Carbon-Efficient Conversion through Hydrogen and Formate-Driven Metabolism in Escherichia coli

Bertrand, R. L.; Panich, J.; Cowan, A. E.; Roberts, J. B.; Artier, J.; Toppari, E.; Baidoo, E. E.; Chen, Y.; Petzold, C. J.; Hudson, G. A.; Shih, P. M.; Singer, S. W.; Keasling, J. D.

doi:10.1101/2025.05.30.657096

bioRxiv · 10.1101/2025.05.30.657096

Carbon-Efficient Conversion through Hydrogen and Formate-Driven Metabolism in Escherichia coli

Bertrand, R. L.·Panich, J.·Cowan, A. E.·Roberts, J. B.·Artier, J.·Toppari, E.·Baidoo, E. E.·Chen, Y.·Petzold, C. J.·Hudson, G. A.·Shih, P. M.·Singer, S. W.·Keasling, J. D.

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Abstract

Product yields for biomanufacturing processes are often constrained by the tight coupling of cellular energy generation and carbon metabolism in sugar-based fermentation systems. To overcome this limitation, we engineered Escherichia coli to utilize hydrogen gas (H2) and formate (HCOO-) as alternative sources of energy and reducing equivalents, thereby decoupling energy generation from carbon metabolism. This approach enabled precise suppression of decarboxylative oxidation during acetate growth, with 86.6 {+/-} 1.6% of electrons from hydrogen gas (via soluble hydrogenase from Cupriavidus necator H16) and 98.4 {+/-} 3.6% of electrons from formate (via formate dehydrogenase from Pseudomonas sp. 101) offsetting acetate oxidation. Hydrogen gas supplementation led to a titratable and stoichiometric reduction in CO2 evolution in acetate-fed cultures. Metabolomic analysis suggests that this metabolic decoupling redirects carbon flux through the glyoxylate shunt, partially bypassing two decarboxylative steps in the TCA cycle. We demonstrated the utility of this strategy by applying it to mevalonate biosynthesis, where formate supplementation during glucose fermentation increased titers by 57.6% in our best-performing strain. Flux balance analysis further estimated that 99.0 {+/-} 2.8% of electrons from formate were used to enhance mevalonate production. These findings highlight a broadly applicable strategy for enhancing biomanufacturing efficiency by leveraging external reducing power to optimize feedstock and energy use. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=65 SRC="FIGDIR/small/657096v2_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@12f77dborg.highwire.dtl.DTLVardef@165d6c1org.highwire.dtl.DTLVardef@f6302forg.highwire.dtl.DTLVardef@d59bb3_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Panich, J. (2025) https://BioRender.com/0tmtp94

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Bertrand, R. L., Panich, J., Cowan, A. E., Roberts, J. B., Artier, J., Toppari, E., Baidoo, E. E., Chen, Y., Petzold, C. J., Hudson, G. A., Shih, P. M., Singer, S. W., Keasling, J. D.. 2025-05-31. Carbon-Efficient Conversion through Hydrogen and Formate-Driven Metabolism in Escherichia coli. https://doi.org/10.1101/2025.05.30.657096

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