Metabolic engineering of Yarrowia lipolytica for high-level production of squalene

Advances in metabolic engineering for enhanced acetyl-CoA availability in yeast

Acetyl-CoA is an intermediate metabolite in cellular central metabolism. It's a precursor for various valuable commercial products, including: terpenoids, fatty acids, and polyketides. With the advancement of metabolic and synthetic biology tools, microbial cell factories have been constructed for the efficient synthesis of acetyl-CoA and derivatives, with the Saccharomyces cerevisiae and Yarrowia lipolytica as two prominent chassis. This review summarized the recent developments in the biosynthetic pathways and metabolic engineering approaches for acetyl-CoA and its derivatives synthesis in these two yeasts. First, the metabolic routes involved in the biosynthesis of acetyl-CoA and derived products were outlined. Then, the advancements in metabolic engineering strategies for channeling acetyl-CoA toward the desired products were summarized, with particular emphasis on: enhancing metabolic flux in different organelles, refining precursor CoA synthesis, optimizing substrate utilization, and modifying protein acetylation level. Finally, future developments in advancing the metabolic engineering strategies for acetyl-CoA and related derivatives synthesis, including: reducing CO2 emissions, dynamically regulating metabolic pathways, and exploring the regulatory functions between acetyl-CoA levels and protein acetylation, are highlighted. This review provided new insights into regulating acetyl-CoA synthesis to create more effective microbial cell factories for bio-manufacturing.

Combinatorial metabolic engineering of Yarrowia lipolytica for high-level production of the plant-derived diterpenoid sclareol

BACKGROUND

Sclareol, a diterpene alcohol derived from Salvia sclarea, is primarily used in the synthesis of ambrox, an alternative to the expensive spice ambergris. However, commercial production of sclareol from plant extraction is costly and environmentally problematic, limiting its scalability. Recent advances in synthetic biology have enabled the construction of efficient cell factories for sclareol synthesis, offering a more sustainable solution.

RESULTS

In this study, we engineered Yarrowia lipolytica to produce sclareol by integrating genes encoding (13E)-8α-hydroxylabden-15-yl diphosphate synthase (LPPS) and sclareol synthase (SCS). Sclareol titers were further enhanced through the fusion of SsSCS and SsLPPS proteins, as well as multi-copy gene integration. To increase the precursor geranylgeranyl diphosphate (GGPP), we overexpressed various geranylgeranyl diphosphate synthases (GGS1), resulting in significant accumulation of GGPP. Additionally, optimization of the mevalonate pathway, coupled with the downregulation of lipid synthesis and upregulation of lipid degradation, directed more acetyl CoA towards sclareol production.

CONCLUSIONS

In this study, we reprogrammed the metabolism of Y. lipolytica by combinatorial metabolic engineering with a sclareol titer of 2656.20 ± 91.30 mg/L in shake flasks. Our findings provide a viable strategy for utilizing Y. lipolytica as a microbial cell factory to produce sclareol.

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.

Biosynthesis and bioactivities of triterpenoids from Centella asiatica: Challenges and opportunities

Centella asiatica (L.) Urban is an herbaceous perennial plant that has long been widely used in traditional medicine, due to its diverse wound-healing, neuroprotection, antioxidant and anti-inflammatory properties. The major functional bioactive secondary metabolites are the triterpenoids asiatic acid, madecassic acid, asiaticoside and madecassoside, collectively known as centellosides. Current extraction methods for C. asiatica are unable to meet market demand for extracts and pure functional components. Biotechnological approaches based on synthetic biology and microbial cell factories are a promising alternative. This review summarises the major secondary metabolites and their biological activities, and the biosynthetic pathway of functional triterpenoids in C. asiatica. Biotechnological production of centellosides is also described, including in vitro plant cultures and construction of microbial cell factories. Finally, current challenges and future perspectives for sustainable production of centellosides are discussed, and guidelines for future engineering are proposed.

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.

Novel cell factory for the production of 24-epi-ergosterol, an un-natural semi-synthetic precursor for the production of brassinolide in Yarrowia lipolytica

Brassinolide (BL) is the most bioactive plant growth regulator among Brassinosteroids (BRs), belonging to the sixth class of plant hormones. However, its low natural abundance limits large-scale agricultural applications. An unnatural sterol, 24-epi-ergosterol, was proposed as a semi-synthetic precursor for economic production of BL. Here, we constructed a synthetic pathway for 24-epi-ergosterol in Yarrowia lipolytica, which has abundant acetyl-CoA content and a hydrophobic intracellular environment. Initially, we introduced a mutant plant-derived Δ24(28) sterol reductase (Dwf1) into Y. lipolytica to enable 24-epi-ergosterol production. The production of 24-epi-ergosterol was subsequently enhanced by regulating sterol homeostasis, optimizing transcriptional regulators, and overexpressing key pathway genes. Next, the accumulation of 24-epi-ergosterol was further improved by increasing acetyl-CoA levels and adjusting lipid metabolism. Finally, the 24-epi-ergosterol production reached 1626.85 mg/L after optimizing the fermentation conditions and performing a fed-batch culture in a 2 L fermenter. This study represents the first successful de novo synthesis of 24-epi-ergosterol in Y. lipolytica, offering a novel approach for the industrial production of BL.

Construction of isopentenol utilization pathway and artificial multifunctional enzyme for miltiradiene synthesis in Saccharomyces cerevisiae

Miltiradiene serves as a pivotal precursor for the synthesis of numerous abietane-type diterpenes with important pharmacological activities. The endogenous mevalonate (MVA) pathway is tightly regulated in Saccharomyces cerevisiae, which limits the availability of precursors for the heterologous production of miltiradiene. In this study, the orthogonal isopentenol utilization pathway (IUP) was constructed and investigated for its adaptability with mitochondria and peroxisomes in S. cerevisiae for the synthesis of miltiradiene. Compartments combinatorial engineering was used to enhance precursor supply and miltiradiene synthesis, thereby elevating the production of miltiradiene to 146.1 mg/L in S. cerevisiae. Furthermore, an artificial multifunctional enzyme, tSmCPS-tSmKSL-PvPT, was constructed by mimicking the natural multifunctional enzyme to enhance the biosynthesis of miltiradiene in S. cerevisiae strain PCM-MT1, which is capable of producing 414.4 mg/L miltiradiene. Finally, the titer of miltiradiene was increased to 1.02 g/L by fed-batch fermentation in a 5 L bioreactor. This study broadens the application of the IUP in S. cerevisiae by integrating compartmentalization and artificial multifunctional enzymes for the synthesis of diterpenes.

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.

Reprograming the Carbon Metabolism of Yeast for Hyperproducing Mevalonate, a Building Precursor of the Terpenoid Backbone

Utilization of microbial hosts to produce natural plant products is regarded as a promising and sustainable approach. However, achieving highly efficient production of terpenoids using microorganisms remains a significant challenge. Here, mevalonate, a building block of terpenoids, was used as a demo product to explore the potential metabolic constraints for terpenoid biosynthesis in Yarrowia lipolytica. First, by regulation of the expression of ERG12 and HMGR, the mevalonate titer was improved by 7660%. Subsequently, the native mevalonate pathway (MVA pathway) was enhanced, and the production of mevalonate increased to 4.16 g/L. To ensure a sufficient supply of acetyl-CoA, the citrate route and TCA cycle were simultaneously engineered, and the mevalonate titer was further improved to 5.25 g/L in shake flasks. Ultimately, the citrate overflow metabolism of Y. lipolytica was eliminated by deleting CEX1, resulting in the highest mevalonate titer of 101 g/L with a yield of 0.255 g/g of glucose in eukaryotes. These insights could be applied to the effective production of terpenoids and biochemicals derived from central carbon metabolic pathways.

Metabolic Engineering for Squalene Production: Advances and Perspectives

Squalene is a linear polyunsaturated triterpene which has multiple physiological functions including anticancer, antioxidant, and skin-care. It has been widely used in the food, medicine, and cosmetics sectors and also serves as a precursor of triterpenes and steroids. Recently, the production of squalene by microbial cell hosts has drawn much attention due to its sustainability, environmental friendliness, and great efficiency. In this review, we first introduce the recent developments in the production of squalene by employing microbial cell factories, especially yeasts. Next, we underscore the primary metabolic strategies, including the biosynthetic pathway engineering, precursor manipulation, cofactor engineering, and organelle engineering. In addition to traditional metabolic engineering strategies, we also discuss some prospective metabolic regulation approaches, including regulation of lipid synthesis, identifying and manipulating related transcription factors, dynamic regulation of the metabolic pathway, and secretion engineering of membrane-impermeable terpenoids. These approaches provide insights for further metabolic engineering of squalene and related terpenoids.

Combined metabolic engineering and lipid droplets degradation to increase vitamin A production in Saccharomyces cerevisiae

BACKGROUND

In microbial cell factories, substrate accessibility to enzyme is a key factor affecting the biosynthesis of natural products. As a robust chassis cells for biofuels and bioproducts, Saccharomyces cerevisiae also encounters the challenge since different enzymes and precursors are typically compartmentalized in different organelles. Such spatial separation could largely limit the efficiency of enzymatic reactions. In this study, the production of the hydrophobic product (vitamin A) was highly improved by metabolic engineering combined with degrading lipid droplets (the primary organelle storing β-carotene) to achieve efficient contact between β-carotene and 15, 15'-β-carotene monooxygenases in Saccharomyces cerevisiae.

RESULTS

To efficiently produce vitamin A in Saccharomyces cerevisiae, ten 15, 15'-β-carotene monooxygenases (BCMOs) were firstly evaluated. The strain carrying marine bacterium 66A03 (Mb. BCMO) achieved the highest vitamin A titer. Co-adding 10% dodecane and 1% dibutylhydroxytoluene increased vitamin A titer to 19.03 mg/L in two-phase fermentation. Since most β-carotene is stored in LDs while BCMO is located in the cytosol, we developed a strategy to release β-carotene from LDs to better contact with BCMO. By overexpressing TGL3 and TGL4 using an ion-responsive promoter after high accumulation of β-carotene in LDs, LDs were sequentially degraded, which dramatically improved vitamin A production. Finally, by overexpressing tHMG1, ERG20, and CrtI and introducing Vitreoscilla hemoglobin, vitamin A titer reached 219.27 mg/L, which was a 10.52-folds increase over the original strain in shake flasks, and finally reached 1100.83 mg/L in fed-batch fermentation. The effectiveness of LDs degradation on promoting the formation of β-carotene cleaved product has also been verified in β-ionone synthesis with 44.07% increased yield.

CONCLUSIONS

Overall, our results highlighted the significance of sequential degrading LDs on vitamin A overproduction in recombinant yeast, and verified that combining metabolic and LDs engineering is an efficient strategy to improve vitamin A production. This integrated strategy can be applied to the overproduction of other hydrophobic compounds with similar characteristics.

Selecting Endogenous Promoters for Improving Biosynthesis of Squalene in Schizochytrium sp

Squalene (C30H50) is an acyclic triterpenoid compound renowned for its myriad physiological functions, such as anticancer and antioxidative properties, rendering it invaluable in both the food and pharmaceutical sectors. Due to the natural resource constraints, microbial fermentation has emerged as a prominent trend. Schizochytrium sp., known to harbor the intact mevalonate acid (MVA) pathway, possesses the inherent capability to biosynthesize squalene. However, there is a dearth of reported key genes in both the MVA and the squalene synthesis pathways, along with the associated promoter elements for their modification. This study commenced by cloning and characterizing 13 endogenous promoters derived from transcriptome sequencing data. Subsequently, five promoters exhibiting varying expression intensities were chosen from the aforementioned pool to facilitate the overexpression of the squalene synthase gene squalene synthetase (SQS), pivotal in the MVA pathway. Ultimately, a transformed strain designated as SQS-3626, exhibiting squalene production 2.8 times greater than that of the wild-type strain, was identified. Finally, the optimization of nitrogen source concentrations and trace element contents in the fermentation medium was conducted. Following 120 h of fed-batch fermentation, the accumulated final squalene yield in the transformed strain SQS-3626 reached 2.2 g/L.

De novo production of bioactive sesterterpenoid ophiobolins in Saccharomyces cerevisiae cell factories

BACKGROUND

Sesterterpenoids are rare species among the terpenoids family. Ophiobolins are sesterterpenes with a 5-8-5 tricyclic skeleton. The oxidized ophiobolins exhibit significant cytotoxic activity and potential medicinal value. There is an urgent need for large amounts of ophiobolins supplication for drug development. The synthetic biology approach has been successfully employed in lots of terpene compound production and inspired us to develop a cell factory for ophiobolin biosynthesis.

RESULTS

We developed a systematic metabolic engineering strategy to construct an ophiobolin biosynthesis chassis based on Saccharomyces cerevisiae. The whole-cell biotransformation methods were further combined with metabolic engineering to enhance the expression of key ophiobolin biosynthetic genes and improve the supply of precursors and cofactors. A high yield of 5.1 g/L of ophiobolin F was reached using ethanol and fatty acids as substrates. To accumulate oxidized ophiobolins, we optimized the sources and expression conditions for P450-CPR and alleviated the toxicity of bioactive compounds to cells through PDR engineering. We unexpectedly obtained a novel ophiobolin intermediate with potent cytotoxicity, 5-hydroxy-21-formyl-ophiobolin F, and the known bioactive compound ophiobolin U. Finally, we achieved the ophiobolin U titer of 128.9 mg/L.

CONCLUSIONS

We established efficient cell factories based on S. cerevisiae, enabling de novo biosynthesis of the ophiobolin skeleton ophiobolin F and oxidized ophiobolins derivatives. This work has filled the gap in the heterologous biosynthesis of sesterterpenoids in S. cerevisiae and provided valuable solutions for new drug development based on sesterterpenoids.

Remodeling the Homologous Recombination Mechanism of Yarrowia lipolytica for High-Level Biosynthesis of Squalene

Squalene is a high-value antioxidant with many commercial applications. The use of microbial cell factories to produce squalene as an alternative to plant and animal extracts could meet increasing market demand. Yarrowia lipolytica is an excellent host for squalene production due to its high levels of acetyl-CoA and a hydrophobic environment. However, the need for precise and complicated gene editing has hindered the industrialization of this strain. Herein, the rapid construction of a strain with high squalene production was achieved by enhancing the homologous recombination efficiency in Y. lipolytica. First, remodeling of the homologous recombination efficiency resulted in a 10-fold increase in the homologous recombination rate. Next, the whole mevalonate pathway was integrated into the chromosome to enhance squalene production. Then, a higher level of squalene accumulation was achieved by increasing the level of acetyl coenzyme A and regulating the downstream steroid synthesis pathway. Finally, the squalene production reached 35 g/L after optimizing the fermentation conditions and performing a fed-batch culture in a 5 L jar fermenter. This is the highest squalene production ever reported to date by de novo biosynthesis without adding any inhibitors, paving a new path toward the industrial production of squalene and its downstream products.

Efficient synthesis of squalene by cytoplasmic-peroxisomal engineering and regulating lipid metabolism in Yarrowia lipolytica

Squalene, a high-value acyclic triterpenoid compound, is broadly used in the food and medical industries. Although the large acetyl-CoA pool and hydrophobic space of Yarrowia lipolytica are suitable for the accumulation of squalene, the current production level in Y. lipolytica is still not sufficient for industrial production. In this study, two rounds of multicopy integration of genes encoding key enzymes were performed to enhance squalene anabolic flux in the cytoplasm. Furthermore, the mevalonate pathway was imported into peroxisomes through the compartmentalization strategy, and the production of squalene was significantly increased. By augmenting the acetyl-CoA supply in peroxisomes and the cytoplasm, the squalene was boosted to 2549.1 mg/L. Finally, the squalene production reached 51.2 g/L by fed-batch fermentation in a 5-L bioreactor. This is the highest squalene production reported to date for microbial production, and this study lays the foundation for the synthesis of steroids and squalene derivatives.