing cells. Sixty-three binding targets, each located at the 5′ end of a gene, were identified. Some targets are adjacent to poorly transcribed genes where FNR has little impact on transcription. In stationary phase, the distribution of FNR was largely unchanged. Control experiments showed that, like FNR, the distribution of the nucleoid-associated protein, IHF, is little altered when cells enter stationary phase, whilst RNA polymerase undergoes a complete redistribution.

The cyclic AMP receptor protein (CRP) activates transcription of the Escherichia coli acs gene, which encodes an acetate-scavenging enzyme required for fitness during periods of carbon starvation. Two promoters direct transcription of acs, the distal acsP1 and the proximal acsP2. In this study, we demonstrated that acsP2 can function as the major promoter and showed by in vitro studies that CRP facilitates transcription by "focusing" RNA polymerase to acsP2. We proposed that CRP activates transcription from acsP2 by a synergistic class III mechanism. Consistent with this proposal, we showed that CRP binds two sites, CRP I and CRP II. Induction of acs expression absolutely required CRP I, while optimal expression required both CRP I and CRP II. The locations of these DNA sites for CRP (centered at positions ؊69.5 and ؊122.5, respectively) suggest that CRP interacts with RNA polymerase through class I interactions. In support of this hypothesis, we demonstrated that acs transcription requires the surfaces of CRP and the C-terminal domain of the ␣ subunit of RNA polymerase holoenzyme (␣-CTD), which is known to participate in class I interactions: activating region 1 of CRP and the 287, 265, and 261 determinants of the ␣-CTD. Other surface-exposed residues in the ␣-CTD contributed to acs transcription, suggesting that the ␣-CTD may interact with at least one protein other than CRP.The Escherichia coli cyclic AMP (cAMP) receptor protein (CRP; also known as the catabolite activator protein) activates transcription from more than 100 promoters. When bound to its allosteric effector, cAMP, the CRP homodimer binds specific DNA sites near target promoters, enhancing the binding of RNA polymerase holoenzyme (RNAP) and facilitating the initiation of transcription. Simple CRP activation operates through two related mechanisms, designated class I and class II. Both mechanisms depend upon specific interactions between CRP and RNAP. At class I promoters, a CRP dimer binds to DNA at a site centered near position Ϫ61.5, Ϫ71.5, Ϫ82.5, or Ϫ92.5. CRP bound at any of these positions uses a defined surface (activating region 1 [AR1]) in the downstream subunit of CRP to contact a specific surface determinant, 287, of the C-terminal domain of the ␣ subunit of RNA polymerase (␣-CTD). Two additional ␣-CTD determinants contribute to class I activation: the 261 determinant, proposed to interact with the subunit of RNAP, and the 265 determinant, known to interact with DNA, especially AϩT-rich sequences, most notably the UP element.Class I interactions appear to recruit RNAP to promoter DNA by increasing the binding constant for closed-complex formation. At class II promoters, a CRP dimer binds to DNA at a site centered near position Ϫ41.5. When bound at this position, CRP uses AR1 of the upstream subunit of CRP to contact the 287 determinant of the ␣-CTD and a second surface (AR2) to contact the 162 to 165 determinant of the Nterminal domain of ␣. The ␣-CTD 265 determinant also contributes by interacting with DNA. Class II interactions appea...