| Итог: | <p>The response to environmental stress shapes the growth and metabolism of
microorganisms under changing environmental conditions, and stress-induced secondary
metabolism is a rich source of valuable bioproducts in various industries. Consequently, it’s necessary to incorporate environmental stress into the modeling of microbial metabolism. However, due to the inherent limitations of conventional flux balance analysis (FBA), most existing FBA-based models cannot account for stress responses. Some researchers have proposed proteome resource allocation models incorporating the effect of environmental stress, but those theoretical models have not yet been implemented in any real-world scenarios with specific microbial systems.</p>
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<p>With the aim to develop computational models for microbial metabolism under
environmental stress, four research projects were conducted in this PhD study to analyze and model the effects of undissociated lactic acid, temperature changes, and acidic pH on microbial metabolism. The selected research object was lactic acid bacteria. Project 1 (<strong>Chapter 3</strong>) and Project 2 (<strong>Chapter 4</strong>) both focused on growth-coupled primary metabolism under stress. Project 1 built a dynamic community FBA model, integrated with constrained proteome allocation, for dominant species in the yogurt starter culture to accurately simulate the central carbon metabolism under the stress of accumulating undissociated lactic acid. Furthermore, the model could account for inter-species metabolic interactions. Subsequently, Project 2 developed a deep learning based predictor of temperature dependent enzyme 𝑘<sub>𝑐𝑎𝑡</sub>, DLTKcat, to model microbial metabolism affected by temperature changes. The temperature sensitive proteome constrained FBA, performed with predicted 𝑘<sub>𝑐𝑎𝑡</sub>, could capture the metabolic responses of lactic acid bacteria to temperature changes, though the quantitative accuracy remained to be improved.</p>
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<p>Regarding stress-induced secondary metabolism, Project 3 (<strong>Chapter 5</strong>) revealed a trade-off in regulatory activities between primary metabolism and acid stress-induced exopolysaccharide (EPS) biosynthesis in <em>Lactiplantibacillus plantarum</em> from the independent component analysis of transcriptomic data. To quantitatively investigate acid stress-induced EPS production in <em>L. plantarum</em>, Project 4 (<strong>Chapter 6</strong>), with multi-omics data at different pH values, identified a proteome trade-off between primary metabolism and EPS biosynthesis, which led to the construction of regulatory proteome constrained flux balance analysis (RPCFBA). As the first mechanistic model that can simulate primary and secondary metabolism simultaneously, RPCFBA model showed good accuracy in predicting growth rates and EPS production fluxes of <em>L. plantarum</em> in the validation with experimental data.</p>
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<p>Overall, FBA-based metabolic models developed in this PhD study demonstrated that modified proteome constrained FBA could overcome the limitations of conventional FBA on microbial metabolism under environmental stress. Moreover, such models have the potential to become computational tools to aid the control and engineering of complex microbial processes.</p>
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