Systems Understanding of Microbial Oxygen-Dependent and Independent Catabolism (SUMO2)

In this project, a multidisciplinary team of scientists, comprising molecular biologists, biochemists, mathematicians and computer scientists will work together and use Systems Biology to study the response of a bacterium to oxygen in its environment. The bacterium is E. coli, a major model organism, study of which has provided much of our current knowledge of basic molecular biology and continues to be the workhorse of the biotechnology sector. The Systems Biology approach to research is a relatively new area of investigation that tries to understand entire biological processes or systems (such as an organism and its behaviour), rather than merely the components of the system (such as atoms, molecules, and individual reactions). In effect, Systems Biology attempts to 'put Humpty Dumpty together again'. Systems Biology can be used to simulate biological processes and predict the outcome of perturbing the system, even before experiments are carried out. This ability to predict leads to the design of more meaningful experiments. We aim to obtain a complete, quantitative description of the metabolism of this bacterium, i.e. understand how carbon foodstuffs are broken down and used to generate energy in fermentation and respiration. The expected results are as follows. (1) Complex experimental results describing: (a) the dynamics of gene expression during the change from fermentative to anaerobic (i.e. without oxygen) respiratory growth; (b) the dynamics of responses to pulses of oxidants (oxygen and chemically related molecules); (c) the effects of mutation of substrate transport processes on physiology under defined aerobiosis conditions (i.e. in air); (d) effects of perturbation of central metabolism by mutation and by switching carbon source; (e) the role of a branched respiratory chain in adapting when conditions change. (2) Multi-scale, multi-level mathematical models describing: (a) the dynamics of gene regulatory networks during perturbations of anaerobic cultures; (b) the regulatory consequences of dynamics within complex networks of gene regulation processes; (c) the regulatory mechanisms of gene promoters; (d) catabolism (break-down) of foodstuffs from their entry into the cell right through to energy generation, including anaerobic pathways; (e) the regulation and action of alternative respiratory chains; (f) single-cell dynamics and cell behaviour in unstable conditions. (3) The formulation of a predictive, quantitative, experimentally validated model of the integrated metabolic sub-systems of E. coli and how these respond to changes in internal and external signals.

SUMO2 aims to obtain a complete, quantitative description of the integrated catabolic subsystems of E. coli, from regulation to energy conservation. The expected results are as follows. (1) Complex experimental datasets describing: (a) the dynamics of the transcriptional responses during transition from fermentative to anaerobic respiratory growth; (b) the dynamics of responses to pulses of electron acceptors; (c) the effects of mutational perturbation of substrate transport on physiology under defined aerobiosis conditions; (d) effects of perturbation of central metabolism by mutation and by switching carbon source; (e) 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 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.

A systems-based study of the dynamics of adaptation is crucially important for understanding many aspects of biology. A paradigm of microbial responses to fluctuating environments is provided by the 'model' enterobacterium Escherichia coli, which exhibits a versatile metabolism (incorporating aerobic respiratory, anaerobic respiratory and fermentative metabolic modes) plus numerous and sometimes complex regulatory networks to achieve optimal growth and survival. One such adaptation that has been widely studied is the response of E. coli to the provision (or not) of oxygen and/or alternative terminal electron acceptors. The foreseeable impacts on the UK and internationally include: 1. High quality training of early-career bio-scientists in the BBSRC priority area of Systems Biology; 2. Publishing quality science in high impact peer-reviewed scientific journals; 3. Establishing generic experimental and modelling tools essential for systems biology research projects; 4. 'Induced' impacts, in which the employment of an individual or stimulating an area of research subsequently results in either economic and social impact; 5. Providing underpinning knowledge and tools that may be applied to other systems, such as other bacteria used in biotechnology and product formation; 6. Encouraging multidisciplinary and collaborative research; 7. Identifying targets in the form of regulatory circuits and metabolic pathways that could be used for enhancing commercial exploitation of bacteria as biofactories in fermenters and commercial 'fermentations', and perhaps the control of infection.