High-Level De Novo Production of (2S)-Eriodictyol in Yarrowia Lipolytica by Metabolic Pathway and NADPH Regeneration Engineering

Identification of two new flavone 4'-O-methyltransferases and their application in de novo biosynthesis of (2S)-hesperetin in Yarrowia lipolytica

Methyltransferases are pivotal enzymes in the biosynthesis of methylated flavonoids, including (2S)-hesperetin. However, existing flavonoid 4'-O-methyltransferase (F4'OMT) enzymes typically exhibit low substrate specificity and catalytic efficiency, which hinders microbial synthesis. To overcome this limitation, this study screened and identified two novel F4'OMTs, CrcOMT-2 and CgtOMT-3, from Chinese citrus varieties Citrus reticulata 'Chachiensis' (CZG) and Citrus grandis Tomentosa (HZY). These enzymes displayed high substrate specificity for (2S)-eriodictyol. A strain capable of de novo synthesis of (2S)-hesperetin was developed by integrating the novel F4'OMTs and other biosynthetic pathway genes at high copy numbers into Yarrowia lipolytica. The engineered strain achieved a remarkable production titre of (2S)-hesperetin (130.2 mg/L), surpassing the yields of previously reported F4'OMTs. Furthermore, availability of the cofactor S-adenosylmethionine (SAM) was optimised to enhance methyltransferase catalytic efficiency, enabling the engineered strain to produce 178.2 mg/L of (2S)-hesperetin during fed-batch fermentation with SAM supplementation, the highest yield reported to date. This study represents the first successful de novo biosynthesis of (2S)-hesperetin in Y. lipolytica, providing valuable insights into the synthesis of other O-methylated flavonoids.

Site-Divergent C-H Bond Functionalization of Free Phenols Enables Hydroxyflavanones

A solvent-controlled strategy to regulate the site-selectivity of free phenols and stereospecificity of 1,4-addition is presented, thereby divergently producing 4'-hydroxyflavanone and 2'-hydroxyflavanone via site-specific C-H bond functionalization. This protocol is applicable to a diverse range of free phenols. Furthermore, this strategy efficiently accesses natural product-like frameworks, including Eriodictyol, Narigenin, (+)-Anastatins A, (+)-Anastatins B, and (+)-Cycloaltilisin 7 with high selectivity. Late-stage modifications of pharmaceuticals, such as Ethinylestradiol, β-Estradiol, Ezetimibe, and Estrone, are certainly enabling. Importantly, the IC50 values of the newly synthesized compounds 4o and 5m were determined to be in the submicromolar range, indicating a notably potent inhibitory effect. This finding for the synthesis of hydroxyflavanones marks a significant stride in overcoming the extraction challenges of natural products.

Advances in synthesizing plant-derived isoflavones and their precursors with multiple pharmacological activities using engineered yeasts

Isoflavones such as daidzein and genistein are naturally occurring compounds found in plants such as legumes. They have diverse pharmacological activities, making them valuable in the food, pharmaceutical, and cosmetic industries. Currently, isoflavones are mainly obtained through the extraction of plant biomass. Chemical synthesis is challenging for most isoflavones due to the complexity of their structures. The limited supply of isoflavones cannot meet the market demands. Advances in synthetic biology have provided a sustainable and efficient solution for the production of isoflavones, with yeasts often serving as the microbial chassis for biosynthesis. This review summarizes the pharmacological properties of specific isoflavones, their biosynthetic pathways, and the technical strategies used in engineered yeasts for isoflavone production. In addition, the development of synthetic biology and state-of-the-art biotechnological strategies for the environmentally friendly production of bioactive isoflavones is discussed.

De Novo Biosynthesis of Chlorogenic Acid in Yarrowia lipolytica through Cis-Acting Element Optimization and NADPH Regeneration Engineering

Chlorogenic acid (CGA) is a natural hydroxycinnamic acid ester with significant applications in food preservation and nutritional health. However, extraction of CGA from plants is challenging, resulting in low purity that fails to meet increasing market demands. Furthermore, the broad substrate specificity of hydroxycinnamoyl-CoA:quinic acid transferase catalysis generating a plethora of byproducts, lack of NADPH regeneration, and the presence of degrading proteins impede microbial synthesis of CGA. This study achieved de novo synthesis of CGA in Yarrowia lipolytica by introducing hydroxylation and condensation modules based on screening synthetic pathway genes and optimizing parallel promoters. Additionally, an NADPH regeneration system was incorporated to enhance the efficiency of hydroxylation, thereby increasing the titer of CGA to 333.16 mg/L. From transcriptome data, 528 significantly upregulated genes were identified, and deletion of YALI0_B21824g significantly slowed the rate of CGA degradation, which increased the titer of CGA to 351.33 mg/L in shake flasks. Applying fed-batch fermentation in a 5 L bioreactor further increased CGA production to 4837.32 mg/L (64 mg/g DCW). This study established de novo synthesis of CGA in Y. lipolytica, providing a foundation for microbial production of coumaric acid and its derivatives.

Engineering Saccharomyces cerevisiae for Efficient Liquiritigenin Production

Production of liquiritigenin, a plant-derived significant flavonoid traditionally extracted from licorice plants, is constrained by ecological and operational inefficiencies. Despite efforts to achieve heterologous reconstruction of liquiritigenin synthesis pathway in microorganisms, the liquiritigenin titers remain low and the process is still at the proof-of-concept stage, insufficient to replace plant extraction. Herein, to achieve the efficient production of liquiritigenin, the galactose induction system in Saccharomyces cerevisiae was reengineered for better decoupling of production and growth stages, making it more suitable for heterologous pathways, and then applied to a naringenin-producing strain and modified to redirect the pathway for liquiritigenin production. To improve liquiritigenin ratio, a dual NADPH supply system was developed to enhance production capabilities. Subsequently, the concept of using endogenous metabolites to regulate the simplification and optimization of heterologous natural product biosynthetic pathways was proposed, and a general metabolic strategy model for flavonoid compounds, the aromatic ester model, was introduced. The final engineered strain achieved 867.67 mg/L liquiritigenin in the 5 L fermenter. These results demonstrated the innovative use of genetic and metabolic modifications to overcome conventional extraction limitations, providing valuable insights for synthesizing flavonoids and other natural products.

Microbial Astaxanthin Synthesis by Komagataella phaffii through Metabolic and Fermentation Engineering

Astaxanthin is a kind of carotenoid with a strong antioxidant ability, which has shown broad applications in the areas of healthcare, medicine, cosmetics, food additives, and aquaculture. With the increasing demand for natural products, the microbial production of astaxanthin has become a new hot spot. In this study, the astaxanthin synthesis pathway was first metabolically constructed in Komagataella phaffii (K. phaffii)(Pichia pastoris). By exploring the combination of different promoters, astaxanthin producers were obtained. Then, the key enzymes in the astaxanthin synthesis pathway were explored, and different enzyme assembly strategies and an increase in NADPH supply were used to improve the astaxanthin production. Furthermore, fermentation parameters including temperature, the concentration of the carbon source, nitrogen sources, metal ions, BHT (2,6-di-tert-butyl-4-methylphenol), and Tween-80 were comprehensively investigated for the microbial growth and astaxanthin synthesis. Finally, the astaxanthin production reached 716.13 mg/L by fed-batch fermentation in a 5 L bioreactor, which was the highest production of astaxanthin synthesized by K. phaffii.

Metabolic engineering of the oleaginous yeast Yarrowia lipolytica for 2-phenylethanol overproduction

The rose fragrance molecule 2-phenylethanol (2-PE) has huge market demand in the cosmetics, food and pharmaceutical industries. However, current 2-PE synthesis methods do not meet the efficiency market requirement. In this study, CRISPR-Cas9-related metabolic engineering strategies were applied to Yarrowia lipolytica for the de novo biosynthesis of 2-PE. Initially, overexpressing exogenous feedback-resistant EcAROGfbr and EcPheAfbr increased 2-PE production to 276.3 mg/L. Subsequently, the ylARO10 and ylPAR4 from endogenous genes were enhanced with the multi-copies to increase the titer to 605 mg/L. Knockout of ylTYR1 and enhancement of shikimate pathway by removing the precursor metabolic bottleneck and overexpressing the genes ylTKT, ylARO1, and ylPHA2 resulted in a significant increase of the 2-PE titer to 2.4 g/L at 84 h, with the yield of 0.06 g/gglu, which is the highest yield for de novo synthesis in yeast. This study provides a valuable precedent for the efficient biosynthesis of shikimate pathway derivatives.

Advances in Flavonoid and Derivative Biosynthesis: Systematic Strategies for the Construction of Yeast Cell Factories

Flavonoids, a significant group of natural polyphenolic compounds, possess a broad spectrum of pharmacological effects. Recent advances in the systematic metabolic engineering of yeast cell factories (YCFs) provide new opportunities for enhanced flavonoid production. Herein, we outline the latest research progress on typical flavonoid products in YCFs. Advanced engineering strategies involved in flavonoid biosynthesis are discussed in detail, including enhancing precursor supply, cofactor engineering, optimizing core pathways, eliminating competitive pathways, relieving transport limitations, and dynamic regulation. Additionally, we highlight the existing problems in the biosynthesis of flavonoid glucosides in yeast, such as endogenous degradation of flavonoid glycosides, substrate promiscuity of UDP-glycosyltransferases, and an insufficient supply of UDP-sugars, with summaries on the corresponding solutions. Discussions also cover other typical postmodifications like prenylation and methylation, and the recent biosynthesis of complex flavonoid compounds in yeast. Finally, a series of advanced technologies are envisioned, i.e., semirational enzyme engineering, ML/DL algorithn, and systems biology, with the aspiration of achieving large-scale industrial production of flavonoid compounds in the future.