Combinatorial metabolic engineering enables the efficient production of ursolic acid and oleanolic acid in Saccharomyces cerevisiae

Metabolic Response of Sanghuangporus baumii to Zn2+ Induction and Biosynthesis of a Key Pharmacological Component: Triterpenoid

Triterpenoids derived from Sanghuangporus baumii exhibit potent antitumor activity, but their yields under natural conditions are relatively low due to their status as secondary metabolites. In this study, we investigated the effects of Zn²⁺ induction on the growth and triterpenoid biosynthesis of S. baumii. The results showed that 0.5 mM Zn²⁺ significantly enhanced the mycelial growth rate (0.43 ± 0.004 cm/d) and biomass (4.8 ± 0.024 g/L), representing increases of 8.71% and 16.95%, respectively, compared with the Zn0 group. This result was mainly caused by an increase in the soluble sugar content. Furthermore, 5 mM Zn²⁺ induced upregulation of genes in the mevalonate (MVA) pathway, thereby promoting triterpenoid accumulation by 167.86% compared with the Zn0 group. Transcriptome analysis identified SbHMGS as the key gene involved in triterpenoid biosynthesis under Zn²⁺ induction. Heterologous expression of SbHMGS in Saccharomyces cerevisiae confirmed its critical role in triterpenoid production. The triterpenoid (squalene) content of the engineered strain (Sc-HMGS) reached 0.88 mg/g under Zn²⁺ induction, which was 208.6% higher than in the non-induced control strain (Sc-NTC). These findings provide a foundation for optimizing the industrial fermentation condition of S. baumii and S. cerevisiae to enhance triterpenoid yields.

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.

Construction of Saccharomyces cerevisiae Platform Strain for the Biosynthesis of Carotenoids and Apocarotenoids

Carotenoids and apocarotenoids, natural compounds with vital biological functions, are now sustainably produced via microbial synthesis as an eco-friendly alternative to inefficient and polluting traditional plant-based extraction methods. In their biosynthesis, β-carotene (BC) plays a crucial role as it is the key intermediate from which different downstream derivatives are formed. Here, we engineered a high-producing Saccharomyces cerevisiae platform strain to produce BC through a combination of systematic metabolic engineering and atmospheric and room temperature plasma mutagenesis. The strain achieved a BC production of 2.09 g/L via fed-batch fermentation in a 5-L bioreactor, the highest yield reported in S. cerevisiae to date. Using this platform strain, we constructed zeaxanthin- and β-ionone-producing strains by introducing key enzyme genes. The engineered strains produced 39.09 mg/L of zeaxanthin and 31.87 mg/L of β-ionone in shake-flask cultures. The engineered BC platform established in this study provides a higher starting point for producing diverse BC derivatives.

Metabolic Engineering of Corynebacterium glutamicum for Producing Different Types of Triterpenoids

Triterpenoids widely exist in nature with diverse structures and possess various functional properties and biological effects. However, research on triterpenoids biosynthesis in Corynebacterium glutamicum is still limited to squalene, which restricts the development of C. glutamicum to produce high-value triterpenoids. In this study, C. glutamicum was developed as an efficient and flexible platform for the biosynthesis of different types of triterpenoids. Squalene was synthesized and the titer was improved to 400.1 mg/L in flask combining strategies of metabolic engineering and fermentation optimization. Particularly, intracellular squalene accounted for more than 97%, addressing the problem of leaking squalene in C. glutamicum, which may restrict the subsequent synthesis of other triterpenoids derived from squalene. Furthermore, 201.9 mg/L (3S)-2,3-oxidosqualene (SQO) and 264.9 mg/L (3S,22S)-2,3,22,23-dioxidosqualene (SDO) were successfully synthesized in strains harboring heterogeneous squalene epoxidase from Arabidopsis thaliana with different expression strengths. Therefore, a platform for de novo triterpenoids synthesis based on SQO or SDO was constructed in C. glutamicum. For instance, biosynthesis of α-amyrin and α-onocerin was achieved for the first time by introducing oxidosqualene cyclases in SQO- and SDO-producing C. glutamicum strains, respectively. After optimization, the titer of α-amyrin and α-onocerin was improved to 65.3 and 136.85 mg/L, respectively. Furthermore, ursolic acid, derived from α-amyrin, was synthesized after expressing cytochrome P450 enzyme and its compatible cytochrome P450 reductases with a titer of 486 μg/L. For the first time, reactions of epoxidation, cyclization, and oxidation from squalene were achieved in C. glutamicum, leading to the production of different types of triterpenoids. Our study provides a new platform for the production of triterpenoids, which will be helpful for the large-scale production of triterpenoids employing C. glutamicum as a chassis strain.

Light-induced programmable solid-liquid phase transition of biomolecular condensates for improved biosynthesis

Keeping condensates in liquid-like states throughout the biosynthesis process in microbial cell factories remains an ongoing challenge. Here, we present a light-controlled phase regulator, which maintains the liquid-like features of synthetic condensates on demand throughout the biosynthesis process upon light induction, as demonstrated by various live cell-imaging techniques. Specifically, the tobacco etch virus (TEV) protease controlled by light cleaves intrinsically disordered proteins (IDPs) to alter their valency and concentration for controlled phase transition and programmable fluidity of cellular condensates. As a proof of concept, we harness this capability to significantly improve the production of squalene and ursolic acid (UA) in engineered Saccharomyces cerevisiae. Our work provides a powerful approach to program the solid-liquid phase transition of biomolecular condensates for improved biosynthesis.

Bioengineered yeast for preventing age-related diseases

The aging process entails a multifaceted decline in the capacity to restore homeostasis in response to stress. A prevalent characteristic of many age-related diseases is the presence of low-grade chronic inflammation, a risk factor contributing significantly to morbidity and mortality in the elderly population. Specific lifestyle interventions, such as regular physical activity, targeted diet, and supplementation, can delay the accumulation of chronic age-associated conditions by mitigating inflammation processes. Bioengineered yeast-producing compounds with distinctive bioactivities, including anti-inflammatory properties, have the potential to provide rich dietary alternatives for the prevention of age-related diseases. This review highlights recent achievements in engineering effective yeast platforms, namely Saccharomyces cerevisiae and Yarrowia lipolytica, that hold promise in retarding the onset of aging and age-related ailments.

Modular Metabolic Engineering of Saccharomyces cerevisiae for Enhanced Production of Ursolic Acid

Ursolic acid, a plant-derived pentacyclic triterpenoid with anti-inflammatory, antioxidant, and other bioactive properties, holds significant potential for use in nutritional supplements and drug development. However, its extraction from medicinal plants is inefficient due to low yield and dependence on seasonality and geography. Herein, we use modular metabolic engineering to enhance ursolic acid production in Saccharomyces cerevisiae by dividing the biosynthetic pathway into five modules. First, the heterologous ursolic acid biosynthesis module was established using Catharanthus roseus α-amyrin synthase (CrMAS) and a fused α-amyrin oxidase (CrOAS) with cytochrome P450 reductase (CPR). Next, the full hybrid mevalonate pathway was overexpressed, and the copy number of CrMAS was optimized. The sterol pathway was further optimized by introducing N-degron tags to relieve the competition pathway and deleting the SSM4 gene to enhance the ERG1 stability. Acetyl-CoA supply was improved via phosphoketolase and acetyl-CoA synthase pathways, combined with fine-tuning of mitochondrial and cytosolic carbon flux. The final engineered strain produced 1083.62 mg/L of ursolic acid in shake-flask cultures and 8.59 g/L in a 5 L bioreactor via fed-batch fermentation, achieving the highest microbial ursolic acid titer reported to date. This study not only demonstrates the potential for efficient biosynthesis of triterpenoid compounds but also provides ideas that can be extended to other microbial hosts for the concentrated use of intracellular carbon sources in the synthesis of complex natural products.

Synthetic evolution of Saccharomyces cerevisiae for biomanufacturing: Approaches and applications

The yeast Saccharomyces cerevisiae is a well-studied unicellular eukaryote with a significant role in the biomanufacturing of natural products, biofuels, and bulk and value-added chemicals, as well as the principal model eukaryotic organism utilized for fundamental research. Robust tools for building and optimizing yeast chassis cells were made possible by the quick development of synthetic biology, especially in engineering evolution. In this review, we focused on methods and tools from synthetic biology that are used to design and engineer S. cerevisiae's evolution. A detailed discussion was held regarding transcriptional regulation, template-dependent and template-free approaches. Furthermore, the applications of evolved S. cerevisiae were comprehensively summarized. These included improving environmental stress tolerance and raising cell metabolic performance in the production of biofuels and bulk and value-added chemicals. Finally, the future considerations were briefly discussed.

Herbal Multiomics Provide Insights into Gene Discovery and Bioproduction of Triterpenoids by Engineered Microbes

Triterpenoids are natural products found in plants that exhibit industrial and agricultural importance. Triterpenoids are typically synthesized through two main pathways: the mevalonate (MVA) and methylerythritol 4-phosphate (MEP) pathways. They then undergo structural diversification with the help of squalene cyclases (OSCs), cytochrome P450 monooxygenases (P450s), UDP glycosyltransferases (UGTs), and acyltransferases (ATs). Advances in multiomics technologies for herbal plants have led to the identification of novel triterpenoid biosynthetic pathways. The application of various analytical techniques facilitates the qualitative and quantitative analysis of triterpenoids. Progress in synthetic biology and metabolic engineering has also facilitated the heterologous production of triterpenoids in microorganisms, such as Escherichia coli and Saccharomyces cerevisiae. This review summarizes recent advances in biotechnological approaches aimed at elucidating the complex pathway of triterpenoid biosynthesis. It also discusses the metabolic engineering strategies employed to increase the level of triterpenoid production in chassis cells.

Efficient 7-Dehydrocholesterol Production by Multiple Metabolic Engineering of Diploid Saccharomyces cerevisiae

7-Dehydrocholesterol (7-DHC), a direct precursor of vitamin D3, has attracted increasing attention in microbial fermentation recently. In this study, 7-DHC biosynthesis in diploid Saccharomyces cerevisiae with robust ergosterol production was achieved by heterologous 24-dehydrocholesterol reductase expression, generating 44.1 mg/L 7-DHC, whereas the titer of ergosterol decreased by 40.5%. The ergosterol biosynthetic pathway was completely blocked by knocking out ERG6 and ERG5, affording a 4.2-fold increase in the 7-DHC titer. Subsequently, the facilitation of the mevalonate and the postsqualene pathways accompanied by elimination of transcriptional repressors enhanced 7-DHC synthesis, and the 7-DHC titer reached 738.5 mg/L in a shake flask. Further validation in a 50 L fermenter demonstrated that the 7-DHC titer reached 3.80 g/L within just 24 h, with productivity reaching 158.3 mg/L/h, setting a new benchmark as the highest reported to date. This study paves the way toward a large-scale and cost-effective manufacture of 7-DHC.

Yeast metabolism adaptation for efficient terpenoids synthesis via isopentenol utilization

Microbial biosynthesis has become the leading commercial approach for large-scale production of terpenoids, a valuable class of natural products. Enhancing terpenoid production, however, requires complex modifications on the host organism. Recently, a two-step isopentenol utilization (IU) pathway relying solely on ATP as the cofactor has been proposed as an alternative to the mevalonate (MVA) pathway, streamlining the synthesis of the common terpenoid precursors. Herein, we find that isopentenol inhibits energy metabolism, leading to reduced efficiency of the IU pathway in Saccharomyces cerevisiae. To overcome this, we engineer an IU pathway-dependent (IUPD) strain, designed for growth-coupled production. The IUPD strain is compelled to enhance the ATP supply, essential for the IU pathway, and incorporates a high-throughput screening method for enzyme evolution. The refined IU pathway surpasses the MVA pathway in synthesizing complex terpenoids. Our work offers valuable insights into developing growth-coupled strains adapted to efficient natural product synthesis.

Hyperproduction of 7-dehydrocholesterol by rewiring the post-squalene module in lipid droplets of Saccharomyces cerevisiae

Lipid droplets (LDs) are specialized organelles that store neutral lipids to reduce the negative effects of lipotoxicity on cells. However, many neutral lipids are precursors for the synthesis of sterols and complex terpenoids, and this sequestration often greatly limits the efficient biosynthesis of sterols and complex terpenoids. In this study, taking 7-dehydrocholesterol (7-DHC) synthesis in Saccharomyces cerevisiae as an example, we revealed the blocking mechanism of LD sequestration on the efficient synthesis of metabolic products and found that LDs can sequester a significant amount of squalene, the precursor of 7-DHC, effectively preventing it from being directed toward the post-squalene pathway. Based on this, a post-squalene pathway was reconstructed on LDs, which resulted in a 28.7% increase in the 7-DHC titer, reaching 684.1 mg/L, whereas the squalene titer was reduced by approximately 97%. Subsequently, the triacylglycerol degradation pathway was weakened to release the storage space in LDs, and the esterification pathway was concurrently strengthened to guide 7-DHC storage within LDs, which further increased 7-DHC production, reaching 792.9 mg/L. Finally, by reducing the NADH/NAD + ratio to alleviate the redox imbalance, the 7-DHC titer reached 867.6 mg/L in shake flask and 5.1 g/L in a 3-L bioreactor, which is the highest reported titer to date. In summary, this study provides new insights into the important role of LDs in sterol synthesis and offers a novel strategy for constructing cell factories for the efficient synthesis of sterol compounds.

Establishing cell suitability for high-level production of licorice triterpenoids in yeast

Yeast has been an indispensable host for synthesizing complex plant-derived natural compounds, yet the yields remained largely constrained. This limitation mainly arises from overlooking the importance of cell and pathway suitability during the optimization of enzymes and pathways. Herein, beyond conventional enzyme engineering, we dissected metabolic suitability with a framework for simultaneously augmenting cofactors and carbon flux to enhance the biosynthesis of heterogenous triterpenoids. We further developed phospholipid microenvironment engineering strategies, dramatically improving yeast's suitability for the high performance of endoplasmic reticulum (ER)-localized, rate-limiting plant P450s. Combining metabolic and microenvironment suitability by manipulating only three genes, NHMGR (NADH-dependent HMG-CoA reductase), SIP4 (a DNA-binding transcription factor)and GPP1 (Glycerol-1-phosphate phosphohydrolase 1), we enabled the high-level production of 4.92 g/L rare licorice triterpenoids derived from consecutive oxidation of β-amyrin by two P450 enzymes after fermentation optimization. This production holds substantial commercial value, highlighting the critical role of establishing cell suitability in enhancing triterpenoid biosynthesis and offering a versatile framework applicable to various plant natural product biosynthetic pathways.

Microalgae growth-promoting bacteria for cultivation strategies: Recent updates and progress

Microalgae growth-promoting bacteria (MGPB), both actinobacteria and non-actinobacteria, have received considerable attention recently because of their potential to develop microalgae-bacteria co-culture strategies for improved efficiency and sustainability of the water-energy-environment nexus. Owing to their diverse metabolic pathways and ability to adapt to diverse conditions, microalgal-MGPB co-cultures could be promising biological systems under uncertain environmental and nutrient conditions. This review proposes the recent updates and progress on MGPB for microalgae cultivation through co-culture strategies. Firstly, potential MGPB strains for microalgae cultivation are introduced. Following, microalgal-MGPB interaction mechanisms and applications of their co-cultures for biomass production and wastewater treatment are reviewed. Moreover, state-of-the-art studies on synthetic biology and metabolic network analysis, along with the challenges and prospects of opting these approaches for microalgal-MGPB co-cultures are presented. It is anticipated that these strategies may significantly improve the sustainability of microalgal-MGPB co-cultures for wastewater treatment, biomass valorization, and bioproducts synthesis in a circular bioeconomy paradigm.

Application of multiple strategies to enhance oleanolic acid biosynthesis by engineered Saccharomyces cerevisiae

Oleanolic acid and its derivatives are widely used in the pharmaceutical, agricultural, cosmetic and food industries. Previous studies have shown that oleanolic acid production levels in engineered cell factories are low, which is why oleanolic acid is still widely extracted from traditional medicinal plants. To construct a highly efficient oleanolic acid production strain, rate-limiting steps were regulated by inducible promoters and the expression of key genes in the oleanolic acid synthetic pathway was enhanced. Subsequently, precursor pool expansion, pathway refactoring and diploid construction were considered to harmonize cell growth and oleanolic acid production. The multi-strategy combination promoted oleanolic acid production of up to 4.07 g/L in a 100 L bioreactor, which was the highest level reported.

Promising Ursolic Acid as a Novel Antituberculosis Agent: Current Progress and Challenges

Tuberculosis (TB) stands as the second most prevalent cause of global human mortality from infectious diseases. In 2022, the World Health Organization documented an estimated number of global TB cases reaching 7.5 million, which causes death for 1.13 million patients. The continuous growth of drug-resistant TB cases due to various mutations in the Mycobacterium tuberculosis (MTB) strain, raises the urgency of the exploration of novel anti-TB treatments. Ursolic acid (UA) is a natural pentacyclic triterpene found in various plants that has shown potential as a novel anti-TB agent. This review aims to provide an overview of the therapeutic prospects of UA against MTB, with a particular emphasis on in silico, in vitro, and in vivo studies. Various mechanisms of action of UA against MTB are briefly recapped from in silico studies, such as enoyl acyl carrier protein reductase inhibitors, FadA5 (Acetyl-CoA acetyltransferase) inhibitors, tuberculosinyl adenosine transferase inhibitors, and small heat shock protein 16.3 inhibitor. The potential of UA to overcome drug resistance and its synergistic effects with existing antituberculosis drugs are briefly explained from in vitro studies using a variety of methods, such as Microplate Alamar Blue Assay, Mycobacteria Growth Indicator Tube 960 and Resazurin Assays, morphological change evaluation using transmission electron microscopy, and in vivo studies using BALB/C infected with multi drug resistant clinical isolates. Besides its promising mechanism as an antituberculosis drug, its complex chemical composition, limited availability and supply, and lack of intellectual property are also reviewed as those are the most frequently occurring challenges that need to be addressed for the successful development of UA as novel anti-TB agent.

Efficient Plant Triterpenoids Synthesis in Saccharomyces cerevisiae: from Mechanisms to Engineering Strategies

Triterpenoids possess a range of biological activities and are extensively utilized in the pharmaceutical, food, cosmetic, and chemical industries. Traditionally, they are acquired through chemical synthesis and plant extraction. However, these methods have drawbacks, including high energy consumption, environmental pollution, and being time-consuming. Recently, the de novo synthesis of triterpenoids in microbial cell factories has been achieved. This represents a promising and environmentally friendly alternative to traditional supply methods. Saccharomyces cerevisiae, known for its robustness, safety, and ample precursor supply, stands out as an ideal candidate for triterpenoid biosynthesis. However, challenges persist in industrial production and economic feasibility of triterpenoid biosynthesis. Consequently, metabolic engineering approaches have been applied to improve the triterpenoid yield, leading to substantial progress. This review explores triterpenoids biosynthesis mechanisms in S. cerevisiae and strategies for efficient production. Finally, the review also discusses current challenges and proposes potential solutions, offering insights for future engineering.

Engineering yeast for the production of plant terpenoids using synthetic biology approaches

Covering: 2011-2022The low amounts of terpenoids produced in plants and the difficulty in synthesizing these complex structures have stimulated the production of terpenoid compounds in microbial hosts by metabolic engineering and synthetic biology approaches. Advances in engineering yeast for terpenoid production will be covered in this review focusing on four directions: (1) manipulation of host metabolism, (2) rewiring and reconstructing metabolic pathways, (3) engineering the catalytic activity, substrate selectivity and product specificity of biosynthetic enzymes, and (4) localizing terpenoid production via enzymatic fusions and scaffolds, or subcellular compartmentalization.

Recent advances in triterpenoid pathway elucidation and engineering

Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.

Mining and modification of Oryza sativa-derived squalene epoxidase for improved β-amyrin production in Saccharomyces cerevisiae

β-Amyrin is a pentacyclic triterpenoid and has anti-viral, anti-bacterial and anti-inflammatory activities. The synthetic pathway of β-amyrin has been analyzed and its heterogeneous synthesis has been achieved in Saccharomyces cerevisiae. Squalene epoxidase (SQE) catalyzes the oxygenation of squalene to form 2,3-oxidosqualene and is rate-limiting in the synthetic pathways of β-amyrin. The endogenous SQE in S. cerevisiae is insufficient for high production of β-amyrin. Herein, eight squalene epoxidases derived from different plants were selected and characterized in S. cerevisiae for improved biosynthesis of β-amyrin. Among them, the squalene epoxidase from Oryza sativa (OsSQE52) showed the best performance compared to other plant-derived sources. Through protein remodeling, the mutant OsSQE52L256R, obtained based on modeling analysis, increased the titer of β-amyrin by 2.43-fold compared to that in the control strain with ERG1 overexpressed under the same conditions. Moreover, the expression of OsSQE52L256R was optimized with the improvement of precursor supply to further increase the production of β-amyrin. Finally, the constructed strains produced 66.97 mg/L β-amyrin in the shake flask, which was 6.45-fold higher than the original strain. Our study provides alternative SQEs for efficient production of β-amyrin as well as other triterpenoids derived from 2,3-oxidosqualene.

Metabolic Engineering of Saccharomyces cerevisiae for Efficient Retinol Synthesis

Retinol, the main active form of vitamin A, plays a role in maintaining vision, immune function, growth, and development. It also inhibits tumor growth and alleviates anemia. Here, we developed a Saccharomyces cerevisiae strain capable of high retinol production. Firstly, the de novo synthesis pathway of retinol was constructed in S. cerevisiae to realize the production of retinol. Second, through modular optimization of the metabolic network of retinol, the retinol titer was increased from 3.6 to 153.6 mg/L. Then, we used transporter engineering to regulate and promote the accumulation of the intracellular precursor retinal to improve retinol production. Subsequently, we screened and semi-rationally designed the key enzyme retinol dehydrogenase to further increase the retinol titer to 387.4 mg/L. Lastly, we performed two-phase extraction fermentation using olive oil to obtain a final shaking flask retinol titer of 1.2 g/L, the highest titer reported at the shake flask level. This study laid the foundation for the industrial production of retinol.