Rewiring the microbial metabolic network for efficient utilization of mixed carbon sources

Abstract

Carbon sources represent the most dominant cost factor in the industrial biomanufacturing of products. Thus, it has attracted much attention to seek cheap and renewable feedstocks, such as lignocellulose, crude glycerol, methanol, and carbon dioxide, for biosynthesis of value-added compounds. Co-utilization of these carbon sources by microorganisms not only can reduce the production cost but also serves as a promising approach to improve the carbon yield. However, co-utilization of mixed carbon sources usually suffers from a low utilization rate. In the past few years, the development of metabolic engineering strategies to enhance carbon source co-utilization efficiency by inactivation of carbon catabolite repression has made significant progress. In this article, we provide informative and comprehensive insights into the co-utilization of two or more carbon sources including glucose, xylose, arabinose, glycerol, and C1 compounds, and we put our focus on parallel utilization, synergetic utilization, and complementary utilization of different carbon sources. Our goal is not only to summarize strategies of co-utilization of carbon sources, but also to discuss how to improve the carbon yield and the titer of target products.

Keywords: Carbon source; Co-utilization; Crude glycerol; Lignocellulosic hydrolysates; Methanol.

Fig. 1.

Schematic representation of carbon sources’ co-utilization strategies in microbes. (a) Parallel carbon utilization strategy. (b) Synergetic carbon utilization strategy. (c) Carbon-supplement co-utilization strategy.

Fig. 2.

Metabolic pathways of xylose, arabinose, and glucose co-utilization in microbes. Blue-colored characters indicate Dahms pathway; purple-colored characters indicate Weimberg pathway; and black-colored dash lines indicate the CCR. EMP, Embden–Meyerhof–Parnas pathway; PPP, pentose phosphate pathway; TCA, tricarboxylic acid cycle; PTS, phosphotransferase system; GK, glucose kinase; Pgi, glucose-6-phosphate isomerase; Pyk, pyruvate kinase; G6pdh, glucose 6-phosphate dehydrogenase; XylA, xylose isomerase; XylB, xylulokinase; XDH, xylose dehydrogenase; XL, xylonolactonase; XD, xylonate dehydratase; KdxD, 2-keto-3-deoxy-D-xylonate dehydratase; DPDH, 2,5-dioxopentanoate dehydrogenase; AL, aldolase; GR, glycolaldehyde reductase; GD, glycolaldehyde dehydrogenase; GO, glycolate oxidase; AraA, L-arabinose isomerase; AraB, ribulokinase; AraD, L-ribulose 5-phosphate epimerase. Metabolites: PEP, phosphoenolpyruvate; PYR, pyruvate; AcCoA, acetyl coenzyme A; X5P, D-xylulose 5-phosphate; Ru5P, ribulose 5-phosphate.

Fig. 3.

Glucose and glycerol co-utilization strategies in microbes. (a) Glucose and glycerol co-utilization strategy for the production of redox-demanding products. Black-colored arrows indicate the native metabolic pathways. Blue-colored arrows indicate the chemical biosynthesis pathways of glycerol. (b) Glucose and glycerol synergetic utilization strategy for the production of glucose derived products. Black-colored arrows indicate the native metabolic pathways; blue-colored arrows indicate the main metabolic pathways of glycerol for cell growth; and purple-colored arrows indicate the chemical biosynthesis pathways of glucose. G3P, glyceraldehyde 3-phosphate; DHA, dihydroxyacetone; DHAP, dihydroxyacetone phosphate; PEP, phosphoenolpyruvate; PYR, pyruvate; G6P, glucose 6-phosphate; EMP, Embden–Meyerhof–Parnas pathway; PPP, pentose phosphate pathway; TCA, tricarboxylic acid cycle; glpF, glycerol facilitator; glpK, glycerol kinase; gldA, glycerol dehydrogenase; glf, glucose facilitator; PTS, phosphotransferase system; pgi, encoding phosphoglucose isomerase; zwf, encoding glucose 6-phosphate dehydrogenase; pykAF, encoding pyruvate kinase.

Fig. 4.

Metabolic pathways of methanol assimilation with other carbon sources. Black-colored arrows indicate the native metabolic pathways in most microbes; blue-colored arrows with blue-colored enzymes and metabolites indicate the ribulose monophosphate (RuMP) pathway; purple-colored arrows indicate the natural serine cycle; and yellow-colored arrows indicate the modified serine cycle. PPP, pentose phosphate pathway; TCA, tricarboxylic acid cycle; Mdh, methanol dehydrogenase; Hps, 3-hexulose-6-phosphate synthase; Phi, 6-phospho-3-hexuloisomerase; XylA, xylose isomerase; XylB, xylulokinase; AI, L-arabinose isomerase; RK, ribulokinase; RPE, ribulose 5-phosphate epimerase; Faldh, formaldehyde dehydrogenase; Fae, formaldehyde-activating enzyme; Mtd, NADP-dependent methylene-tetrahydromethanopterin/methylene-tetrahydrofolate dehydrogenase; Mch, N(5), N(10)-methenyltetrahydromethanopterin cyclohydrolase; Fhc, formyltransferase/hydrolase complex; Fthfl, formate THF ligase; Fch, methenyltetrahydrofolate cyclohydrolase. Metabolites: G6P, glucose 6-phosphate; H6P, hexulose 6-phosphate; F6P, fructose 6-phosphate; GAP, 3-phosphoglyceraldehyde; PEP, phosphoenolpyruvate; PYR, pyruvate; X5P, xylulose 5-phosphate.