Environmental Signal Sensing and Integration
Our major research interest is focussed on the underlying molecular mechanism by which bacteria perceive their surroundings through regulatory signals, and how they integrate multiple and sometimes conflicting signals to effect appropriate changes in their gene expression and ultimately their behaviour. The experimental system is derived from a soil dwelling Pseudomonad (Pseudomonas putida CF600) that can completely mineralise (methyl)phenol environmental pollutants via a specialised suite of catabolic enzymes encoded by the dimethylphenol dmp- genes.
Regulatory systems that control the expression of the specialised catabolic enzymes lie at the top of the hierarchy of events that allow bacteria to utilise aromatic compounds as carbon sources. They determine under what conditions, and in response to what compounds, the metabolically expensive production of the catabolic enzymes is undertaken, and control behavioural responses that allow bacteria to relocate to more optimal niches. Three interrelated research areas address the molecular mechanisms underlying the integrated decision-making process:
A) The sensor regulator DmpR: The DmpR regulatory protein that controls transcriptional activation of the dmp-genes acts as the direct sensor of the system by virtue of activation upon binding specific aromatic compounds. DmpR activates transcription in conjunction with the unusual alternative form of RNA polymerase utilising s54 (sN , RpoN). Conversion of the stable closed complexes to open complexes and thus transcriptional initiation requires DmpR binding and hydrolysis of ATP that triggers a dimer to multimer transitions (see Shingler 2003, Shingler 2004 for reviews). Current aims are to determining how structural changes render DmpR competent to promote transcription.
B) ppGpp/DksA mediated global regulation: The aromatic-responsive DmpR circuit is essentially mute under high-energy conditions. A second regulatory signal, the bacterial alarmone ppGpp that heralds metabolic stress, is responsible for this level of global regulation. This level of regulation operates through the formation and/or functioning of s54 -RNA polymerase, and is integrated within the specific DmpR-mediated circuit to ensure that the specialised enzymes are not made if energetically more favourable carbon sources are present (see Laurie et al., 2003). We are currently elucidating the mechanism(s) by which ppGpp and its co-factor DksA re-orchestrate transcription to subvert the specific DmpR-mediated regulatory circuit to allow expression only under the low-energy conditions that prevail in the soil environment.
3) Metabolism-dependent taxis: Once expressed, growth at the expense of (methyl)phenols allows the bacteria to move towards the source of compound by metabolism-dependent taxis. Current research is directed towards resolving how metabolism-dependent energy-taxis towards (methyl)phenol is coupled to the central motility pathway of Pseudomonads through cyclic di-GMP signalling and an energy-sensory transducer.