Design principles for engineering bacteria to maximise chemical production from batch cultures

Ahmad A. Mannan, Alexander P. S. Darlington (), Reiko J. Tanaka and Declan G. Bates ()
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Ahmad A. Mannan: Imperial College London
Alexander P. S. Darlington: University of Warwick
Reiko J. Tanaka: Imperial College London
Declan G. Bates: University of Warwick

Nature Communications, 2025, vol. 16, issue 1, 1-10

Abstract: Abstract Bacteria can be engineered to manufacture chemicals, but it is unclear how to optimally engineer a single cell to maximise production performance from batch cultures. Moreover, the performance of engineered production pathways is affected by competition for the host’s native resources. Here, using a ‘host-aware’ computational framework which captures competition for both metabolic and gene expression resources, we uncover design principles for engineering the expression of host and production enzymes at the cell level which maximise volumetric productivity and yield from batch cultures. However, this does not break the fundamental growth-synthesis trade-off which limits production performance. We show that engineering genetic circuits to switch cells to a high synthesis-low growth state after first growing to a large population can further improve performance. By analysing different circuit topologies, we show that highest performance is achieved by circuits that inhibit host metabolism to redirect it to product synthesis. Our results should facilitate construction of microbial cell factories with high and efficient production capabilities.

Date: 2025
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DOI: 10.1038/s41467-024-55347-y

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