Enzyme and Metabolic Engineering Strategies for Biosynthesis of α-Farnesene in Saccharomyces cerevisiae

Sucrose-driven carbon redox rebalancing eliminates the Crabtree effect and boosts energy metabolism in yeast

Saccharomyces cerevisiae primarily generates energy through glycolysis and respiration. However, the manifestation of the Crabtree effect results in substantial carbon loss and energy inefficiency, which significantly diminishes product yield and escalates substrate costs in microbial cell factories. To address this challenge, we introduce the sucrose phosphorolysis pathway and delete the phosphoglucose isomerase gene PGI1, effectively decoupling glycolysis from respiration and facilitating the metabolic transition of yeast to a Crabtree-negative state. Additionally, a synthetic energy system is engineered to regulate the NADH/NAD+ ratio, ensuring sufficient ATP supply and maintaining redox balance for optimal growth. The reprogrammed yeast strain exhibits significantly higher yields of various non-ethanol compounds, with lactic acid and 3-hydroxypropionic acid production increasing by 8- to 11-fold comparing to the conventional Crabtree-positive strain. This study describes an approach for overcoming the Crabtree effect in yeast, substantially improving energy metabolism, carbon recovery, and product yields.

Beyond CEN.PK - parallel engineering of selected S. cerevisiae strains reveals that superior chassis strains require different engineering approaches for limonene production

Genetically engineered microbes are increasingly utilized to produce a broad range of high-value compounds. However, most studies start with only a very narrow group of genetically tractable type strains that have not been selected for maximum titers or industrial robustness. In this study, we used high-throughput screening and parallel metabolic engineering to identify and optimize Saccharomyces cerevisiae chassis strains for the production of limonene, a monoterpene with applications in flavors, fragrances, and biofuels. We screened 921 genetically and phenotypically distinct S. cerevisiae strains for limonene tolerance and lipid content to identify optimal chassis strains for precision fermentation of limonene. In parallel, we also evaluated 16 different plant limonene synthases. Our results revealed that two of the selected strains showed approximately a 2-fold increase in titers compared to CEN.PK2-1C, the type strain that is often used as a chassis for limonene production, with the same genetic modifications in the mevalonate pathway. Intriguingly, the most effective engineering strategy proved strain-specific. Metabolic profiling revealed that this difference is likely explained by differences in native mevalonate production. Ultimately, by using strain-specific engineering strategies, we achieved 844 mg/L in a new strain, 40 % higher than the titer (605 mg/L) achieved by CEN.PK2-1C. Our findings demonstrate the potential of leveraging genetic diversity in S. cerevisiae for monoterpene bioproduction and highlight the necessity for tailoring metabolic engineering strategies to specific strains.

Metabolic Engineering of Yeast

Microbial cell factories have been developed to produce various compounds in a sustainable and economically viable manner. The yeast Saccharomyces cerevisiae has been used as a platform cell factory in industrial biotechnology with numerous advantages, including ease of operation, rapid growth, and tolerance for various industrial stressors. Advances in synthetic biology and metabolic models have accelerated the design-build-test-learn cycle in metabolic engineering, significantly facilitating the development of yeast strains with complex phenotypes, including the redirection of metabolic fluxes to desired products, the expansion of the spectrum of usable substrates, and the improvement of the physiological properties of strain. Strains with enhanced titer, rate, and yield are now competing with traditional petroleum-based industrial approaches. This review highlights recent advances and perspectives in the metabolic engineering of yeasts for the production of a variety of compounds, including fuels, chemicals, proteins, and peptides, as well as advancements in synthetic biology tools and mathematical modeling.

Multiomics reveals the molecular mechanism of unsaturated fatty acid-induced terpenoid biosynthesis in Sanghuangporus lonicericola

Treatment with C18:1 and C18:2, but not C18:0, increased the triterpenoid content of the medicinal fungus Sanghuangporus lonicericola. We identified 413 terpenoids, including 210 volatile terpenoids. Eight upregulated terpenoids, including 3,13,15-trihydroxyoleanane-12-one, dulcioic acid and serrat-14-ene-3,20,24,29-tetrol, were shared between the C18:1 and C18:2 treatments but not the C18:0 treatment. The C18:1 and C18:2 treatments increased the levels of 12 and 7 odour-related terpenoids, respectively, and increased the level of alpha-farnesene (herbal odour). Gene set enrichment analysis revealed that compared with C18:0, C18:1 and C18:2 produced stronger activation of the terpenoid biosynthesis, fatty acid degradation, and MAPK signalling pathways and stronger inhibition of basal transcription factors at both the transcript and protein levels. Finally, two-way orthogonal partial least squares analysis revealed that gene and protein expression in the identified pathways was correlated with levels of unsaturated fatty acid-induced terpenoid metabolites. Together, our integrated multiomics data revealed the key pathways involved in unsaturated fatty acid-induced terpenoid biosynthesis in S. lonicericola.

Heterologous Biosynthesis of Terpenoids in Saccharomyces cerevisiae

Terpenoids are widely distributed in nature and have various applications in healthcare products, pharmaceuticals, and fragrances. Despite the significant potential that terpenoids possess, traditional production methods, such as plant extraction and chemical synthesis, face challenges in meeting current market demand. With the advancement of synthetic biology and metabolic engineering, it becomes feasible to construct efficient microbial cell factories for large-scale production of terpenoids. This article primarily centers on the heterologous expression of terpenoids in Saccharomyces cerevisiae, detailing the expression of terpenoid biosynthesis pathways through the utilization of cellular microcompartments, strategies for the efficient expression of key P450 enzymes in the synthesis pathway, and the regulation and optimization of host metabolism to enhance flux to terpenoids synthesis. Additionally, we analyze current challenges and propose solutions to further refine yeast chassis for more effective terpenoids production.

Advances in recombinant protein production in microorganisms and functional peptide tags

Recombinant protein production in prokaryotic and eukaryotic cells is a fundamental technology for both research and industry. Achieving efficient protein synthesis is key to accelerating the discovery, characterization, and practical application of proteins. This review focuses on recent advances in recombinant protein production and strategies for more efficient protein production, especially using Escherichia coli and Saccharomyces cerevisiae. Additionally, this review summarizes the development of various functional peptide tags that can be employed for protein production, modification, and purification, including translation-enhancing peptide tags developed by our research group.

Comprehensive Engineering Strategies for Heterologous Production of Zealexin A1 in Saccharomyces cerevisiae

Zealexin A1 is a nonvolatile sesquiterpene phytoalexin, which not only exhibits extensive antifungal and insecticidal activities but also has the ability to enhance the drought resistance of plants, and thus has potential applications in agricultural and food fields. In this study, the biosynthetic pathway of zealexin A1 was constructed in Saccharomyces cerevisiae for the first time, and the highest production of zealexin A1 reported to date was achieved. First, through screening of sesquiterpene synthases from various plants, BdMAS11 had a stronger (S)-β-macrocarpene synthesis ability was obtained, and the heterologous synthesis of zealexin A1 was achieved by coexpressing BdMAS11 with cytochrome P450 oxygenase ZmCYP71Z18. Subsequently, after the site-directed mutagenesis of BdMAS11, fusion expression of farnesyl diphosphate synthase ERG20 and BdMAS11, and tailored truncation of BdMAS11 and ZmCYP71Z18, the strain coexpressing the manipulated BdMAS11 and original ZmCYP71Z18 produced 119.31 mg/L of zealexin A1 in shake-flask fermentation. Finally, the production of zealexin A1 reached 1.17 g/L through fed-batch fermentation in a 5 L bioreactor, which was 261.7-fold that of the original strain. This study lays the foundation for the industrial production of zealexin A1 and other terpenoids.

Efficient production of 22(R)-hydroxycholesterol via combination optimization of Saccharomyces cerevisiae

22(R)-hydroxycholesterol (22(R)-HCHO) is a crucial precursor of steroids biosynthesis with various biological functions. However, the production of 22(R)-HCHO is expensive and unsustainable due to chemical synthesis and extraction from plants or animals. This study aimed to construct a microbial cell factory to efficiently produce 22(R)-HCHO through systems metabolic engineering. First, we tested 7-dehydrocholesterol reductase (Dhcr7s) and cholesterol C22-hydroxylases from different sources in Saccharomyces cerevisiae, and the titer of 22(R)-HCHO reached 128.30 mg L-1 in the engineered strain expressing Dhcr7 from Columba livia (ClDhcr7) and cholesterol 22-hydroxylase from Veratrum californicum (VcCyp90b27). Subsequently, the 22(R)-HCHO titer was significantly increased to 427.78 mg L-1 by optimizing the critical genes involved in 22(R)-HCHO biosynthesis. Furthermore, hybrid diploids were constructed to balance cell growth and 22(R)-HCHO production and to improve stress tolerance. Finally, the engineered strain produced 2.03 g L-1 of 22(R)-HCHO in a 5-L fermenter, representing the highest 22(R)-HCHO titer reported to date in engineered microbial cell factories. The results of this study provide a foundation for further applications of 22(R)-HCHO in various industrially valuable steroids.

New advances in protein engineering for industrial applications: Key takeaways

Recent advancements in protein/enzyme engineering have enabled the production of a diverse array of high-value compounds in microbial systems with the potential for industrial applications. The goal of this review is to articulate some of the most recent protein engineering advances in bacteria, yeast, and other microbial systems to produce valuable substances. These high-value substances include α-farnesene, vitamin B12, fumaric acid, linalool, glucaric acid, carminic acid, mycosporine-like amino acids, patchoulol, orcinol glucoside, d-lactic acid, keratinase, α-glucanotransferases, β-glucosidase, seleno-methylselenocysteine, fatty acids, high-efficiency β-glucosidase enzymes, cellulase, β-carotene, physcion, and glucoamylase. Additionally, recent advances in enzyme engineering for enhancing thermostability will be discussed. These findings have the potential to revolutionize various industries, including biotechnology, food, pharmaceuticals, and biofuels.

Integrated HS-GC-IMS and UPLC-Q-Orbitrap HRMS-based metabolomics revealed the characteristics and differential volatile and nonvolatile metabolites of different citrus peels

Citrus is an important genus in the Rutaceae family, and citrus peels can be used in both food and herbal medicine. However, the bulk of citrus peels are discarded as waste by the fruit processing industry, causing environmental pollution. This study aimed to provide guidelines for the rational and effective use of citrus peels by elucidating the volatile and nonvolatile metabolites within them using metabolomics based on headspace-gas chromatography-ion mobility spectrometry and ultra-high-performance liquid chromatography-Q-Orbitrap high-resolution mass spectrometry. In addition, the antioxidant activities of the citrus peels were evaluated using DPPH radical scavenging, ABTS radical scavenging, and ferric reducing antioxidant power. In total, 103 volatile and 53 nonvolatile metabolites were identified and characterized. Alcohols, aldehydes, and terpenes constituted 87.36% of the volatile metabolites, while flavonoids and carboxylic acids accounted for 85.46% of the nonvolatile metabolites. Furthermore, (Z)-2-penten-1-ol, L-pipecolinic acid, and limonin were identified as characteristic components of Citrus reticulata Blanco cv. Ponkan (PK), C. reticulata 'Unshiu' (CLU), and C. reticulata 'Wo Gan' (WG), respectively. Principal component analysis and partial least squares discriminant analysis indicated that C. reticulata Blanco 'Chun Jian' (CJ), PK, CLU, and C. reticulata 'Dahongpao' (DHP) were clustered together. DHP is a traditional Chinese medicine documented in the Chinese Pharmacopoeia, suggesting that the chemical compositions of CJ, PK, and CLU may also have medicinal values similar to those of DHP. Moreover, DHP, PK, C. reticulata 'Ai Yuan 38'(AY38), CJ, C. reticulata 'Gan Ping'(GP), and C. reticulata 'Qing Jian'(QJ) displayed better antioxidant activities, recommending their use as additives in cosmetics and food. Correlation analysis suggested that some polyphenols including tangeritin, nobiletin, skullcapflavone II, genistein, caffeic acid, and isokaempferide were potential antioxidant compounds in citrus peel. The results of this study deepen our understanding of the differences in metabolites and antioxidant activities of different citrus peel varieties and ultimately provide guidance for the full and rational use of citrus peels.

Catalytic Mechanism and Heterologous Biosynthesis Application of Sesquiterpene Synthases

Sesquiterpenes comprise a diverse group of natural products with a wide range of applications in cosmetics, food, medicine, agriculture, and biofuels. Heterologous biosynthesis is increasingly employed for sesquiterpene production, aiming to overcome the limitations associated with chemical synthesis and natural extraction. Sesquiterpene synthases (STSs) play a crucial role in the heterologous biosynthesis of sesquiterpene. Under the catalysis of STSs, over 300 skeletons are produced through various cyclization processes (C1-C10 closure, C1-C11 closure, C1-C6 closure, and C1-C7 closure), which are responsible for the diversity of sesquiterpenes. According to the cyclization types, we gave an overview of advances in understanding the mechanism of STSs cyclization from the aspects of protein crystal structures and site-directed mutagenesis. We also summarized the applications of engineering STSs in the heterologous biosynthesis of sesquiterpene. Finally, the bottlenecks and potential research directions related to the STSs cyclization mechanism and application of modified STSs were presented.

Biosynthesis Progress of High-Energy-Density Liquid Fuels Derived from Terpenes

High-energy-density liquid fuels (HED fuels) are essential for volume-limited aerospace vehicles and could serve as energetic additives for conventional fuels. Terpene-derived HED biofuel is an important research field for green fuel synthesis. The direct extraction of terpenes from natural plants is environmentally unfriendly and costly. Designing efficient synthetic pathways in microorganisms to achieve high yields of terpenes shows great potential for the application of terpene-derived fuels. This review provides an overview of the current research progress of terpene-derived HED fuels, surveying terpene fuel properties and the current status of biosynthesis. Additionally, we systematically summarize the engineering strategies for biosynthesizing terpenes, including mining and engineering terpene synthases, optimizing metabolic pathways and cell-level optimization, such as the subcellular localization of terpene synthesis and adaptive evolution. This article will be helpful in providing insight into better developing terpene-derived HED fuels.

Combining Metabolic Engineering and Lipid Droplet Assembly to Achieve Campesterol Overproduction in Saccharomyces cerevisiae

Campesterol is a kind of important functional food additive. Therefore, stable and efficient campesterol biosynthesis is significant. Herein, we first knocked out the sterol 22-desaturase gene in Saccharomyces cerevisiae and expressed sterol Δ7-reductase from Pangasianodon hypophthalmus, obtaining a strain that produced 6.6 mg/L campesterol. Then, the modular expression of campesterol synthesis enzymes was performed, and a campesterol titer of 88.3 mg/L was achieved. Because campesterol is a lipid-soluble macromolecule, we promoted lipid droplet formation by exploring regulatory factors, and campesterol production was improved to 169.20 mg/L. Next, triacylglycerol lipase was used to achieve compartment campesterol synthesis. After enhancing the expression of sterol Δ7-reductase and screening cations, the campesterol titer reached 438.28 mg/L in a shake flask and 1.44 g/L in a 5 L bioreactor, which represents the highest campesterol titer reported to date. Metabolic regulation combined with lipid droplet engineering may be useful for the synthesis of other steroids as well.