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Metab Eng. 2017 May;41:202-211. doi: 10.1016/j.ymben.2017.04.007. Epub 2017 Apr 23.

Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum.

Author information

1
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia.
2
LanzaTech Inc., Skokie, USA.
3
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia; Metabolomics Australia, AIBN, The University of Queensland, Brisbane, Australia.
4
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia; Metabolomics Australia, AIBN, The University of Queensland, Brisbane, Australia; School of Pharmacy, The University of Queensland, Brisbane, Australia.
5
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia. Electronic address: e.marcellin@uq.edu.au.

Abstract

Acetogens are attractive organisms for the production of chemicals and fuels from inexpensive and non-food feedstocks such as syngas (CO, CO2 and H2). Expanding their product spectrum beyond native compounds is dictated by energetics, particularly ATP availability. Acetogens have evolved sophisticated strategies to conserve energy from reduction potential differences between major redox couples, however, this coupling is sensitive to small changes in thermodynamic equilibria. To accelerate the development of strains for energy-intensive products from gases, we used a genome-scale metabolic model (GEM) to explore alternative ATP-generating pathways in the gas-fermenting acetogen Clostridium autoethanogenum. Shadow price analysis revealed a preference of C. autoethanogenum for nine amino acids. This prediction was experimentally confirmed under heterotrophic conditions. Subsequent in silico simulations identified arginine (ARG) as a key enhancer for growth. Predictions were experimentally validated, and faster growth was measured in media containing ARG (tD~4h) compared to growth on yeast extract (tD~9h). The growth-boosting effect of ARG was confirmed during autotrophic growth. Metabolic modelling and experiments showed that acetate production is nearly abolished and fast growth is realised by a three-fold increase in ATP production through the arginine deiminase (ADI) pathway. The involvement of the ADI pathway was confirmed by metabolomics and RNA-sequencing which revealed a ~500-fold up-regulation of the ADI pathway with an unexpected down-regulation of the Wood-Ljungdahl pathway. The data presented here offer a potential route for supplying cells with ATP, while demonstrating the usefulness of metabolic modelling for the discovery of native pathways for stimulating growth or enhancing energy availability.

KEYWORDS:

Acetogen; Arginine catabolism; Clostridium autoethanogenum; Genome-scale modelling; RNA-sequencing; Syngas

PMID:
28442386
DOI:
10.1016/j.ymben.2017.04.007
[Indexed for MEDLINE]

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