Evolutionary engineering of methylotrophic E. coli enables fast growth on methanol

Liang-Yu Nieh, Frederic Y.-H. Chen, Hsin-Wei Jung, Kuan-Yu Su, Chao-Yin Tsuei, Chun-Ting Lin, Yue-Qi Lee and James C. Liao ()
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Liang-Yu Nieh: Academia Sinica
Frederic Y.-H. Chen: Academia Sinica
Hsin-Wei Jung: Academia Sinica
Kuan-Yu Su: Academia Sinica
Chao-Yin Tsuei: Academia Sinica
Chun-Ting Lin: Academia Sinica
Yue-Qi Lee: Academia Sinica
James C. Liao: Academia Sinica

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract As methanol can be derived from either CO2 or methane, methanol economy can play an important role in combating climate change. In this scenario, rapid utilization of methanol by an industrial microorganism is the first and crucial step for efficient utilization of the C1 feedstock chemical. Here, we report the development of a methylotrophic E. coli strain with a doubling time of 3.5 hours under optimal conditions, comparable or faster than native model methylotrophs Methylorubrum extorquens AM1 (Td~4hr) and Bacillus methanolicus at 37°C (Td~5hr). To accomplish this, we develop a bacterial artificial chromosome (BAC) with dynamic copy number variation (CNV) to facilitate overcoming the formaldehyde-induced DNA-protein cross-linking (DPC) problem in the evolution process. We track the genome variations of 75 cultures along the evolution process by next-generation sequencing, and identified the features of the fast-growing strain. After stabilization, the final strain (SM8) grows to 20 g/L of cell mass within 77 hrs in a bioreactor. This study illustrates the potential of dynamic CNV as an evolution tool and synthetic methylotrophs as a platform for sustainable biotechnological applications.

Date: 2024
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DOI: 10.1038/s41467-024-53206-4

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