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.

The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.

The structure of this pleiotropic activator of gene transcription in bacteria and its interaction sites at promoter DNA's as well as the role of this protein in the RNA polymerase-promoter interactions are reviewed.

Chromatin immunoprecipitation and high-density microarrays have been used to monitor the distribution of the global transcription regulator Escherichia coli cAMP-receptor protein (CRP) and RNA polymerase along the E. coli chromosome. Our results identify targets occupied by CRP and genes transcribed by RNA polymerase in vivo. Many of the loci of CRP binding are at known CRP regulated promoters. However, our results show that CRP also interacts with thousands of weaker sites across the whole chromosome and that this ''background'' binding can be used as a probe for organization within the E. coli folded chromosome. In rapidly growing cells, we show that the major sites of RNA polymerase binding are Ϸ90 transcription units that include genes needed for protein synthesis. Upon the addition of rifampicin, RNA polymerase is distributed among >500 functional promoters. We show that the chromatin immunoprecipitation and high-density-microarrays methodology can be used to study the redistribution of RNA polymerase induced by environmental stress, revealing previously uncharacterized aspects of RNA polymerase behavior and providing an alternative to the ''transcriptomics'' approach for studying global transcription patterns.chromatin immunoprecipitation ͉ genomics ͉ stringent response ͉ transcription I n growing Escherichia coli, Ϸ2,000 RNA polymerase molecules are distributed unevenly among 4,300 genes, and Ͼ150 transcription factors play a key role in managing this distribution (1-3). It is important to understand the genome-wide profile of RNA polymerase binding and the role of each of the transcription factors. Here, we describe the use of chromatin immunoprecipitation (ChIP) and high-density microarrays (known as the ChIP-chip approach) to study the whole-genome DNA-binding properties of E. coli cAMP-receptor protein (CRP), one of the principal global transcription regulators in E. coli, and RNA polymerase.CRP is one of the seven ''global'' transcription factors in E. coli known to regulate Ͼ50% of the cell's transcription units (3). CRP's activity is triggered by binding of the second messenger cAMP in response to glucose starvation and other stresses (4). Many catalogues of CRP regulated promoters have been assembled, based on either transcriptome analysis (5-7) or bioinformatics (8, 9). These analyses conclude that CRP directly affects up to 200 promoters, although neither approach directly measures CRP binding at promoters. The computational analysis of Robison et al. (8) identified Ϸ200 high-affinity DNA targets for CRP, predominantly located in noncoding parts of the E. coli chromosome. That study also predicted Ͼ10,000 lower-affinity CRP targets scattered throughout the chromosome, with little bias to noncoding sequences. In this work, we used ChIP-chip analysis to take snapshots of the distribution of CRP in living E. coli cells. The advantage of this methodology (reviewed in ref. 10) is that it provides a direct measure of binding at different targets, enabling us to identify specific sites where CRP binds...

In eukaryotes, the location of a gene on the chromosome is known to affect its expression, but such position effects are poorly understood in bacteria. Here, using Escherichia coli K-12, we demonstrate that expression of a reporter gene cassette, comprised of the model E. coli lac promoter driving expression of gfp, varies by ∼300-fold depending on its precise position on the chromosome. At some positions, expression was more than 3-fold higher than at the natural lac promoter locus, whereas at several other locations, the reporter cassette was completely silenced: effectively overriding local lac promoter control. These effects were not due to differences in gene copy number, caused by partially replicated genomes. Rather, the differences in gene expression occur predominantly at the level of transcription and are mediated by several different features that are involved in chromosome organization. Taken together, our findings identify a tier of gene regulation above local promoter control and highlight the importance of chromosome position effects on gene expression profiles in bacteria.