CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium

Yixin Rong, Adrian Frey, Emre Özdemir, Arrate Larrea, Songyuan Li, Alex Toftgaard Nielsen and Sheila Ingemann Jensen ()
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Yixin Rong: Technical University of Denmark
Adrian Frey: Technical University of Denmark
Emre Özdemir: Technical University of Denmark
Arrate Larrea: Technical University of Denmark
Songyuan Li: Technical University of Denmark
Alex Toftgaard Nielsen: Technical University of Denmark
Sheila Ingemann Jensen: Technical University of Denmark

Nature Communications, 2024, vol. 15, issue 1, 1-8

Abstract: Abstract Replacing petrochemicals with compounds from bio-based manufacturing processes remains an important part of the global effort to move towards a sustainable future. However, achieving economic viability requires both optimized cell factories and innovative processes. Here, we address this challenge by developing a fermentation platform, which enables two concurrent fermentations in one bioreactor. We first construct a xylitol producing Escherichia coli strain in which CRISPRi-mediated gene silencing is used to switch the metabolism from aerobic to anaerobic, even when the bacteria are under oxic conditions. The switch also decouples growth from production, which further increases the yield. The strain produces acetate as a byproduct, which is subsequently metabolized under oxic conditions by a secondary E. coli strain. Through constraint-based metabolic modelling this strain is designed to co-valorize glucose and the excreted acetate to a secondary product. This unique syntrophic consortium concept facilitates the implementation of “two fermentations in one go”, where the concurrent fermentation displays similar titers and productivities as compared to two separate single strain fermentations.

Date: 2024
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DOI: 10.1038/s41467-024-53381-4

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