Transcription initiation in bacteria depends on a catalytic core RNA polymerase with five key subunits: α2ββ’ω. In order to match gene expression to the needs of the organism, RNA polymerase needs to be carefully controlled in terms of where it binds (at promoters), how frequently it initiates transcription, its elongation rate, and its site of termination. Factors that bind to RNA polymerase to control these parameters include small molecules (e.g. ppGpp), small regulatory RNAs (e.g. 6S RNA) and proteins (sigma factors, elongation factors etc). Many of these elicit global effects on gene expression and therefore can contribute to large scale changes in gene expression associated with stationary phase when antibiotic spare produced.
Current projects include:
The RNA polymerase-binding protein RbpA
RbpA is a novel small protein found only in the actinomycetes. In Streptomyces coelicolor the protein is required for normal rapid growth and basal levels of resistance to the antibiotic Rifampicin. In vitro experiments show that RbpA stimulates transcription. We are addressing three key questions: how does RbpA stimulate transcription; what is the structural nature of the RNA polymerase-RbpA interface; what genes are influenced by RbpA.
Collaborators: Prof Seth Darst and Dr Liz Campbell, Rockefeller University; Prof Steve Matthews, Imperial College London; Prof Colin Smith, University of Surrey
The SigR-based response to disulphide stress
SigR is a sigma factor widely conserved in actinomycetes. During oxidative stress, the sigma factor binds to RNA polymerase and directs it to promoters for the expression of at least 70 genes including thioredoxins, ATP-dependent proteases and chaperones. In the absence of stress, SigR is held inactive by an "anti-sigma factor" called RsrA. RsrA senses oxidative stress directly, through the formation of an intramolecular disulphide bond, which causes a conformational change and the subsequent release of SigR. The SigR-RsrA system is highly conserved in actinomycetes including M. tuberculsosis, where it is required for pathogenesis.
Collaborators: Prof Colin Kleanthous, University of York; Prof Mark Buttner, John Innes Centre, Norwich.