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bioRxiv · 10.1101/2019.12.27.888545

Maximization of non-nitrogenous metabolite production in E. coli using population systems biology

Rajagopal, S.·Ghatak, A.·Mookherjee, D.·Hmar, R. V.·Shanbhag, A. P.·Venkataraman, J.·Katagihallimath, N.·S, R. K.·Datta, S.
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Abstract

The E. coli metabolome is an interconnected set of enzymes that has measurable kinetic parameters ascribed for the production of most of its metabolites. Flux Balance Analysis (FBA) or Ordinary Differential Equation (ODE) models are used to increase product yield using defined media. However, they either give a range (FBA) or exact amount (ODE) of metabolite yield which isnt true as the transcriptome diversity of individual cells isnt considered. We formulate the metabolic-behaviour of individual cells by using a POpulation SYstems-Biology ALgorithm (POSYBAL) which predicts multiple-gene knockouts for increasing industrially relevant metabolites. We validate this prediction for producing isobutanol (Heterogenous metabolite) and shikimate (Homogenous metabolite) where, the product-yield was increased by 40 times (~2000 ppm) and 42 times (~3000 ppm) respectively. Also, we introduce a nitrogen-swap in standard media to its low-nitrogen counterpart during post-growth phase to redistribute flux towards non-nitrogenous pathways for increasing overall product-yield. Further, our model shows growth-phase diversity in bacterial population even under normal glucose-uptake, portraying a real-world scenario of diverse and robust environment thus, making it evolutionarily favourable to threats such as anti-bacterial attack.

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Rajagopal, S., Ghatak, A., Mookherjee, D., Hmar, R. V., Shanbhag, A. P., Venkataraman, J., Katagihallimath, N., S, R. K., Datta, S.. 2019-12-28. Maximization of non-nitrogenous metabolite production in E. coli using population systems biology. https://doi.org/10.1101/2019.12.27.888545

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