Feeding the growing human population is a critical issue: one of the BBSRC's strategic research goals is increasing food security. Crop plants are limited in their ability to grow largely by a lack of bio-available nitrogen in the soil. Nitrogen fixing bacteria are one of the very few organisms able to fix atmospheric nitrogen into bioavailable forms by using the nitrogenase protein. A simulation of these bacteria is therefore of great interest for the biological modelling community and agricultural professionals to increase our understanding
of these bacteria and to exploit their nitrogen fixing ability.
In order to explore nitrogen metabolism generally, I have constructed a whole cell model of amino acid metabolism in bacteria and examined the applications of this amino acid model. I then go on to construct a separate whole cell model of nitrogenase in bacteria, both with and without amino acid metabolism. The end products of this thesis are three whole cell models: an amino acid model, a nitrogen fixing model, and a combined amino acid and nitrogen fixing model.
It was found that there is a trade-off between the level of fixed nitrogen and the growth of the bacterial cell population, with a maximal yield of nitrogen occurring at high nitrogenase transcription levels and medium levels of transcription of metabolic proteins. These are the first nitrogen complete whole cell models available to the biological modelling community therefore I expect these models will improve future in silico experiments on bacteria and make their findings more translatable to the real world.