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bioRxiv · 10.1101/2022.04.04.487013

Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

Anand, A.·Patel, A.·Chen, K.·Olson, C. A.·Phaneuf, P. V.·Lamoureux, C.·Hefner, Y.·Szubin, R.·Feist, A.·Palsson, B.
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Abstract

Respiration requires organisms to have an electron transport system (ETS) for the generation of proton motive force across the membrane that drives ATP synthase. Although the molecular details of the ETS are well studied and constitute textbook material, few studies have appeared to elucidate its systems biology. The most thermodynamically efficient ETS consists of two enzymes, an NADH: quinone oxidoreductase (NqRED) and a dioxygen reductase (O2RED), which facilitate the shuttling of electrons from NADH to oxygen. However, evolution has produced variations within ETS which modulate the overall energy efficiency of the system even within the same organism 1-3. The system-level impact of these variations and their individual physiological optimality remain poorly determined. To mimic varying ETS efficiency we generated four Escherichia coli deletion strains (named ETS-1H, 2H, 3H, and 4H) harboring unbranched ETS variants that pump 1, 2, 3, or 4 proton(s) per electron respectively. We then used a combination of synergistic methods (laboratory evolution, multi-omic analyses, and computation of proteome allocation) to characterize these ETS variants. We found that: (a) all four ETS variants evolved to a similar optimized growth rate, (b) the evolution of ETS variants was enabled by specific rewiring of major energy-generating pathways that couple to the ETS to optimize their ATP production capability, (c) proteome allocation per ATP generated was the same for all the variants, (d) the aero-type, that designates the overall ATP generation strategy 4 of a variant, remained conserved during its laboratory evolution, with the exception of the ETS-4H variant, and (e) integrated computational analysis of then data supported a proton-to-ATP ratio of 10 protons per 3 ATP for ATP synthase for all four ETS variants. We thus have defined the Aero-Type System (ATS) as a generalization of the aerobic bioenergetics, which is descriptive of the metabolic systems biology of respiration and demonstrates its plasticity.

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Anand, A., Patel, A., Chen, K., Olson, C. A., Phaneuf, P. V., Lamoureux, C., Hefner, Y., Szubin, R., Feist, A., Palsson, B.. 2022-04-05. Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity. https://doi.org/10.1101/2022.04.04.487013

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