With the emergence of "omics" techniques, it has become essential to develop tools to utilise the vast amount of data produced by these methods. Genome-scale metabolic models represent the mathematical essence of metabolism and can easily be linked to the data from omics sources. Such models can be used for various analyses, including the investigation of metabolic responses to changing environmental conditions. Legumes are known for their ability to form a nitrogen-fixing symbiosis with rhizobia, a vital process that provides the biosphere with the majority of its nitrogen content. In the present thesis, a genome-scale metabolic model for the legume Medicago truncatula was reconstructed, based on the annotated genome sequence and the MedicCyc database. A novel approach was employed to define the compartmentalisation of the plant's metabolism. The model was used to calculate the biosynthetic costs of biomass precursors (e.g. amino acids, sugars, fatty acids, nucleotides), and its capability to produce biomass in experimentally observed ratios was demonstrated using flux balance analysis. Further investigation was carried out into how the biosynthesis fluxes and costs change with respect to different nitrogen sources. The precise charge balancing of all reactions in the model allowed the investigation of the effects of charge transport over the cellular membrane. The simulations showed a good agreement with experimentaldata in using different sources of nitrogen (ammonium and nitrate) to minimise the charge transport of the membrane. To allow the investigation of the symbiotic relationship, two rhizobial models were used. The first model, for Sinorhizobium meliloti, was reconstructed from the MetaCyc database (MC-model); the second model was a recently published model for S. meliloti specialised for symbiotic nitrogen xation (SNF-model). Combined models were created for both rhizobial networks using a specialised nodule submodel of the plant model. Potential interactions were extracted from the literature and investigated, with the analysis suggesting that oxygen availability is the main limitation factor in symbiotic nitrogen fixation. Within the analysis the SNF-model appeared to be too restricted and lacking the potential for sufficient nitrogen xation; therefore, further analysis was carried out using the MC-model, upon which it was observed that the availability of oxygen can also influence how nitrogen is supplied to the plant. At high oxygen concentrations ammonia is the primary form of nitrogen supplied by the rhizobium. However, the simulations, in accordance with experimental data, show that at lower concentrations of oxygen, alanine takes precedence. The findings also support the concept of amino acid cycling as a potential way to improve nitrogen fixation. The more flexible MetaCyc based model has allowed other potential genetic engineering approaches for higher nitrogen fixation yields to be proposed.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:582686 |
| Date | January 2013 |
| Creators | Pfau, Thomas |
| Publisher | University of Aberdeen |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=202144 |
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