Constructing efficient bacterial cell factories to enable one-carbon utilization based on quantitative biology: A review

Developing methylotrophic cell factories that can efficiently catalyze organic one-carbon (C1) feedstocks derived from electrocatalytic reduction of carbon dioxide into bio-based chemicals and biofuels is of strategic significance for building a carbon-neutral, sustainable economic and industrial system. With the rapid advancement of RNA sequencing technology and mass spectrometer analysis, researchers have used these quantitative microbiology methods extensively, especially isotope-based metabolic flux analysis, to study the metabolic processes initiating from C1 feedstocks in natural C1-utilizing bacteria and synthetic C1 bacteria. This paper reviews the use of advanced quantitative analysis in recent years to understand the metabolic network and basic principles in the metabolism of natural C1-utilizing bacteria grown on methane, methanol, or formate. The acquired knowledge serves as a guide to rewire the central methylotrophic metabolism of natural C1-utilizing bacteria to improve the carbon conversion efficiency, and to engineer non-C1-utilizing bacteria into synthetic strains that can use C1 feedstocks as the sole carbon and energy source. These progresses ultimately enhance the design and construction of highly efficient C1-based cell factories to synthesize diverse high value-added products. The integration of quantitative biology and synthetic biology will advance the iterative cycle of understand-design-build-testing-learning to enhance C1-based biomanufacturing in the future.