Genome-scale approach towards investigating bacterial gene regulation
(Bugbears Research page)

We take a genome-scale approach towards tackling our questions of interest. Genomics complements the detailed findings of reductionist molecular biology and biochemistry by describing general principles and identifying exceptions. The large-scale nature and the gaining popularity of genomic studies together generate a flood of biological data, the interpretation of which requires computational tools and expertise.

Towards understanding bacterial regulatory systems on a genomic scale, we perform computational studies which integrate large-scale data of diverse types: (a) genome and proteome sequences; (b) measurements of gene expression derived from DNA microarrays and high throughput parallel sequencing; (c) protein expression data based on fluorescence measurements and mass-spectrometry; (d) regulatory networks, primarily transcriptional regulatory networks described using chromatin-immunoprecipitation followed by DNA microarray hybridisation (ChIP-chip) or sequencing (ChIP-seq); (e) other functional genomic information including metabolic and protein-protein interaction networks sourced from genome annotations and experimental techniques such as yeast two-hybrid and TAP-tagging-mass-spectrometry. In addition to these, we generate primary data dealing with genome-wide gene expression and binding of DNA-binding proteins to the chromosome in enterobacteriaciae.

Projects carried out in Cambridge
Our projects so far were carried out in Nicholas Luscombe’s group at the EMBL-European Bioinformatics Institute (Hinxton, Cambridge), in collaboration with Gillian Fraser (Department of Pathology, University of Cambridge, UK), Madan Babu Mohan (MRC-Laboratory of Molecular Biology, Cambridge, UK) and Vladimir Benes (Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany). These include the following:

Global regulation of E. coli gene expression by promoter sequence, DNA topology and nucleoid-associated proteins:
DNA sequence content at the promoter is a foundation for permitting transcription initiation; however it is a temporally static property that does not determine, on its own, condition-specific transcriptional responses. Using public data, we have investigated how other cis- and trans-acting players in E. coli - DNA supercoiling and nucleoid-associated proteins - supersede and aid DNA sequence content in permitting broad responses to drastic alterations in environmental and cellular conditions (with Karthikeyan Sivaraman, Madan Babu Mohan, Nicholas Luscombe, Alexander Cole). In a second, experimental genomics project, we are using high-throughput parallel sequencing and DNA microarrays to understand the role of certain nucleoid-associated proteins in transcriptional control in E. coli during the growth phase (with Christina Kahramanoglou, Anabel Prieto, Vladimir Benes, Gillian Fraser, Nicholas Luscombe).

General principles underlying regulation of the metabolic system in E. coli:
Any cellular or environmental signal can potentially participate in regulating a process by acting not only at the transcriptional stage, but also in the post-transcriptional and post-translational stages. Metabolism is an area where both transcriptional and post-translational regulatory mechanisms are prevalent. Much of this is due to small molecule signals, which are part of the metabolic system itself. We have studied how transcriptional and post-translational regulation, both initiated by small molecules, complement each other in controlling metabolism in E. coli (with Madan Babu Mohan, Gillian Fraser, Nicholas Luscombe).

Comparative genomics of bacterial regulatory systems:
Any adaptive response is likely to be initiated by the sensing of environmental or cellular signals by receptors.  The signal is then transduced, largely to a transcriptional change. Non-transcriptional outputs are also possible and include enzymatic activities such as the synthesis of second messengers like cyclic-di-GMP and the methyltransferase activity involved in chemotaxis. Bacteria can be expected to vary their repertoire of signal-sensing, signal-transducing and output-generating proteins - collectively called regulatory proteins - depending on their habitat and lifestyles. We have used comparative genomics approaches to understand how different second messenger systems are temporally and spatially separated, and how regulatory complexity might be associated with ‘complex’ organism lifestyles (with Madan Babu Mohan, Gillian Fraser, Nicholas Luscombe).

Future projects
Our new group, to be established in NCBS, while maintaining our relationship with our collaborators in Cambridge, will extend our interest in bacterial genomics in the following directions:

1. Genomic analysis of the impact of E. coli nucleoid-associated proteins on chromosome topology and global gene expression.
2. Impact of horizontal gene acquisition on the conserved gene regulatory network in enterobacteria.
3. Genomic analysis of the impact of distinct second messenger signalling systems on enterobacterial gene expression.
4. Genomic analysis of factors influencing DNA methylation in bacteria.
5. Generation and analysis of metagenomic data towards understanding genotype-phenotype relationships in the context of adaptation to an environment.
6. Genomic characterisation of clinical strains of enterobacterial pathogens.