Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica

Efficient production of astaxanthin in Yarrowia lipolytica through metabolic and enzyme engineering

Astaxanthin is a natural red carotenoid, commonly used as an additive in the pharmaceutical industry and as a nutritional supplement owing to its notable antioxidant benefits. However, a complex biosynthetic pathway poses a challenge to de novo biosynthesis of astaxanthin. Here, Yarrowia lipolytica was engineered through multiple strategies for high level production of astaxanthin using a cheap mineral medium. For the production of β-carotene, a platform strain was constructed in which 411.7 mg/L of β-carotene was produced at a shake-flask level. Integration of algal β-carotene ketolase and β-carotene hydroxylase led to the production of 12.3 mg/L of astaxanthin. Furthermore, construction of HpBKT and HpCrtZ as a single enzyme complex along with the enhanced catalytic activity of the enzymes led to the accumulation of 41.0 mg/L of astaxanthin. Iterative gene integration into the genome and direction of the astaxanthin production pathway into sub-organelles substantially increased astaxanthin production (172.1 mg/L). Finally, restoration of the auxotrophic markers and medium optimization further improved astaxanthin production to 237.3 mg/L. The aforementioned approaches were employed in fed-batch fermentation to produce 2820 mg/L of astaxanthin (229-fold improvement regarding the starter strain), with an average productivity of 434 mg/L/d and a yield of 5.6 mg/g glucose, which is the highest reported productivity in Y. lipolytica.

Engineering Komagataella phaffii to produce lycopene sustainably from glucose or methanol

Lycopene, a potent carotenoid with high antioxidant capacity and extensive applications, holds significant potential for sustainable production via microbial engineering, particularly with the rising interest in methanol as an ideal non-grain feedstock for a carbon-negative economy. In this study, Komagataella phaffii was systematically engineered to enhance lycopene production using glucose and renewable methanol as alternative carbon sources. Firstly, we demonstrated that the cytoplasmic FPP could penetrate into the peroxisome, and thus achieved the dual-localized lycopene synthesis. Subsequently, the cytoplasmic FPP pool was expanded by dynamically regulating squalene synthase and enhancing the mevalonate pathway, and FPP was redirected to lycopene synthesis via assembling critical enzymes. Furthermore, the synthesis of lycopene from methanol was improved by reprogramming the methanol metabolic pathway. In the above process, we found that the engineered strains would degrade significantly in the process of passing culture. Comparative transcriptomic analysis revealed that nitrogen metabolism genes contributed significantly to strain degeneration, and a gene (PAS_chr2-2_0003) that positively influenced lycopene synthesis was identified. Finally, two strains were successfully engineered: strain zw327, which produced 8.4 g/L lycopene from glucose, and strain zw352, which achieved 10.2 g/L from methanol and glycerol. The latter represents the highest reported titer from methanol to date, underscoring the potential of K. phaffii as a robust one-carbon platform for industrial terpenoid biosynthesis.

An engineered Yarrowia lipolytica with rapid growth and efficient lipid utilization

Yarrowia lipolytica, a safe yeast, efficiently metabolizes lipids for the production of food additives and agricultural products. Boosting its growth and lipid utilization capabilities is crucial to enhancing the overall efficiency Y. lipolytica. Herein, an integrated strategy was implemented to enhance lipid uptake, accumulation and metabolism and systematically promote the growth and lipid utilization of the commonly used Y. lipolytica Po1f strain. The engineered strain had a specific growth rate of 0.32 h-1 and a lipid content of 67.66 % (g/g DCW), which were 54 % and 26 % greater than those of the original strain. β-Carotene was used to verify the production of lipophilic natural compounds, and the highest yield was obtained 48 h earlier using the engineered strain compared to the original strain when consuming same carbon source. These findings show promise in using engineered Y. lipolytica for rapid growth and improved lipid utilization to boost efficiency of lipophilic product production.

Engineered β-Carotene Hydroxylase with Excellent Thermostability Promotes Zeaxanthin Production in Yeast

Zeaxanthin, as an important natural pigment and nutrient, is applied in food and cosmetics industries. Zeaxanthin is converted from β-carotenoid by the β-carotene hydroxylase (CrtZ). Limited by the thermostability of CrtZ, zeaxanthin and its derivatives tend to be fermented in Saccharomyces cerevisiae at low temperatures. In this study, CrtZ mutants with improved thermostability and catalytic efficiency were designed via the position-specific scoring matrix (PSSM), and the beneficial mutants were verified in vitro. Moreover, molecular dynamics simulations revealed the thermostability mechanisms of the mutants. Subsequently, CrtZ mutant M83L was introduced into the S. cerevisiae chassis, and the zeaxanthin titer increased by 121.2% compared with that of the CrtZ, reaching 156.8 mg/L in shake flask fermentation at 30 °C. Furthermore, the oxidoreductase RFNR/FD3 system was introduced to match the overexpressed M83L, and the zeaxanthin titer further increased by 138.9% (reaching 374.6 mg/L). Ultimately, 814.6 mg/L zeaxanthin was produced in S. cerevisiae in 5.0 L fed-batch fermentation at 30 °C, which is the highest reported titer in S. cerevisiae. This study not only provides a useful strategy to increase the thermostability of key enzymes but also describes an efficient platform for the biosynthesis of zeaxanthin and its high-value derivatives.

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.

Enhancing caproate production in lactate-containing effluents by Megasphaera hexanoica through acetate modulation

The anaerobic bacterium Megasphaera hexanoica has great potential for caproate production through reverse β-oxidation using lactate, acetate, and butyrate as substrates. This study assessed the effect of acetate concentrations (10-50 mM) on caproate biosynthesis, lactate oxidation, and cell synthesis in M. hexanoica. At 30 mM acetate, caproate production reached 42.83 mM, with an electron efficiency of 67.03 % and a specific productivity of 4.47 gCA·h-1·gDCW-1. Subsequent fed-batch experiments with lactate, acetate, and butyrate maintained continuous caproate production, achieving 65.21 mM. Bioreactor assays further validated the strategy, yielding 65.25 mM caproate over 180 h. Mechanistic analysis demonstrated that 30 mM acetate optimized acetyl-CoA flux and enhanced caproyl-CoA transferase activity (3.5 U‧mg-1), supporting caproate synthesis. Kinetic modeling demonstrated the Logistic model fit lactate consumption (R2 = 0.991), while the Fitzhugh model captured caproate production (R2 = 0.991, NRMSE = 1.137). The findings offer practical insights for industrial-scale caproate production.

A versatile genetic toolkit for engineering Wickerhamomyces ciferrii for tetraacetyl phytosphingosine production

Wickerhamomyces ciferrii: a non-conventional yeast with significant industrial potential for tetraacetyl phytosphingosine (TAPS), remains underutilized due to the lack of a comprehensive genetic toolbox. In this study, we developed a modular genetic system tailored for Wickerhamomyces ciferrii to enable strain engineering and metabolic pathway optimization. This toolkit includes episomal plasmids incorporating multiple selectable markers, replication origins, and fluorescent reporters. Systematic evaluation of four antibiotic resistance markers demonstrated that nourseothricin, geneticin, and zeocin effectively confer resistance, whereas hygromycin B did not support selection in this host. Among three tested replication origins, 2μ and CEN6/ARS4 enabled stable episomal maintenance, whereas panARS failed to replicate. Expression analysis of six fluorescent proteins under the endogenous PGK1 promoter revealed significant variability in transcript levels, which correlated with codon adaptation index values, emphasizing the importance of codon optimization for heterologous expression. Additionally, characterization of the endogenous TDH3, PGK1, and PDA1 promoters using two highly expressed fluorescent proteins confirmed that promoter strength is largely independent of the downstream coding sequence. To demonstrate the functional application of this toolkit, we overexpressed a phosphorylation-insensitive mutant of acetyl-CoA carboxylase (ACC1 S26A-S1161A ), resulting in a 2.4-fold increase in TAPS production. Collectively, this study establishes a versatile genetic platform for W. ciferrii, providing a robust foundation for future synthetic biology and metabolic engineering applications.

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.

Synthetic Biology in Natural Product Biosynthesis

Synthetic biology has played an important role in the renaissance of natural products research during the post-genomics era. The development and integration of new tools have transformed the workflow of natural product discovery and engineering, generating multidisciplinary interest in the field. In this review, we summarize recent developments in natural product biosynthesis from three different aspects. First, advances in bioinformatics, experimental, and analytical tools to identify natural products associated with predicted biosynthetic gene clusters (BGCs) will be covered. This will be followed by an extensive review on the heterologous expression of natural products in bacterial, fungal and plant organisms. The native host-independent paradigm to natural product identification, pathway characterization, and enzyme discovery is where synthetic biology has played the most prominent role. Lastly, strategies to engineer biosynthetic pathways for structural diversification and complexity generation will be discussed, including recent advances in assembly-line megasynthase engineering, precursor-directed structural modification, and combinatorial biosynthesis.

Biotechnological Production of Carotenoids Using Yarrowia lipolytica

Carotenoids are a group of tetraterpenoid natural products with a variety of physiological activities, which led to their application in food, cosmetics, agriculture, and other industries with broad market prospects. The fermentation of carotenoids using engineered microbial hosts has emerged as an efficient, sustainable, and environmentally friendly production method with significant potential for further development. Yarrowia lipolytica (Y. lipolytica), an unconventional oleaginous yeast, has intrinsic advantages as a host strain for the production of carotenoids. This review outlines the functions of some well-studied carotenoids, including lycopene, β-carotene, and astaxanthin. Furthermore, the biotechnological strategies for carotenoid production in Y. lipolytica are categorized and summarized. Finally, potentially feasible future strategies for further improvement of carotenoid production in Y. lipolytica are also prospected.

Engineering a Yeast Cell Factory to Sustainably Biosynthesize Parthenolide

The sesquiterpene lactone parthenolide is a promising anticancer drug. Its biosynthesis via a microbial cell factory has been considered as a sustainable alternative to plant extraction. Herein, systematic metabolic engineering approaches, as well as the introduction of a novel noncanonical tricarboxylic acid (TCA) cycle, were employed to enhance the production of the key precursor germacrene A. By identifying two new dehydrogenases and controlling the expression of parthenolide synthase, we further achieved the elimination of byproducts and enhanced parthenolide production. A two-stage fermentation approach and in situ product extraction using macroreticular resin were further applied to relieve the nocuous effect of costunolide and parthenolide on the growth of yeast cell factories, ultimately achieving a titer of 549.7 mg/L for parthenolide and 972.7 mg/L for costunolide in a 10 L fermenter, which represents the highest reported titer obtained by microbial fermentation. The strategies should also contribute to the microbial cell factory-construction for other natural products exhibiting toxicity.

Synthetic Biology Strategies for the Production of Natural Colorants and Their Non-Natural Derivatives

Colorants are widely used in our daily lives to give colors to diverse chemicals and materials, including clothes, food, drugs, cosmetics, and paints. Although synthetic colorants derived from fossil fuels have been predominantly used due to their low cost, there is a growing need to replace them with natural alternatives. This shift is driven by increasing concerns over the climate crisis caused by excessive fossil fuel use, as well as health issues associated with the consumption of foods, beverages, and cosmetics containing petroleum-derived chemicals. In addition, many natural colorants show health-promoting properties such as antioxidant and antimicrobial activities. Despite such advantages, natural colorants could not be readily commercialized and distributed in the market due to their low stability, limited color spectrum, and low yields from natural resources. To this end, synthetic biology approaches have been developed to efficiently produce natural colorants from renewable resources with high yields. Strategies to diversify natural colorants to produce non-natural derivatives with enhanced properties and an expanded color spectrum have been also developed. In this Review, we discuss the recent synthetic biology strategies developed for enhancing the production of natural colorants and their non-natural derivatives, together with accompanying examples. Challenges ahead and future perspectives are also discussed.

Recent Advancements in the Biomanufacturing of Crocetin and Crocins: Key Enzymes and Metabolic Engineering

Crocetin and crocins are high-value apocarotenoids recognized for their role as food colorants as well as for their numerous industrial and therapeutic applications. Biotechnological platforms have the potential to replace traditional plant-based extraction of these compounds with a more sustainable approach. This review first introduced the catalytic characteristics of key enzymes involved in the biosynthetic pathway of crocetin and crocins, including carotenoid cleavage dioxygenases, aldehyde dehydrogenases, and uridine diphosphate glycosyltransferases. Next, we highlighted advanced metabolic engineering strategies aimed at enhancing crocetin and crocin production, such as increasing the pool of precursors and cofactors, protein mining and engineering, tuning protein expression, biosensor, genomic integration, and process optimization. Finally, the paper proposed potential strategies and tools associated with further boosting the heterologous production of crocetin and crocins to meet commercial-scale demands.

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.

Engineering Yarrowia lipolytica to Enhance the Production of Malonic Acid via Malonyl-CoA Pathway at High Titer

Malonic acid (MA) is a high-value-added chemical with significant applications in the polymers, pharmaceutical, and food industries. Microbial production of MA presents enzyme inefficiencies, competitive metabolic pathways, and dispersive carbon flux, which collectively limit its biosynthesis. Here, the non-conventional oleaginous yeast Yarrowia lipolytica is genetically engineered to enhance MA production. Initially, the malonyl-CoA pathway, comprising a malonyl-CoA hydrolase from Saccharomyces cerevisiae, is confirmed as the most efficient for MA production in Y. lipolytica. To further enhance MA production, two novel malonyl-CoA hydrolases exhibiting higher activity than the hydrolase from S. cerevisiae, are identified from Y. lipolytica and Fusarium oxysporum, respectively. The introduction of the malonyl-CoA hydrolase from F. oxysporum increases the MA titer to 6.3 g L-1. Subsequently, advanced metabolic engineering strategies are performed to ensure a sufficient flux of the precursors acetyl-CoA and malonyl-CoA for MA production, resulting in a production of 13.8 g L-1 MA in shaking-flasks. Finally, by employing the fermentation conditions and feeding strategies, a maximum concentration of 63.6 g L-1 of MA is achieved at 156 h with a productivity of 0.41 g L-1 h-1 in fed-batch fermentation. This study provides a new way for engineering Y. lipolytica to enhance MA production at high titer.

Designing synthetic microbial communities with the capacity to upcycle fermentation byproducts to increase production yields

Microbial cell factories, which convert feedstocks into a product of value, have the potential to help transition toward a bio-based economy with more sustainable ways to produce food, fuels, chemicals, and materials. One common challenge found in most bioconversions is the co-production, together with the product of interest, of undesirable byproducts or overflow metabolites. Here, we designed a strategy based on synthetic microbial communities to address this issue and increase overall production yields. To achieve our goal, we created a Yarrowia lipolytica co-culture comprising a wild-type (WT) strain that consumes glucose to make biomass and citric acid (CA), and an 'upcycler' strain, which consumes the CA produced by the WT strain. The co-culture produced up to two times more β-carotene compared with the WT monoculture using either minimal medium or hydrolysate. The proposed strategy has the potential to be applied to other bioprocesses and organisms.

Engineering Yarrowia lipolytica for the production of β-carotene by carbon and redox rebalancing

BACKGROUND

β-Carotene is a natural product that has garnered significant commercial interest. Considerable efforts have been made to meet such demand through the metabolic engineering of microorganisms, yet there is still potential for improvement. In this study, engineering approaches including carbon and redox rebalancing were used to maximize β-carotene production in Yarrowia lipolytica.

RESULTS

The initial production level was increased by iterative overexpression of pathway genes with lycopene inhibition removal. For further improvement, two approaches that redirect the central carbon pathway were evaluated to increase NADPH regeneration and reduce ATP expenditure. Pushing flux through the pentose phosphate pathway and introducing NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase were found to be more effective than the phosphoketolase-phosphotransacetylase (PK-PTA) pathway. Furthermore, flux to the lipid biosynthesis pathway was moderately increased to better accommodate the increased β-carotene pool, resulting in the production level of 809.2 mg/L.

CONCLUSIONS

The Y. lipolytica-based β-carotene production chassis was successfully developed through iterative overexpression of multiple pathways, central carbon pathway engineering and lipid pathway flux adjustment. The approach presented here provides insights into future endeavors to improve microbial terpenoid production capability.

Multiple Strategies Enhance 7-Dehydrocholesterol Production from Kitchen Waste by Engineered Yarrowia lipolytica

7-Dehydrocholesterol (7-DHC) is an important precursor of vitamin D3. The microbial synthesis of 7-DHC has attracted substantial attention. In this study, multiple strategies were developed to create a sustainable green route for enhancing 7-DHC yield from kitchen waste by engineered Yarrowia lipolytica. Y. lipolytica strains were engineered and combined with various Δ24-dehydrocholesterol reductases. Overexpressing all the genes in the mevalonate pathway improved the precursor pool, increasing the 7-DHC titer from 21.8 to 145.6 mg/L. Additionally, optimizing medium components using the response surface method significantly raised the 7-DHC titer to 391.0 mg/L after shake flask cultivation. The engineered strain yielded a record 7-DHC titer of 3.5 g/L in a 5-L bioreactor when kitchen waste was used as a carbon source. Overall, these results demonstrate that engineered Y. lipolytica efficiently synthesizes 7-DHC from waste lipid feedstock, offering a promising route for its bioproduction.

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 of Yarrowia lipolytica for the production and secretion of the saffron ingredient crocetin

BACKGROUND

Crocetin is a multifunctional apocarotenoid natural product derived from saffron, holding significant promises for protection against various diseases and other nutritional applications. Historically, crocetin has been extracted from saffron stigmas, but this method is hindered by the limited availability of high-quality raw materials and complex extraction processes. To overcome these challenges, metabolic engineering and synthetic biology can be applied to the sustainable production of crocetin.

RESULTS

We constructed a Yarrowia lipolytica strain using hybrid promoters and copy number adjustment, which was able to produce 2.66 g/L of β-carotene, the precursor of crocetin. Next, the crocetin biosynthetic pathway was introduced, and we observed both the production and secretion of crocetin. Subsequently, the metabolite profiles under varied temperatures were studied and we found that low temperature was favorable for crocetin biosynthesis in Y. lipolytica. Therefore, a two-step temperature-shift fermentation strategy was adopted to optimize yeast growth and biosynthetic enzyme activity, bringing a 2.3-fold increase in crocetin titer. Lastly, fermentation media was fine-tuned for an optimal crocetin output of 30.17 mg/L, bringing a 51% higher titer compared with the previous highest report in shake flasks. Concomitantly, we also generated Y. lipolytica strains capable of achieving substantial zeaxanthin production, yielding 1575.09 mg/L, doubling the previous highest reported titer.

CONCLUSIONS

Through metabolic engineering and fermentation optimization, we demonstrated the first de novo biosynthesis of crocetin in the industrial yeast Yarrowia lipolytica. In addition, we achieved a higher crocetin titer in flasks than all our known reports. This work not only represents a high production of crocetin, but also entails a significant simultaneous zeaxanthin production, setting the stage for sustainable and cost-effective production of these valuable compounds.

Triune Engineering Approach for (+)-valencene Overproduction in Yarrowia lipolytica

The sesquiterpene (+)-valencene, with its flavor and diverse biological functions, holds promise for applications in the food, fragrance, and pharmaceutical industries. However, the low concentration in nature and high cost of extraction limit its application. This study aimed to construct a microbial cell factory to efficiently produce (+)-valencene. The strain Yarrowia lipolytica YL238, possessing a stronger capacity for (+)-valencene synthesis, was selected and utilized as the chassis for further modifications. By fine-tuning the mevalonate and squalene synthesis pathways we achieved a remarkable 13.2-fold increase in (+)-valencene titer compared to the original strain. Following directed evolution was employed to screen for efficient (+)-valencene synthase, which further enhanced (+)-valencene production by 138%. Consequently, the engineered strain overproduced 813 mg/L of (+)-valencene in shake flasks, marking the highest titer reported in microbials to date. Furthermore, in fed-batch fermentation, this engineered strain showed the capacity to produce 3.3 g/L of (+)-valencene. This study offers a successful model for the application of the "strain-pathway-enzyme" triune strategy in the metabolic engineering of Y. lipolytica, and these methodologies could be broadly utilized for the synthesis of other natural terpenes.

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.

The potency of mitochondria enlargement for mitochondria-mediated terpenoid production in yeast

Terpenoids are widely used in the food, beverage, cosmetics, and pharmaceutical industries. Microorganisms have been extensively studied for terpenoid production. In yeast, the introduction of the mevalonate (MVA) pathway in organelles in addition to the augmentation of its own MVA pathway have been challenging. Introduction of the MVA pathway into mitochondria is considered a promising approach for terpenoid production because acetyl-CoA, the starting molecule of the MVA pathway, is abundant in mitochondria. However, mitochondria comprise only a small percentage of the entire cell. Therefore, we hypothesized that increasing the total mitochondrial volume per cell would increase terpenoid production. First, we ascertained that the amounts of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the final molecules of the MVA pathway, were 15-fold higher of the strain expressing the MVA pathway in mitochondria than in the wild-type yeast strain. Second, we found that different deletion mutants induced different mitochondrial volumes by measuring the mitochondrial volume in various deletion mutants affecting mitochondrial morphology; for example,Δmdm32 increased mitochondrial volume, and Δfzo1 decreased it. Finally, the effects of mitochondrial volume on amounts of IPP/DMAPP and terpenoids (squalene or β-carotene) were investigated using mutants harboring large or small mitochondria expressing the MVA pathway in mitochondria. Amounts of IPP/DMAPP and terpenoids (squalene or β-carotene) increased when the mitochondrial volume expanded. Introducing the MVA pathway into mitochondria for terpenoid production in yeast may become more attractive by enlarging the mitochondrial volume. KEY POINTS: • IPP/DMAPP content increased in the strain expressing the MVA pathway in mitochondria • IPP/DMAPP and terpenoid contents are positively correlated with mitochondrial volume • Enlarging the mitochondria may improve mitochondria-mediated terpenoid production.

Pretreated sugarcane bagasse matches performance of synthetic media for lipid production with Yarrowia lipolytica

Engineered strains of Yarrowia lipolytica with modified lipid profiles and other desirable properties for microbial oil production are widely reported but are almost exclusively characterized in synthetic laboratory-grade media. Ensuring translatable performance between synthetic media and industrially scalable lignocellulosic feedstocks is a critical challenge. Yarrowia lipolytica growth and lipid production were characterized in media derived from two-step acid-catalyzed glycerol pretreatment of sugarcane bagasse. Fermentation performance was benchmarked against laboratory-grade synthetic growth media, including detailed characterization of media composition, nitrogen utilization, biomass and lipid production, and fatty acid product profile. A Yarrowia lipolytica strain modified to enable xylose consumption consumed all sugars, glycerol, and acetic acid, accumulating lipids to 34-44 % of cell dry weight. Growth and lipid content when grown in sugarcane bagasse-derived media were equivalent to or better than that observed with synthetic media. These sugarcane bagasse-derived media are suitable for transferable development of Yarrowia lipolytica fermentations from synthetic media.

Biotechnological approaches for producing natural pigments in yeasts

Pigments are widely used in the food, cosmetic, textile, pharmaceutical, and materials industries. Demand for natural pigments has been increasing due to concerns regarding potential health problems and environmental pollution from synthetic pigments. Microbial production of natural pigments is a promising alternative to chemical synthesis or extraction from natural sources. Here, we discuss yeasts as promising chassis for producing natural pigments with their advantageous traits such as genetic amenability, safety, rapid growth, metabolic diversity, and tolerance. Metabolic engineering strategies and optimizing strategies in downstream process to enhance production of natural pigments are thoroughly reviewed. We discuss the challenges, including expanding the range of natural pigments and improving their feasibility of industrial scale-up, as well as the potential strategies for future development.

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.

Efficient Production of the Colorless Carotenoid Phytoene in Yarrowia lipolytica through Metabolic Engineering

Phytoene, a colorless carotenoid with unique ultraviolet (UV)-B absorption properties, offers potential for applications in functional food, cosmetics, and therapeutics. However, their low natural yield poses a challenge for large-scale production. This study aims to enhance phytoene production in the oleaginous yeast Yarrowia lipolytica by introducing a heterologous phytoene synthase gene combined with metabolic engineering approaches. We enhanced phytoene synthesis by overexpressing key genes in the mevalonate pathway and compartmentalizing the biosynthetic pathway within peroxisomes. Moreover, we inhibited the glyoxylate cycle to increase the accumulation of peroxisomal acetyl-CoA available for phytoene production. Our engineered strains demonstrated a significant increase in phytoene production, reaching up to 1.34 g/L titer and 58.74 mg/gDCW yield in the flask-scale fed-batch culture, which are the highest levels reported to date. These results underscore the potential of Y. lipolytica as a robust platform for producing phytoenes and other terpenoids on an industrial scale, offering valuable insights for future efforts in metabolic engineering.

Understanding Cytochrome P450 Enzyme Substrate Inhibition and Prospects for Elimination Strategies

Cytochrome P450 (CYP450) enzymes, which are widely distributed and pivotal in various biochemical reactions, catalyze diverse processes such as hydroxylation, epoxidation, dehydrogenation, dealkylation, nitrification, and bond formation. These enzymes have been applied in drug metabolism, antibiotic production, bioremediation, and fine chemical synthesis. Recent research revealed that CYP450 catalytic kinetics deviated from the classic Michaelis-Menten model. A notable substrate inhibition phenomenon that affects the catalytic efficiency of CYP450 at high substrate concentrations was identified. However, the substrate inhibition of various reactions catalyzed by CYP450 enzymes have not been comprehensively reviewed. This review describes CYP450 substrate inhibition examples and atypical Michaelis-Menten kinetic models, and provides insight into mechanisms of these enzymes. We also reviewed 3D structure and dynamics of CYP450 with substrate binding. Outline methods for alleviating substrate inhibition in CYP450 and other enzymes, including traditional fermentation approaches and protein engineering modifications. The comprehensive analysis presented in this study lays the foundation for enhancing the catalytic efficiency of CYP450 by deregulating substrate inhibition.

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.

Progress in the Metabolic Engineering of Yarrowia lipolytica for the Synthesis of Terpenes

Terpenes are natural secondary metabolites with isoprene as the basic structural unit; they are widely found in nature and have potential applications as advanced fuels, pharmaceutical ingredients, and agricultural chemicals. However, traditional methods are inefficient for obtaining terpenes because of complex processes, low yields, and environmental unfriendliness. The unconventional oleaginous yeast Yarrowia lipolytica, with a clear genetic background and complete gene editing tools, has attracted increasing attention for terpenoid synthesis. Here, we review the synthetic biology tools for Y. lipolytica, including promoters, terminators, selection markers, and autonomously replicating sequences. The progress and emerging trends in the metabolic engineering of Y. lipolytica for terpenoid synthesis are further summarized. Finally, potential future research directions are envisioned.

Sustainable production of C50 carotenoid bacterioruberin from methane using soil-enriched microbial consortia

Bacterioruberin is widely used in medicine, food, and cosmetics owing to its prominent characteristics of antioxidants and bioactivities. Bioconversion of methane into bacterioruberin is a promising way to address biomanufacturing substrate costs and greenhouse gas emissions but has not been achieved yet. Herein, this study aimed to upcycle methane to bacterioruberin by microbial consortia. The microbial consortia consist of Methylomonas and Methylophilus capable of synthesizing carotenoids from methane was firstly enriched from paddy soil. Through this microbial community, methane was successfully converted into C50 bacterioruberin for the first time. The bioconversion process was then optimized by the response surface methodology. Finally, the methane-derived bacterioruberin reached a record yield of 280.88 ± 2.94 μg/g dry cell weight. This study presents a cost-effective and eco-friendly approach for producing long-chain carotenoids from methane, offering a significant advancement in the direct conversion of greenhouse gases into value-added products.

Synthesis, characterization and application of microbial pigments in foods as natural colors

Colorants have played a crucial role in various applications, particularly in food processing, with natural sources such as mineral ores, plants, insects, and animals being commonly used. However, the nineteenth century saw the development of synthetic dyes, which replaced these natural colorants. In recent years, there has been a growing demand for natural products, driving an increased interest in natural colorants. Microbial pigments have emerged as promising sources of natural pigments due to their numerous health benefits. They can be produced in large quantities rapidly and from more affordable substrates, making them economically attractive. This review focuses on the current advancements in the low-cost synthesis of microbial pigments, exploring their biological activities and commercial applications. Microbial pigments offer a sustainable and economically viable alternative to natural and synthetic colorants, meeting the growing demand for natural products. These pigments are relatively nontoxic and exhibit significant health benefits, making them suitable for a wide range of applications. As interest in natural products continues to rise, microbial pigments hold great potential in shaping the future of colorant production across various sectors.

Advances in Metabolic Engineering for the Accumulation of Astaxanthin Biosynthesis

Astaxanthin, a lipophilic carotenoid renowned for its strong antioxidant activity, holds significant commercial value across industries such as feed, food, and cosmetics. Although astaxanthin can be synthesized through chemical methods, it may contain toxic by-products in the synthesized astaxanthin, limiting its application in medicine or functional food. Natural astaxanthin can be extracted from algae, however, the cultivation cycle of algae is relatively longer compared to microorganisms. With the advancement of synthetic biology and metabolic engineering, the method of microbial fermentation has emerged as a promising strategy for the large-scale production of astaxanthin. This article provides a comprehensive overview of the research progress in astaxanthin biosynthesis, highlighting the use of the natural host Xanthophyllomyces dendrorhous, and the heterologous hosts Yarrowia lipolytica and Saccharomyces cerevisiae. Additionally, future research prospects are also discussed.

From β-Carotene to Retinoids: A Review of Microbial Production of Vitamin A

Vitamin A (retinoids) is crucial for human health, with significant demand across the food, pharmaceutical, and animal feed industries. Currently, the market primarily relies on chemical synthesis and natural extraction methods, which face challenges such as low synthesis efficiency and complex extraction processes. Advances in synthetic biology have enabled vitamin A biosynthesis using microbial cell factories, offering a promising and sustainable solution to meet the increasing market demands. This review introduces the key enzymes involved in the biosynthesis of vitamin A from β-carotene, evaluates achievements in vitamin A production using various microbial hosts, and summarizes strategies for optimizing vitamin A biosynthesis. Additionally, we outline the remaining challenges and propose future directions for the biotechnological production of vitamin A.

Biosynthesis and Extraction of Chlorophyll, Carotenoids, Anthocyanins, and Betalaine In Vivo and In Vitro

As natural bioactive compounds, plant pigments play crucial roles not only in plant phenotype, growth, development, and adaptation to stress but also hold unique value in biotechnology, healthcare, and industrial applications. There is growing interest in the biosynthesis and acquisition of plant pigments. Thus, this paper explores emerging extraction methods of natural pigments and elucidates the biosynthesis pathways of four key plant pigments, chlorophylls, carotenoids, anthocyanins, and betalaine in vivo and in vitro. We comprehensively discuss the application of solvent, supercritical fluid [extraction], ultrasonic, and microwave-assisted extraction techniques, as well as introducing key enzymes, precursors, and synthetic pathways involved in pigment synthesis. δ-Aminolevulinic acid represents a pivotal initiating enzyme for chlorophyll synthesis, whereas isopentenylpyrophosphate, (IPP) and dimethylallyl pyrophosphate, (DMAPP) are closely associated with carotenoid biosynthesis. Phenylalanine and tyrosine are critical substances for anthocyanin and betalaine synthesis, respectively. Hence, crucial genes such as chlI, crtB, PGT8, CYP76AD1, and BvDODA can be employed for heterologous biosynthesis in vitro to meet the demand for increased plant pigment amount. As a pivotal determinant of plant coloration, an in-depth exploration into the high-quality acquisition of plant pigments can provide a basis for developing superior pigments and offer new insights into increasing pigment yield.

Metabolomic Analysis of Carotenoids Biosynthesis by Sphingopyxis sp. USTB-05

Carotenoids belonging to the class of tetraterpenoids have extensive applications in medicine, food, nutrition, cosmetics, and feed. Among them, lutein and zeaxanthin can prevent macular degeneration in the elderly, which is very important for protecting vision. Here, we introduce the first metabolomic analysis of Sphingopyxis sp. USTB-05, aiming to shed light on the biosynthesis of carotenoids. Sphingopyxis sp. USTB-05 has the complete methylerythritol 4-phosphate (MEP) pathway and carotenoid biosynthesis pathway, especially involved in the bioconversion of zeaxanthin, violaxanthin, and astaxanthin. Metabolomic profiling identified seven carotenes and six xanthophylls synthesized by Sphingopyxis sp. USTB-05. Zeaxanthin, in particular, was found to be the most abundant, with a content of 37.1 µg/g dry cells. Collectively, the results presented herein greatly enhance our understanding of Sphingopyxis sp. USTB-05 in carotenoids biosynthesis, and thus further accelerate its fundamental molecular investigations and biotechnological applications.

The Mechanism of Sodium Sulfate Coupled with Anaerobic Methane Oxidation Mitigating Methane Production in Beef Cattle

The aim of this experiment is to explore the effect of sodium sulfate (Na2SO4) on methane reduction in the rumen, and its impact on anaerobic methane-oxidizing archaea (ANME). Using mixed rumen fluid from four Angus cattle fistulas, this study conducted an in vitro fermentation. Adding Na2SO4 to the fermentation substrate resulted in sulfur concentrations in the substrate of 0.4%, 0.6%, 0.8%, 1.0%, 1.2%, 1.4%, 1.6%, 1.8%, 2.0%, 2.2%, and 2.4%. The gas production rate and methane yield were measured using an in vitro gas production method. Subsequently, the fermentation fluid was collected to determine the fermentation parameters. The presence of ANME in the fermentation broth, as well as the relationship between the number of bacteria, archaea, sulfate reducing bacteria (SRB), ANME, and the amount of Na2SO4 added to the substrate, were measured using qPCR. The results showed that: (1) the addition of Na2SO4 could significantly reduce CH4 production and was negatively correlated with CO2 production; (2) ANME-1 and ANME-2c did exist in the fermentation broth; (3) the total number of archaea, SRB, ANME-1, and ANME-2c increased with the elevation of Na2SO4. The above results indicated that Na2SO4 could mitigate methane production via sulfate-dependent anaerobic methane oxidation (S-DAMO) in the rumen. In the future management of beef cattle, including sodium sulfate in their diet can stimulate S-DAMO activity, thereby promoting a reduction in methane emissions.

CRISPR-Cas9-based genome-editing technologies in engineering bacteria for the production of plant-derived terpenoids

Terpenoids are widely used as medicines, flavors, and biofuels. However, the use of these natural products is largely restricted by their low abundance in native plants. Fortunately, heterologous biosynthesis of terpenoids in microorganisms offers an alternative and sustainable approach for efficient production. Various genome-editing technologies have been developed for microbial strain construction. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9) is the most commonly used system owing to its outstanding efficiency and convenience in genome editing. In this review, the basic principles of CRISPR-Cas9 systems are briefly introduced and their applications in engineering bacteria for the production of plant-derived terpenoids are summarized. The aim of this review is to provide an overview of the current developments of CRISPR-Cas9-based genome-editing technologies in bacterial engineering, concluding with perspectives on the challenges and opportunities of these technologies.

Systematic metabolic engineering enables highly efficient production of vitamin A in Saccharomyces cerevisiae

Vitamin A is a micronutrient critical for versatile biological functions and has been widely used in the food, cosmetics, pharmaceutical, and nutraceutical industries. Synthetic biology and metabolic engineering enable microbes, especially the model organism Saccharomyces cerevisiae (generally recognised as safe) to possess great potential for the production of vitamin A. Herein, we first generated a vitamin A-producing strain by mining β-carotene 15,15'-mono(di)oxygenase from different sources and identified two isoenzymes Mbblh and Ssbco with comparable catalytic properties but different catalytic mechanisms. Combinational expression of isoenzymes increased the flux from β-carotene to vitamin A metabolism. To modulate the vitamin A components, retinol dehydrogenase 12 from Homo sapiens was introduced to achieve more than 90 % retinol purity using shake flask fermentation. Overexpressing POS5Δ17 enhanced the reduced nicotinamide adenine dinucleotide phosphate pool, and the titer of vitamin A was elevated by almost 46 %. Multi-copy integration of the key rate-limiting step gene Mbblh further improved the synthesis of vitamin A. Consequently, the titer of vitamin A in the strain harbouring the Ura3 marker was increased to 588 mg/L at the shake-flask level. Eventually, the highest reported titer of 5.21 g/L vitamin A in S. cerevisiae was achieved in a 1-L bioreactor. This study unlocked the potential of S. cerevisiae for synthesising vitamin A in a sustainable and economical way, laying the foundation for the commercial-scale production of bio-based vitamin A.

Dual-Regulation in Peroxisome and Cytoplasm toward Efficient Limonene Biosynthesis with Rhodotorula toruloides

Rhodotorula toruloides is a potential workhorse for production of various value-added chemicals including terpenoids, oleo-chemicals, and enzymes from low-cost feedstocks. However, the limited genetic toolbox is hindering its metabolic engineering. In the present study, four type I and one novel type II peroxisomal targeting signal (PTS1/PTS2) were characterized and employed for limonene production for the first time in R. toruloides. The implant of the biosynthesis pathway into the peroxisome led to 111.5 mg/L limonene in a shake flask culture. The limonene titer was further boosted to 1.05 g/L upon dual-metabolic regulation in the cytoplasm and peroxisome, which included employing the acetoacetyl-CoA synthase NphT7, adding an additional copy of native ATP-dependent citrate lyase, etc. The final yield was 0.053 g/g glucose, which was the highest ever reported. The newly characterized PTSs should contribute to the expansion of genetic toolboxes forR. toruloides. The results demonstrated that R. toruloides could be explored for efficient production of terpenoids.

Comparative transcriptome analysis reveals the redirection of metabolic flux from cell growth to astaxanthin biosynthesis in Yarrowia lipolytica

Engineering Yarrowia lipolytica to produce astaxanthin provides a promising route. Here, Y. lipolytica M2 producing a titer of 181 mg/L astaxanthin was isolated by iterative atmospheric and room-temperature plasma mutagenesis and diphenylamine-mediated screening. Interestingly, a negative correlation was observed between cell biomass and astaxanthin production. To reveal the underlying mechanism, RNA-seq analysis of transcriptional changes was performed in high producer M2 and reference strain M1, and a total of 1379 differentially expressed genes were obtained. Data analysis revealed that carbon flux was elevated through lipid metabolism, acetyl-CoA and mevalonate supply, but restrained through central carbon metabolism in strain M2. Moreover, upregulation of other pathways such as ATP-binding cassette transporter and thiamine pyrophosphate possibly provided more cofactors for carotenoid hydroxylase and relieved cell membrane stress caused by astaxanthin insertion. These results suggest that balancing cell growth and astaxanthin production may be important to promote efficient biosynthesis of astaxanthin in Y. lipolytica.

Microbial chassis as the platform for production of dihydroxy xanthophyll-based carotenoids: an overview of recent advances in biomanufacturing

Physiological and environmental cues prompt microbes to synthesize diverse carotenoids, including dihydroxy xanthophylls, facilitating their adaptation and survival. Lutein and its isomeric counterpart, zeaxanthin, are notable dihydroxy xanthophylls with bioactive properties such as antioxidative, anti-inflammatory, anticancer, and neuroprotective effects, particularly beneficial for human ocular health. However, global natural resources for co-producing lutein and zeaxanthin are scarce, with zeaxanthin lacking commercial sources, unlike lutein sourced from marigold plants and microalgae. Traditionally, dihydroxy xanthophyll production primarily relies on petrochemical synthetic routes, with limited biological sourcing reported. Nonetheless, microbiological synthesis presents promising avenues as a commercial source, albeit challenged by low dihydroxy xanthophyll yield at high cell density. Strategies involving optimization of physical and chemical parameters are essential to achieve high-quality dihydroxy xanthophyll products. This overview briefly discusses dihydroxy xanthophyll biosynthesis and highlights recent advancements, discoveries, and industrial benefits of lutein and zeaxanthin production from microorganisms as alternative biofactories.

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.

Exploiting synthetic biology platforms for enhanced biosynthesis of natural products in Yarrowia lipolytica

With the rapid development of synthetic biology, researchers can design, modify, or even synthesize microorganisms de novo, and microorganisms endowed with unnatural functions can be considered "artificial life" and facilitate the development of functional products. Based on this concept, researchers can solve critical problems related to the insufficient supply of natural products, such as low yields, long production cycles, and cumbersome procedures. Due to its superior performance and unique physiological and biochemical characteristics, Yarrowia lipolytica is a favorable chassis cell used for green biomanufacturing by numerous researchers. This paper mainly reviews the development of synthetic biology techniques for Y. lipolytica and summarizes the recent research progress on the synthesis of natural products in Y. lipolytica. This review will promote the continued innovative development of Y. lipolytica by providing theoretical guidance for research on the biosynthesis of natural products.

Advances in the metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica for the production of -carotene

β-Carotene is one kind of the most important carotenoids. The major functions of β-carotene include the antioxidant and anti-cardiovascular properties, which make it a growing market. Recently, the use of metabolic engineering to construct microbial cell factories to synthesize β-carotene has become the latest model for its industrial production. Among these cell factories, yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica have attracted the most attention because of the: security, mature genetic manipulation tools, high flux toward carotenoids using the native mevalonate pathway and robustness for large-scale fermentation. In this review, the latest strategies for β-carotene biosynthesis, including protein engineering, promoters engineering and morphological engineering are summarized in detail. Finally, perspectives for future engineering approaches are proposed to improve β-carotene production.

Biosynthetic pathway redesign in non-conventional yeast for enhanced production of cembratriene-ol

Cembratriene-ol (CBT-ol), a plant-derived macrocyclic diterpene with notable insecticidal activity, has attracted considerable attention with respect to the development of sustainable and green biopesticides. Currently, CBT-ol production is limited by an inefficient and costly plant extraction strategy. Herein, CBT-ol production was enhanced by redesigning the CBT-ol biosynthetic pathway in Candida tropicalis, with subsequent truncation of CBT-ol synthase further increasing CBT-ol production. Moreover, bottlenecks in the CBT-ol biosynthetic pathway were eliminated by adjusting the gene dosage of the rate-limiting enzymes. Ultimately, the resulting strain C. tropicalis CPPt-03D produced 129.17 mg/L CBT-ol in shaking flasks (a 144-fold increase relative to that of the initial strain C01-CD) with CBT-ol production reaching 1,425.76 mg/L in a 5-L bioreactor, representing the highest CBT-ol titer reported to date. These findings provide a green process and promising platform for the industrial production of CBT-ol and lays the foundation for organic farming.

Metabolic Pathway Coupled with Fermentation Process Optimization for High-Level Production of Retinol in Yarrowia lipolytica

Retinol is a lipid-soluble form of vitamin A that is crucial for human visual and immune functions. The production of retinol through microbial fermentation has been the focus of recent exploration. However, the obtained titer remains limited and the product is often a mixture of retinal, retinol, and retinoic acid, necessitating purification. To achieve efficient biosynthesis of retinol in Yarrowia lipolytica, we improved the metabolic flux of β-carotene to provide sufficient precursors for retinol in this study. Coupled with the optimization of the expression level of β-carotene 15,15'-dioxygenase, de novo production of retinol was achieved. Furthermore, Tween 80 was used as an extractant and butylated hydroxytoluene as an antioxidant to extract intracellular retinol and prevent retinol oxidation, respectively. This strategy significantly increased the level of retinol production. By optimizing the enzymes converting retinal to retinol, the proportion of extracellular retinol in the produced retinoids reached 100%, totaling 1042.3 mg/L. Finally, total retinol production reached 5.4 g/L through fed-batch fermentation in a 5 L bioreactor, comprising 4.2 g/L extracellular retinol and 1.2 g/L intracellular retinol. This achievement represents the highest reported titer so far and advances the industrial production of retinol.

Strategies for the efficient biosynthesis of β-carotene through microbial fermentation

β-Carotene is an orange fat-soluble compound, which has been widely used in fields such as food, medicine and cosmetics owing to its anticancer, antioxidant and cardiovascular disease prevention properties. Currently, natural β-carotene is mainly extracted from plants and algae, which cannot meet the growing market demand, while chemical synthesis of β-carotene cannot satisfy the pursuit for natural products of consumers. The β-carotene production through microbial fermentation has become a promising alternative owing to its high efficiency and environmental friendliness. With the rapid development of synthetic biology and in-depth study on the synthesis pathway of β-carotene, microbial fermentation has shown promising applications in the β-carotene synthesis. Accordingly, this review aims to summarize the research progress and strategies of natural carotenoid producing strain and metabolic engineering strategies in the heterologous synthesis of β-carotene by engineered microorganisms. Moreover, it also summarizes the adoption of inexpensive carbon sources to synthesize β-carotene as well as proposes new strategies that can further improve the β-carotene production.

De Novo Biosynthesis of Lutein in Yarrowia lipolytica

Lutein is a high-value tetraterpenoid carotenoid that is widely used in feed, cosmetics, food, and drugs. Microbial synthesis of lutein is an important method for green and sustainable production, serving as an alternative to plant extraction methods. However, an inadequate precursor supply and low catalytic efficiency of key pathway enzymes are the main reasons for the low efficacy of microbial synthesis of lutein. In this study, some strategies, such as enhancing the MVA pathway and localizing α-carotene synthase OluLCY within the subcellular organelles in Yarrowia lipolytica, were adopted to enhance the synthesis of precursor α-carotene, which resulted in a 10.50-fold increase in α-carotene titer, reaching 38.50 mg/L. Subsequently, by improving hydroxylase activity with truncated N-terminal transport peptide and locating hydroxylases to subcellular organelles, the final strain L9 producing 75.25 mg/L lutein was obtained. Eventually, a lutein titer of 675.40 mg/L (6.13 mg/g DCW) was achieved in a 5 L bioreactor by adding the antioxidant 2,6-ditert-butyl-4-methylphenol. This study realizes de novo synthesis of lutein in Y. lipolytica for the first time and achieves the highest lutein titer reported so far.