Microbial cell factories

Microbial cell factories are among the key subjects in synthetic biology research. Microbial cell factories produce bulk chemicals and natural products through renewable biomass resources. These green and clean biological manufacturing routes can supplement nonrenewable petrochemical resources and rare plant resources; thus, these routes can partially replace petrochemical manufacturing and plant extraction routes, which consume high amounts of energy and generate high pollution levels. The green routes provide an important method for society to address resource, energy and environmental problems. To successfully commercialize microbial cell factories, the regulatory mechanisms that microorganisms use to efficiently produce chemicals were investigated from two perspectives, including carbon metabolism and energy metabolism. Regarding carbon metabolism, a synthetic biology platform for enzyme mining was established, and the synthetic pathways of several triterpenoids were characterized using this platform. Furthermore, some cell factories that produce triterpenoids, such as hawthorn acid, corosolic acid and trichoparic acid, were created by Saccharomyces cerevisiae. In addition, precision pathway regulation technologies, including simultaneous modulation of multiple genes in chromosomes and glycosylase base editor (GBE), were developed and could improve the rate of xylose utilization by 3-fold compared with that of the control. The rate-limiting steps of the synthetic pathways for a series of chemicals were identified, and the rate-limiting enzymes were activated to increase the rate of chemical production by 2.5- to 600-fold; thus, the adaptation problems between enzyme parts and synthetic pathways were solved. When considering energy metabolism, four new modules of generating energy through glucose metabolism were designed according to the requirements of synthetic products; thus, the imbalance problems between the supply and the necessity of reducing equivalents in the synthetic pathway were solved. Based on the knowledge of the regulatory mechanisms for synthetic metabolism, efficient microbial cell factories were constructed by our research team to produce a series of chemicals. Technologies to microbially produce 14 chemicals have been licensed. Among these chemicals, four have been successfully commercialized, and the annual production of each chemical can reach over 10000 t. In addition, one company realized IPO. All these factors have promoted the industrial application of microbial cell factories. The future directions of research on microbial cell factories are discussed at the end of this paper. Most of the synthetic pathways of these cell factories are based on existing biosynthetic pathways in nature. However, for the vast majority of chemicals, the biosynthetic pathways are often unknown or do not occur in nature. How to microbially synthesize these chemicals is among the difficulties encountered when constructing a microbial cell factory. The principle of designing new pathways and new enzymes, the regulation of energy metabolism based on nonnatural coenzymes and the mechanism of chemical stress on cells can be studied in substance metabolism, energy metabolism, and physiological metabolism, respectively.