A computational study of bacterial gene regulation and adaptation ...

Chapter 1: Global regulators of bacterial transcription initiation1.2. IntroductionInitiation of transcription at a bacterial promoter requires its recognition by RNA polymerasethrough interactions with a !-factor. The structure thus formed, comprising the DNA and theRNA polymerase holoenzyme, is called the closed complex. This is followed by theunwinding of the DNA duplex to form the transcription-capable open complex, and thentranscription initiation and subsequently elongation. Initiation of transcription is probably themost important control point in gene expression. It is determined by factors including theDNA around the promoter and trans-acting regulators: proteins such as transcription factorsand regulatory small-molecules that can directly influence !-factor activity (Browning andBusby 2004). Various levels of regulation that influence transcription initiation are depicted inFigure 1.1.DNA sequence is, by itself, an important determinant of transcriptional activity. Regions ofDNA where transcription initiation occurs have higher AT-content than other non-genicregions and genes (Mitchison 2005). Enrichments of specific short sequence motifs at regionsinvolving transcription initiation over internal-to-operon intergenic regions, where initiation isunlikely, may be explained by such differential AT-content (Janga et al. 2006). Sinceoligonucleotides that are over-represented in intergenic regions are embedded within thisspace of high AT-content, this space was perceived as an ‘address’ for a promoter (Sivaramanet al. 2005). This property of the DNA sequence is justified by the proposal that binding ofproteins to the DNA is favoured by high-AT sequences probably due to the high bendabilityof the DNA around such regions (Mitchison 2005). Further, because of weaker inter-strandbase-pairing at AT-rich stretches, unwinding of the DNA is significantly favoured, thuspromoting the formation of the open complex. Here we emphasise that DNA stability is notentirely explained by AT-content (Champ et al. 2006; Ussery et al. 2002): for example, purinetracts are thermodynamically stable, whereas alternating purine-pyrimidine stretches (such asruns of TA) are easier to melt. A-tracts form stable DNA curvatures, which haveconsequences for protein-DNA interactions.DNA sequence, on its own, is a static property. Whereas it could determine whether a regionis transcription-capable or not, it is temporally fixed, except under long evolutionary timescales.Therefore, it does not, on its own again, allow modulation of transcriptional activity in27