Building Yarrowia lipolytica Cell Factories for Advanced Biomanufacturing: Challenges and Solutions

Enhancing Cordycepin Biosynthesis in Yarrowia lipolytica via Lipid Droplets Compartmentalization Engineering and Optimized Fermentation Strategies

Cordycepin, a physiologically active nucleoside compound with broad applications in healthcare, is biosynthesized in Cordyceps militaris through a protein complex formed by CmCns1 and CmCns2. To enhance cordycepin heterologous production in Yarrowia lipolytica, this study confirmed the colocalization of CmCns1 and CmCns2 on lipid droplets, with CmCns1 dominating this process by recruiting CmCns2 from the cytoplasm to lipid droplets via strong interactions. Critical lipid-droplet-targeting motifs within CmCns1 were identified. On this basis, an engineered strain YL-CD3 was developed by expanding the lipid droplets and CmCns3-NK compartmentalization. Then, the fermentation parameters were optimized to increase the yield of cordycepin to 2008.23 mg/L in shake flasks. Finally, fed-batch fermentation in a 2.4 L bioreactor for 144 h achieved 4780.75 mg/L (150.1 mg/OD600 and 66.57 mg/g glucose), marking the highest reported titer in Y. lipolytica. This work establishes Y. lipolytica as a high-potential platform for efficient cordycepin biosynthesis.

Expanding the genetic toolkit of Yarrowia lipolytica: Dynamic promoter engineering enables high-titer biosynthesis of 3-hydroxypropionic acid

The oleaginous yeast Yarrowia lipolytica has emerged as a promising microbial chassis for biosynthesis of platform chemicals such as 3-hydroxypropionic acid (3-HP). However, its industrial potential has been limited by the scarcity of precisely regulated genetic tools. To address this gap, we developed a comprehensive promoter toolkit for Y. lipolytica through transcriptome profiling and functional screening. This toolkit includes 82 gradient-strength promoters and 34 growth phase-responsive promoters. Additionally, we identified three strong promoters (PU12, PU13, and PC48) incorporating novel upstream activating sequences (UAS1PC48 and UAS1PU13), which exhibited 0.76-1.00 × higher activity than common promoter pTEFin. By modularly deploying these tools, we optimized 3-HP biosynthesis: gradient promoters balanced expression levels between different functional domains of malonyl-CoA reductase, growth phase-downregulated promoters dynamically attenuated competitive flux of fatty acid synthesis, and strong promoters boosted malonyl-CoA precursor supply. The engineered strain achieved a record-breaking 100.37 g/L 3-HP-the highest titer reported in any yeast system-with a yield of 0.21 g/g glucose and a productivity of 0.48 g/L/h. This work not only significantly expands Y. lipolytica's genetic toolbox but also establishes a blueprint for engineering dynamic microbial cell factories, addressing the urgent demand for sustainable, high-efficiency biomanufacturing platforms.

Enhancing Precursor Supply and Engineering Efflux Systems to Improve Abscisic Acid Production and Secretion in Yarrowia lipolytica

Abscisic acid is a sesquiterpene phytohormone with extensive applications in agriculture and human health. Currently, it is produced through fermentation of Botrytis cinerea, a plant pathogenic filamentous fungus. The process requires morphology controls, which complicates production and strain optimization. In this study, the abscisic acid production strain Yarrowia lipolytica SM309 was optimized by enhancing the precursor supply using a "push-pull-restrain" strategy focusing on acetyl-CoA, which increased abscisic acid production from 266.34 to 328.51 mg/L. Subsequently, in silico prediction and analysis were used to obtain the docking conformations and binding affinity of ABC transporters for abscisic acid. Overexpression of ABC transporter YlGcn20 further enhanced abscisic acid production by 10.88%, reaching 354.21 mg/L. Additionally, low temperature and dodecane addition were employed as auxiliary strategies to promote abscisic acid synthesis, resulting in a titer of 605.92 mg/L. Finally, the engineered strain achieved an abscisic acid titer of 2056.64 mg/L in a 5 L bioreactor, representing the highest titer reported for a yeast de novo synthesis system to date.

Biosynthesis of Edible Terpenoids: Hosts and Applications

Microbial foods include microbial biomass, naturally fermented foods, and heterologously synthesized food ingredients derived from microbial fermentation. Terpenoids, using isoprene as the basic structure, possess various skeletons and functional groups. They exhibit diverse physicochemical properties and physiological activities, such as unique flavor, anti-bacterial, anti-oxidant, anti-cancer, and hypolipemic, making them extensively used in the food industry, such as flavor, fragrance, preservatives, dietary supplements, and medicinal health food. Compared to traditional strategies like direct extraction from natural species and chemical synthesis, microbial cell factories for edible terpenoids have higher titers and yields. They can utilize low-cost raw materials and are easily scaling-up, representing a novel green and sustainable production mode. In this review, we briefly introduce the synthetic pathway of terpenoids and the applications of microbial cell factories producing edible terpenoids. Secondly, we highlight several typical and non-typical microbial chassis in edible terpenoid-producing cell factories. In addition, we reviewed the recent advances of representative terpenoid microbial cell factories with a gram-scale titer in food flavor, food preservation, nutritional enhancers, and medicinal health foods. Finally, we predict the future directions of microbial cell factories for edible terpenoids and their commercialization process.

Paradigm of engineering recalcitrant non-model microorganism with dominant metabolic pathway as a biorefinery chassis

The development and implementation of microbial chassis cells have profound impacts on circular economy. Non-model bacterium Zymomonas mobilis is an excellent chassis owing to its extraordinary industrial characteristics. Here, the genome-scale metabolic model iZM516 is improved and updated by integrating enzyme constraints to simulate the dynamics of flux distribution and guide pathway design. We show that the innate dominant ethanol pathway of Z. mobilis restricts the titer and rate of these biochemicals. A dominant-metabolism compromised intermediate-chassis (DMCI) strategy is then developed through introducing low toxicity but cofactor imbalanced 2,3-butanediol pathway, and a recombinant D-lactate producer is constructed to produce more than 140.92 g/L and 104.6 g/L D-lactate (yield > 0.97 g/g) from glucose and corncob residue hydrolysate, respectively. Additionally, techno-economic analysis (TEA) and life cycle assessment (LCA) demonstrate the commercialization feasibility and greenhouse gas reduction capability of lignocellulosic D-lactate. This work thus establishes a paradigm for engineering recalcitrant microorganisms as biorefinery chassis.

Synthetic Biology of Natural Products Engineering: Recent Advances Across the Discover-Design-Build-Test-Learn Cycle

Advances in genome engineering and associated technologies have reinvigorated natural products research. Here we highlight the latest developments in the field across the discover-design-build-test-learn cycle of bioengineering, from recent progress in computational tools for AI-supported genome mining, enzyme and pathway engineering, and compound identification to novel host systems and new techniques for improving production levels, and place these trends in the context of responsible research and innovation, emphasizing the importance of anticipatory analysis at the early stages of process development.

Recent Advances in the Biosynthesis of Mid- and Long-Chain Dicarboxylic Acids Using Terminally Oxidizing Unconventional Yeasts

As high-performance monomers for the manufacture of polyamide materials, mid- and long-chain dicarboxylic acids (DCAi, i ≥ 6) have received extensive attention from researchers. Biosynthesis is gradually replacing chemical synthesis due to its outstanding advantages in the industrial production of mid- and long-chain dicarboxylic acids, which is mostly achieved by using the strong terminal oxidation ability of nonmodel microorganisms such as Candida tropicalis to oxidize hydrophobic substrates such as alkanes. Here, we first summarize the metabolic pathways of oxidative alkane conversion into dicarboxylic acid by terminally oxidizing unconventional yeasts and the corresponding metabolic engineering strategies. Then, we summarize the research progress on new dicarboxylic acid production processes. Finally, the future development directions in the biosynthesis of mid- and long-chain dicarboxylic acids are prospected from synthetic biology and bioprocess engineering, which can also provide a reference for the synthesis of other biobased chemicals and biomaterials.