Systems Understanding of Microbial Oxygen-Dependant and Independant Catabolism (SUMO²)

Escherichia coli has a versatile metabolism (incorporating aerobic respiratory, anaerobic respiratory and fermentative metabolic modes) plus numerous, complex regulatory networks to achieve optimal growth and survival. One adaptation crucial to the bacteriums lifestyle as a commensal is the response to the provision (or not) of oxygen and/or alternative terminal electron acceptors. Our aim in SUMO2 is to extend our SysMO project (SUMO, Systems Understanding of Microbial Oxygen Responses) to obtain a complete, quantitative description of the integrated catabolic subsystems of E. coli, from regulation to energy conservation. Our work plan centres on 3 interlinked Themes: (1) system dynamics during transition to anaerobic respiration and in response to pulses of electron acceptors; (2) adaptive responses to different catabolic modes; (3) multi-scale and multi-level modelling of catabolism. We will collect fully compatible datasets at molecular, single-cell and population levels and assemble these into multi-scale complementary models. Interactions of the modelling approaches and the experimental work in SUMO2. Only when all approaches are applied together, are we able to obtain an overall view of the system. The expected results from SUMO2 are: (1) Complex experimental datasets describing: (i) the dynamics of transcriptional responses during transition from fermentative to anaerobic respiratory growth; (ii) the dynamics of responses to pulses of electron acceptors; (iii) the effects of mutational perturbation of substrate transport on physiology under defined aerobiosis conditions; (iv) effects of perturbation of central metabolism by mutation and by switching carbon source; (v) the role of a branched electron transport chain in adapting when electron donor and/or electron acceptor availabilities change. (2) Multi-scale, multi-level models describing: (a) the dynamics of transcription factor activities and regulatory networks during perturbations of anaerobic cultures (probabilistic model); (b) the regulatory consequences of dynamics within transcription factor hierarchical structures (probabilistic model); (c) the regulatory mechanisms of complex promoters (probabilistic and kinetic models); (d) catabolism from carbohydrate transport to ATP generation including anaerobic respiratory pathways (reduced-order model); (e) the regulation and action of the alternative electron transport chains (detailed kinetic and agent models); (f) single-cell dynamics and bi-stable behaviour (agent models). (3) The formulation of a predictive, quantitative, experimentally validated model of the integrated catabolic sub-systems of E. coli and how these respond to changes in internal (metabolic) and external (e.g. electron acceptor availability) signals. SUMO2 is firmly founded on a large body of experimental data based on an agreed set of protocols and approaches, progress in multi-scale modelling, and the strong cooperative working relationships of the scientific team. These features exploit the resources generated by SUMO (including the adoption of standard conditions, strains and protocols, data and model compatibility), and aid in embedding the adoption of systems approaches in the future careers of SUMOs young bio-scientists.