Applications of Metabolic Modelling: Understanding Energy Production in Electricity-Producing Shewanella oneidensis MR-1 and Lipid-Producing Nannochloropsis gaditana

With the improvement of computational technology in recent years, new research fields such as systems biology have been developed thanks to the interdisciplinary interface between computer science and traditional biology. Distinct from traditional biology, systems biology focuses on cellular activity at a systematic level rather than individual molecular scales. A new technique called ‘Omics’ data analysis has been introduced to systems biology to help understand bio-activities on a greater scale. For instance, proteomics is the study of various protein levels simultaneously. This type of research provides an overall picture of the organism, helping us understand how cellular activities interact with each other.
To further understand subcellular activities, computational modelling was developed with techniques including elementary mode analysis, flux balance analysis, metabolic flux analysis, et cetera.
In this report, two projects related to systems biology have been carried out. The first project is a model-driven metabolic analysis of electron-producing bacteria, called Shewanella oneidensis MR-1. In this project, the aerobic and anaerobic respiration was studied. The relation between electron productivity and carbon source has been described. A gene-knockout simulation was also carried out. It was found that the knockout of two ubiquinone-8 related reactions increased the total electron productivity by about 31%. This increase may be because with two knockouts, the flux through the tricarboxylic acid cycle (TCA) cycle maintains a low level, reducing cell growth. Thus, more energy can be converted into electricity. The main electron donor in the electron transport chain is nicotinamide adenine dinucleotide + hydrogen (NADH).
The second project is a metabolic reconstruction of Nannochloropsis gaditana. As a result, over 300 reactions were included in the model reconstruction of Nannochloropsis gaditana and the biomass reaction is needed for further predictions. Together with the biomass reaction, this model can be further used for prediction via flux balance analysis (FBA). In the FBA model of S. oneidensis, it was found that the model had a better performance under carbon-limited conditions rather than oxygen-limited conditions. The theoretical electron transfer efficiency to the anode was found to be extremely low (less than 0.01% in direct electron transfer (DET) mode or 20% in mediated electron transfer (MET) mode).