Co-utilization of carbon sources in microorganisms for the bioproduction of chemicals

The fast development of metabolic engineering has enhanced the capability of microorganisms to produce value-added chemicals using a wide range of carbon sources, including various sugars, organic acids, fatty acids, and so forth. However, when growing in a mixture of carbon sources, microorganisms are specific about the priority of the uptake and metabolism of carbon sources. For most microorganisms, glucose is a preferred carbon source with high catabolic priority and efficiency. When co-present with other carbon sources, glucose is usually preferentially depleted, followed by the sequential utilization of other carbon sources. In an era of intense material and energy competition, the maximum use of different carbon sources in bioproduction is vital to economic efficiency. Nevertheless, the diauxic growth of microorganisms with a lag phase occurs owing to the sequential utilization of mixed carbon sources, often leading to prolonged fermentation periods and reduced productivities/yields of target products. Thus, significant efforts have been made to clarify the diauxic growth phenomenon. Now, it has been universally accepted that diauxic growth is mainly caused by carbon catabolite repression (CCR) mediated via two types of mechanisms. One mechanism is the global transcriptional regulation, where the utilization of a preferred carbon source represses the expression of genes involved in the transport and metabolism of alternative carbon sources. The other mechanism is called inducer exclusion, where the presence of a preferred carbon source inhibits the entry of inducers to the catabolic regulons of alternative carbon sources. The specific mechanisms of CCR vary in different microorganisms, and have not been fully understood.

The demand for the application of low-cost nonfood carbon sources has surged to cope with the global food crisis. For example, lignocellulosic hydrolysate with abundant glucose and xylose (Sun et al., 2023), and crude glycerol that is the byproduct of biodiesel synthesis, are promising carbon sources to meet the aforementioned requirements. Yet, efficient simultaneous consumption of glucose and xylose should be achieved first to expand the industrial application of lignocellulosic biomass. Hence, the efficient co-utilization of mixed carbon sources is of great significance for future industrial biotechnology.

Co-utilizing carbon sources is highly advantageous for industrial microbial production in some cases compared to using a single carbon source (Liu et al., 2020). First, co-utilizing carbon sources can benefit cell growth (Wang et al., 2019b). The precursors of biomass components can be better enriched by the combined supply of carbon sources. Besides, the cell growth and biosynthesis of target products can be rebalanced by co-utilizing carbon sources for high titer/yield/productivity. The yields in the production of glucose derivatives, such as D-glucaric acid (Shiue et al., 2015), D-gluconic acid, N-acetyl-glucosamine (Ma et al., 2021), myo-inositol (Tang et al., 2020), from glucose are low because of the competition between cell growth and product synthesis. During the synthesis of such target products, the utilization of a secondary carbon source to support cell growth, such as glycerol (Ma et al., 2021), xylose (Fujiwara et al., 2020), can divert more glucose for product synthesis, thereby increasing the yields of target products. Apart from the aforementioned merits, co-utilizing carbon sources also benefits the synthesis of products with long synthesis routes (Liu et al., 2020). The metabolism burden can be significantly relieved, and the optimization of different synthesis modules becomes easier by dividing the whole synthetic pathway into different modules in various workhorses (Li et al., 2022a). Undeniably, the use of mixed carbon sources increases the complexity of the fermentation process to some extent compared with using a single carbon source. However, industrial production necessitates a careful balancing act between inputs and outputs. For instance, if a more complex input results in a notable enhancement in production efficiency as the output, it would undoubtedly be worthwhile to pursue. From this perspective, the benefits of utilizing mixed carbon sources in boosting production efficiency have the potential to pave the way for economically viable bioproduction of value-added chemicals.

Co-utilization of carbon sources has been explored via rational metabolic engineering and evolutionary approaches (Fig. 1). Various solutions to alleviate CCR have been proposed, including engineering of the global regulators, inactivation of the phosphotransferase system (PTS), and so forth. Engineering of the transport and metabolism of secondary carbon sources is usually required to enhance the utilization rate of nonpreferred carbon sources. The coupling of co-utilizing carbon sources to cell growth can lead to the compulsive co-utilization of carbon sources in a single culture, and the orthogonal utilization of carbon sources and division of labor in the biosynthetic pathway can achieve the co-utilization of carbon sources in microbial cocultures (Li et al., 2022a). Besides, the evolutionary approaches, including directed evolution for efficient transporters and adaptive evolution of microorganisms, are effective tools for further enhancing co-utilization efficiencies. This review summarized the strategies for co-utilizing carbon sources and their applications in the microbial production of value-added chemicals.

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