Design and engineering of E. coli metabolic sensor strains with a wide sensitivity range for glycerate

Microbial biosensors are used to detect the presence of compounds provided externally or produced internally. The latter case is commonly constrained by the need to screen a large library of enzyme or pathway variants to identify those that can efficiently generate the desired compound. To address t...

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Bibliographic Details
Published in:Metabolic engineering 2020-01, Vol.57, p.96-109
Main Authors: Aslan, Selçuk, Noor, Elad, Benito Vaquerizo, Sara, Lindner, Steffen N., Bar-Even, Arren
Format: Article
Language:English
Subjects:
Auxotrophy
Biosensing Techniques
Constraint-based metabolic model
Escherichia coli - genetics
Escherichia coli - metabolism
Glyceric Acids - analysis
Glyceric Acids - metabolism
Growth selection
Metabolic Engineering
Metabolic Networks and Pathways
Synthetic biology
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Summary:Microbial biosensors are used to detect the presence of compounds provided externally or produced internally. The latter case is commonly constrained by the need to screen a large library of enzyme or pathway variants to identify those that can efficiently generate the desired compound. To address this limitation, we suggest the use of metabolic sensor strains which can grow only if the relevant compound is present and thus replace screening with direct selection. We used a computational platform to design metabolic sensor strains with varying dependencies on a specific compound. Our method systematically explores combinations of gene deletions and identifies how the growth requirement for a compound changes with the media composition. We demonstrate this approach by constructing a set of E. coli glycerate sensor strains. In each of these strains a different set of enzymes is disrupted such that central metabolism is effectively dissected into multiple segments, each requiring a dedicated carbon source. We find an almost perfect match between the predicted and experimental dependence on glycerate and show that the strains can be used to accurately detect glycerate concentrations across two orders of magnitude. Apart from demonstrating the potential application of metabolic sensor strains, our work reveals key phenomena in central metabolism, including spontaneous degradation of central metabolites and the importance of metabolic sinks for balancing small metabolic networks. •Metabolic sensor strains can grow only if the relevant compound is present.•We developed a computational platform to design metabolic sensor strains.•We constructed glycerate sensor strains, dissecting central metabolism to segments.•We find a perfect match between predicted and experimental dependence on glycerate.•Metabolic sensor strains reveal key phenomena in central metabolism.
ISSN:1096-7176
1096-7184
DOI:10.1016/j.ymben.2019.09.002