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Growth of E. coli on formate and methanol via the reductive glycine pathway

Abstract

Engineering a biotechnological microorganism for growth on one-carbon intermediates, produced from the abiotic activation of CO2, is a key synthetic biology step towards the valorization of this greenhouse gas to commodity chemicals. Here we redesign the central carbon metabolism of the model bacterium Escherichia coli for growth on one-carbon compounds using the reductive glycine pathway. Sequential genomic introduction of the four metabolic modules of the synthetic pathway resulted in a strain capable of growth on formate and CO2 with a doubling time of ~70 h and growth yield of ~1.5 g cell dry weight (gCDW) per mol-formate. Short-term evolution decreased doubling time to less than 8 h and improved biomass yield to 2.3 gCDW per mol-formate. Growth on methanol and CO2 was achieved by further expression of a methanol dehydrogenase. Establishing synthetic formatotrophy and methylotrophy, as demonstrated here, paves the way for sustainable bioproduction rooted in CO2 and renewable energy.

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Fig. 1: The synthetic rGlyP is similar in structure to the rAcCoAP.
Fig. 2: Modular establishment of the rGlyP.
Fig. 3: Short-term evolution improves growth on formate.
Fig. 4: Labeling pattern of proteinogenic amino acids confirms the activity of the rGlyP.
Fig. 5: Engineered growth on methanol.

Data availability

Complete information on the experimental setup as well as detailed results are available from the corresponding author upon reasonable request.

Code availability

MATLAB code used for the analysis of the experiments is available from the corresponding author upon request.

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Acknowledgements

We thank C. Cotton, N. Claassens, H. He, R. Milo, E. Noor, N. Antonovsky, A. Flamholz, Y. Bar-On, W. Newell, D. Bonder, A. Satanowski, T. Erb and M. Bouzon for helpful discussions and suggestions. This work was funded by the Max Planck Society, by the German Ministry of Education and Research grant FormatPlant (part of BioEconomy 2030, Plant Breeding Research for the Bioeconomy) and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 763911 (Project eForFuel).

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A.B.-E. designed and supervised the research and wrote the paper. S.K., S.N.L., S.A. and O.Y. genetically engineered E. coli for growth on formate and methanol, and performed the growth experiments. S.K. and S.N.L. measured biomass yield on formate and methanol. S.A. performed the qPCR experiments. S.W. and K.S. cloned the methanol dehydrogenase and formaldehyde dehydrogenase genes, and assisted in the growth experiments on methanol. S.K., S.N.L., S.A., O.Y., S.W., K.S. and A.B.-E. analyzed the data.

Corresponding author

Correspondence to Arren Bar-Even.

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Competing interests

A.B.-E. is cofounder of b.fab, exploring the commercialization of microbial bioproduction using formate as feedstock. The company was not involved in any way in performing or funding this study.

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Supplementary Table 1, Figs. 1–12 and Note.

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Kim, S., Lindner, S.N., Aslan, S. et al. Growth of E. coli on formate and methanol via the reductive glycine pathway. Nat Chem Biol 16, 538–545 (2020). https://doi.org/10.1038/s41589-020-0473-5

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