Maximization of non-nitrogenous metabolite production inE. coliusing population systems biology

Abstract

1 5 1 6The E. coli metabolome is an interconnected set of enzymes that has measurable kinetic parameters ascribed for 1 7 the production of most of its metabolites. Flux Balance Analysis (FBA) or Ordinary Differential Equation 1 8 (ODE) models are used to increase product yield using defined media. However, they either give a range (FBA) 1 9 or exact amount (ODE) of metabolite yield which isn't true as the transcriptome diversity of individual cells 2 0 isn't considered. We formulate the metabolic-behaviour of individual cells by using a POpulation SYstems- 1Biology ALgorithm (POSYBAL) which predicts multiple-gene knockouts for increasing industrially relevant 2 2 metabolites. We validate this prediction for producing isobutanol (Heterogenous metabolite) and shikimate 2 3 (Homogenous metabolite) where, the product-yield was increased by 40 times (~2000 ppm) and 42 times 2 4 (~3000 ppm) respectively. Also, we introduce a nitrogen-swap in standard media to its low-nitrogen counterpart 2 5 during post-growth phase to redistribute flux towards non-nitrogenous pathways for increasing overall product-2 6 yield. Further, our model shows growth-phase diversity in bacterial population even under normal glucose-2 7 uptake, portraying a real-world scenario of diverse and robust environment thus, making it evolutionarily 2 8 favourable to threats such as anti-bacterial attack.2 9 3 0