Signal responsive transcriptional control in bacteria is mediated through both specific and global regulatory circuits to attune promoter output to prevailing conditions. Divergent transcription of a regulatory gene and a cognate promoter under its control provides an opportunity for interplay between transcription dependent on RNA polymerases utilizing various σ-factors, each of which programs the holoenzyme to recognize different classes of promoters. The work presented in this thesis analyses the consequences and mechanisms behind interplay between σ54- and σ70-dependent transcription within the dmp-system of Pseudomonas sp. CF600. The dmp-system confers the ability to grow at the expense of (methyl)phenols and is controlled by two promoters that drive non-overlapping divergent transcription from a common intergenic region: i) the σ54-Po promoter, which controls an operon encoding a suit of specialized catabolic enzymes, and ii) the σ70-Pr promoter, which controls production of the aromatic sensor DmpR - a mechano-activator whose transcription-promoting activity is obligatory for activity of the σ54-Po promoter. The σ54-Po promoter and its dependence on two non-classical transcriptional regulators - the alarmone ppGpp and its co-factor DksA that directly target RNA polymerase - are the focus of the first part of the thesis. These studies utilized ppGpp and DksA deficient strains, mutant RNA polymerases that bypass the need for ppGpp and DksA, reconstituted in vitro transcription systems, and a series of DmpR-regulated hybrid σ54-promoters with different affinities for σ54-RNA polymerase, together with analysis of protein levels of key transcriptional components. Collectively with previous work, these studies provide the experimental support for a robust but purely passive mechanism for ppGpp and DksA global regulation of σ54-transcription, which is likely to also be pertinent for transcription mediated via any alternative σ-factor (Papers I-III). The second part of the thesis focuses on additional roles of ppGpp and DksA through their direct and indirect effects on the activity of the σ70-Pr promoter. These studies unexpectedly revealed that the σ70-Pr promoter is regulated by a novel mechanism in which σ54-RNA polymerase occupancy and activity at the σ54-Po promoter stimulates σ70-Pr output. Evidence is presented that ppGpp and DksA, through DmpR levels, control a feed forward loop to reinforce silence of the σ54-Po promoter under high energy conditions with robust transcription from σ54-Po when the catabolic enzymes are needed. The interplay outlined above effectively places a σ70-dependent promoter under dual control of two forms of RNA polymerases, and also makes it subservient to regulatory signals that elicit activity of σ54-RNA polymerase. The possibility that such dual sensitivity may be a prevalent, but previously unappreciated, mechanism by which bacteria integrate diverse and/or conflicting signals to gain appropriate transcriptional control is discussed.

In bacteria, the RNA polymerase (RNAP) consists of the following subunits: α2, β, β’, ω and σ. The core RNAP (α2ββ’ω) possesses the polymerising activity and it associates with one of the sigma factors to initiate transcription from a promoter region on the DNA template. All bacteria carry an essential housekeeping sigma factor and a number of extra cytoplasmic function (ECF) sigma factors. During alternate physiological states, a major part of transcriptional regulation is carried out by sigma factors, which act as transcriptional switches, thus, making it possible for bacteria to adapt to varied environmental signals by transcribing the necessary set of genes. Bacteriophages utilise various mechanisms for subverting the bacterial biochemical machinery for their advantage. One such example in E. coli is AsiA protein encoded by an early gene of T4 bacteriophage. Because of its property of binding to σ70, AsiA can inhibit transcription from E. coli promoters bearing –10 and –35 DNA sequences leading to inhibition of growth. σ70 of E. coli is also regulated by a stationary phase specific protein, Rsd, whose major function seems to be helping the cell in switching the transcription in favour of stationary phase genes. In this study we have investigated the mechanism of interaction of T4 AsiA and E. coli Rsd to σ70 of E. coli and also tried to determine the basis of differential inhibition of E. coli growth by AsiA and Rsd. In chapter one we have reviewed the published literature on regulation of transcription in bacteria. Some of the well known mechanisms of regulating gene expression are: DNA supercoiling, two component signal transduction system (TCS), regulation by alarmone ppGpp and 6S RNA, and sigma-antisigma interactions. Most bacteria carry a number of sigma factors and each of them is dedicated to transcribing genes in response to environmental signals. Intracellular levels of sigma factors and their binding affinity to core RNAP are deciding factors for initiating transcription from specific subsets of genes. In addition, sigma factor activity is also controlled by specific proteins, which bind to sigma factors (anti-sigma factors) under certain environmental conditions. A number of anti-sigma factors have been isolated from a variety of bacteria and the mechanisms of action of binding to cognate sigma factors have been worked out by using genetic, biochemical and structural tools. In chapter two, using yeast two hybrid assay (YTH), we have identified the regions of σ70 which interact with AsiA, and it was observed that amino acid residues from 547-603, encompassing region 4.1 and 4.2 are involved in binding to σ70. Interestingly, we found that truncated σ70 fragments lacking the N-terminal regions, apparently bound to AsiA with higher affinity compared to full length σ70. As AsiA expression, because of its transcription inhibitory activity, is inhibitory to E.coli growth, co-expression of the truncated C-terminal σ70 fragments (e.g. residues 493-613, σ70C121), which bind to σ70 with high affinity, could relieve growth inhibition. The complex of GST:AsiA-σ70C121 could be purified from E. coli cells. GST:AsiA purified from E .coli cells was found to be associated with RNAP subunits. Since further studies on this interaction required GST:AsiA preparation devoid of RNAP subunits, we decided to express this protein in S. cerevisiae. Bioinformatics analysis indicated the absence of a σ70 homologue in S.cerevisiae. As expected, GST:AsiA purified from the yeast was found to be free from any RNAP like proteins. The protein purified from yeast was used for in-vitro binding experiments. Our YTH analysis had indicated that deletion a part of region 4.1 or 4.2 of σ70 leads to loss of binding to AsiA. However, the published NMR structure of AsiA in complex with peptides corresponding to region 4 of σ70, showed that either region 4.1 or 4.2 alone can bind to AsiA indicating at the possible existence of two binding sites for AsiA. In order to confirm the physiological significance of this finding, we studied the interaction of truncated σ70 fragments lacking either region 4.1 or 4.2 with AsiA in-vivo in E. coli and in-vitro by affinity pull down assays. It was observed that σ70 fragments lacking either region 4.1 (σ70∆4.1) or 4.2 (σ70∆4.2), did not neutralize the GST:AsiA toxicity, indicating lack of interaction. The affinity purified GST:AsiA from these E. coli cells did not have σ70∆4.1 or σ70∆4.2 associated with it. Similar results were obtained from pull down assays in-vitro, where we found that σ70∆4.1 or σ70∆4.2 do not show any observable interaction with AsiA. This clearly established that the minimum region of σ70 required for physiologically relevant interaction with AsiA consists of both the regions 4.1 and 4.2. Chapter 3 of this thesis has been devoted to this aspect of AsiA-σ70 interaction. Having defined the minimum region of σ70 interacting with AsiA, we sought to identify the regions and amino acid residues of AsiA, which are critical for interaction with σ70. The approach for identification of mutants and their characterisation has been discussed in chapter 4. For this purpose, we made systematic deletions in the N and C-terminal regions of the protein and also isolated random mutants of AsiA, which lack binding to σ70 and thus are non-inhibitory to E. coli growth. It was found that deletion of 5 amino acids from N-terminus and 17 amino acids from C-terminus did not alter the inhibitory activity of AsiA. In contrast, deletion of N-terminal 10 amino residues led to complete loss of activity, while in the C-terminus, a gradual loss of activity was observed when amino acid residues beyond 17 amino acids were deleted. A 34 amino acids C-terminal deletion mutant was found to be completely inactive. E10K mutant was found to be inactive, but changes of E to other amino acids such as S, Y, L, A and Q were tolerated, indicating that negative charge at E10 is not a crucial element for interaction with σ70. Inactive mutants could be overexpressed in E. coli and showed reduced binding in YTH assay and were also poor inhibitors of in-vivo transcription in E. coli. We concluded that the primary σ70 binding site of AsiA is present in the N-terminus, yet C-terminal 64-73 amino acid residues are required for effective binding in-vivo. These studies also correlate the inhibitory potential of AsiA with its σ70 binding proficiency. In chapter 5, we have made a comparative analysis of mechanism of interaction of AsiA and Rsd to E. coli RNAP. Overexpression of Rsd was found to be less inhibitory to E. coli cell growth than that of AsiA. The affinity purified GST-AsiA from E. coli was found to have all the RNAP subunits associated with it, whereas, only σ70 was found to be associated with similarly purified GST:Rsd, pointing towards differences in binding to RNAP. In affinity pull down assays, in-vitro, it was found that both AsiA and Rsd do not show any observable binding to core RNAP. Binding of AsiA to σ70 in holo RNAP led to the formation of a ternary complex, whereas no ternary complex was observed when Rsd was made to interact with holo RNAP. Analysis of protein-protein interaction by YTH showed that region 4.1 and 4.2 are critical for binding of both AsiA and Rsd to σ70. However, in the case of Rsd, the surface of interaction is not limited to this region only and other regions of σ70 make significant contribution to this binding. Possibly, the interaction of Rsd with the core binding regions of σ70 prevents its association with core RNAP. Kinetic analysis of binding by surface plasmon resonance (SPR) showed that binding affinities (Kd) of AsiA and Rsd to σ70 are in similar range. Therefore, we concluded that the ability of AsiA to trap the holo RNAP is, probably, responsible for higher inhibitory activity of this protein compared to that of Rsd. Thus, T4 AsiA and E. coli Rsd, which share regions of interaction on σ70, have evolved differences in their mechanism of binding to RNAP such that T4 AsiA, by trapping the holo RNAP subverts the complete bacterial transcription machinery to transcribe its own genes. Rsd, on the other hand, has evolved to interact primarily with σ70, which favours the utilisation of core RNAP by other sigma factors.