A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnological producer of β-carotene

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.

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 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.

Substrate-dependent lipid and β-carotene production in engineered Yarrowia lipolytica: a comparative study

This study evaluates the influence of various substrates (glucose, glycerol, and acetic acid) on the growth and metabolite production of Yarrowia lipolytica in fed-batch bioreactors. The primary aim is to understand how substrate choice impacts lipid and β-carotene production, critical for bioenergy and bioproducts. The study demonstrates that the choice of substrate significantly influences biomass yield, lipid content, and β-carotene levels. Among the substrates tested, glycerol yielded the highest biomass concentration of 5.31 g/L. Glucose led to the highest lipid content, with a yield of 35.8% (g lipids/g biomass), while acetic acid resulted in the highest lipid concentration, reaching 1.42 g/L. In terms of β-carotene production, glucose showed the highest content per cell at 63.3 mg/g, whereas glycerol led to the highest overall concentration of 202 mg/L. These findings highlight Y. lipolytica's versatility and potential as a flexible platform to produce lipids and β-carotene, which are essential for developing sustainable biofuels and bioproducts. The study underscores the significant variations in metabolite production based on substrate choice, emphasizing on the importance of tailored strategies to optimize industrial applications. Further research may explore optimizing fermentation conditions to enhance production yields, making this yeast a viable option for various biotechnological applications.

Efficient biosynthesis of β-caryophyllene by engineered Yarrowia lipolytica

BACKGROUND

β-Caryophyllene, a sesquiterpenoid, holds considerable potential in pharmaceutical, nutraceutical, cosmetic, and chemical industries. In order to overcome the limitation of β-caryophyllene production by the extraction from plants or chemical synthesis, we aimed the microbial production of β-caryophyllene in non-conventional yeast Yarrowia lipolytica in this study.

RESULTS

Two genes, tHMG1 from S. cerevisiae to boost the mevalonate pool and QHS1 from Artemisia annua, were expressed under different promoters and copy numbers in Y. lipolytica. The co-expression of 8UAS pEYK1-QHS1 and pTEF-tHMG1 in the obese strain yielded 165.4 mg/L and 201.5 mg/L of β-caryophyllene in single and double copies, respectively. Employing the same combination of promoters and genes in wild-type-based strain with two copies resulted in a 1.36-fold increase in β-caryophyllene. The introduction of an additional three copies of 8UAS pEYK1-tHMG1 further augmented the β-caryophyllene, reaching 318.5 mg/L in flask fermentation. To maximize the production titer, we optimized the carbon source ratio between glucose and erythritol as well as fermentation condition that led to 798.1 mg/L of β-caryophyllene.

CONCLUSIONS

A biosynthetic pathway of β-caryophyllene was firstly investigated in Y. lipolytica in this study. Through the modulation of key enzyme expression, we successfully demonstrated an improvement in β-caryophyllene production. This strategy suggests its potential extension to studies involving the microbial production of various industrially relevant terpenes.

Upcycling of Enzymatically Recovered Amino Acids from Textile Waste Blends: Approaches for Production of Valuable Second-Generation Bioproducts

Tremendous quantities of textile waste generated and primarily landfilled annually represent a huge risk of contaminating the environment, together with loss of valuable resources. Especially, blended fabrics further pose a challenge for recycling and valorization strategies, while enzymatic hydrolysis offers a highly specific and environmentally friendly solution. In this study, we demonstrate that proteases specifically hydrolyze the wool components in blends with polyester, allowing recovery of pure polyester fibers as well as amino acids and peptides as platform molecules for further valorization. Recovered amino acids and peptides were successfully used as a nitrogen source for cultivation of Chlorella vulgaris and Rhodotorula mucilaginosa for the production of valuable biomolecules including pigments and lipids. Here, 11.3 mg/gCDW chlorophyll and 47% lipid content were obtained from algal biomass, while 1.1 mg/gCDW carotenoids and 35% lipids content were reached from the yeast grown on wool hydrolysate as the sole nitrogen source. These could be applied as natural dyes for textile applications or as biofuels to replace toxic synthetic compounds and fossil resources, respectively. The presented concept demonstrates feasibility of enzymatic recovery and microbial valorization of components of blended textile waste to support the development toward a circular bioeconomy.

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.

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.

Advances in multi-enzyme co-localization strategies for the construction of microbial cell factory

Biomanufacturing, driven by technologies such as synthetic biology, offers significant potential to advance the bioeconomy and promote sustainable development. It is anticipated to transform traditional manufacturing and become a key industry in future strategies. Cell factories are the core of biomanufacturing. The advancement of synthetic biology and growing market demand have led to the production of a greater variety of natural products and increasingly complex metabolic pathways. However, this progress also presents challenges, notably the conflict between natural product production and chassis cell growth. This conflict results in low productivity and yield, adverse side effects, metabolic imbalances, and growth retardation. Enzyme co-localization strategies have emerged as a promising solution. This article reviews recent progress and applications of these strategies in constructing cell factories for efficient natural product production. It comprehensively describes the applications of enzyme-based compartmentalization, metabolic pathway-based compartmentalization, and synthetic organelle-based compartmentalization in improving product titers. The article also explores future research directions and the prospects of combining multiple strategies with advanced technologies.

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.

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.

Screening of novel β-carotene hydroxylases for the production of β-cryptoxanthin and zeaxanthin and the impact of enzyme localization and crowding on their production in Yarrowia lipolytica

Zeaxanthin, a vital dietary carotenoid, is naturally synthesized by plants, microalgae, and certain microorganisms. Large-scale zeaxanthin production can be achieved through plant extraction, chemical synthesis, or microbial fermentation. The environmental and health implications of the first two methods have made microbial fermentation an appealing alternative for natural zeaxanthin production despite the challenges in scaling up the bioprocess. An intermediate between β-carotene and zeaxanthin, β-cryptoxanthin, is found only in specific fruits and vegetables and has several important functions for human health. The low concentration of β-cryptoxanthin in these sources results in low extraction yields, making biotechnological production a promising alternative for achieving higher yields. Currently, there is no industrially relevant microbial fermentation process for β-cryptoxanthin production, primarily due to the lack of identified enzymes that specifically convert β-carotene to β-cryptoxanthin without further conversion to zeaxanthin. In this study, we used genetic engineering to leverage the oleaginous yeast Yarrowia lipolytica as a bio-factory for zeaxanthin and β-cryptoxanthin production. We screened 22 β-carotene hydroxylases and identified eight novel enzymes with β-carotene hydroxylating activity: six producing zeaxanthin and two producing only β-cryptoxanthin. By introducing the β-carotene hydroxylase from the bacterium Chondromyces crocatus (CcBCH), a β-cryptoxanthin titer of 24 ± 6 mg/L was achieved, representing the highest reported titer of sole β-cryptoxanthin in Y. lipolytica to date. By targeting zeaxanthin-producing β-carotene hydroxylase to the endoplasmic reticulum and peroxisomes, we increased the production of zeaxanthin by 54% and 66%, respectively, compared to untargeted enzyme. The highest zeaxanthin titer of 412 ± 34 mg/L was achieved by targeting β-carotene hydroxylases to peroxisomes. In addition, by constructing multienzyme scaffold-free complexes with short peptide tags RIDD and RIAD, we observed a 39% increase in the zeaxanthin titer and a 28% increase in the conversion rate compared to the strain expressing unmodified enzyme. The zeaxanthin titers obtained in this study are not the highest reported; however, our goal was to demonstrate that specific approaches can enhance both titer and conversion rate, rather than to achieve the maximum titer. These findings underscore the potential of Y. lipolytica as a promising platform for carotenoid production and provide a foundation for future research, where further optimization is required to maximize production.

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.

Synthetic, marine, light-driven, autotroph-heterotroph co-culture system for sustainable β-caryophyllene production

Applying low-cost substrate is critical for sustainable bioproduction. Co-culture of phototrophic and heterotrophic microorganisms can be a promising solution as they can use CO2 and light as feedstock. This study aimed to create a light-driven consortium using a marine cyanobacterium Synechococcus sp. PCC 7002 and an industrial yeast Yarrowia lipolytica. First, the cyanobacterium was engineered to accumulate and secrete sucrose by regulating the expression of genes involved in sucrose biosynthesis and transport, resulting in 4.0 g/L of sucrose secretion. Then, Yarrowia lipolytica was engineered to efficiently use sucrose and produce β-caryophyllene that has various industrial applications. Then, co- and sequential-culture were optimized with different induction conditions and media compositions. A maximum β-caryophyllene yield of 14.1 mg/L was obtained from the co-culture. This study successfully established an artificial light-driven consortium based on a marine cyanobacterium and Y. lipolytica, and provides a foundation for sustainable bioproduction from CO2 and light through co-culture systems.

Clostridium carboxidivorans and Rhodosporidium toruloides as a platform for the valorization of carbon dioxide to microbial oils

There is growing scientific interest in oleaginous yeasts producing microbial oils as precursors of biofuels and potential substitutes for fossil fuels. Due to the high cost of substrates commonly metabolized by yeasts, volatile fatty acids (VFAs) are gaining interest as alternative cheap and sustainable carbon sources, which can be obtained from solid, liquid and gas pollutants. In this research, Rhodosporidium toruloides was proven to be able to accumulate microbial oils from VFAs obtained from the fermentation of syngas by Clostridium carboxidivorans. Using CO2 and CO as carbon sources from the syngas mixture and H2 as energy source, this acetogen produced, via the Wood-Ljungdahl pathway, a mixture of acetic, butyric and caproic acids. It was first revealed that R. toruloides exhibited minimal inhibition at concentrations below 12 g/L when exposed to a mixture of VFAs, which included acetic, butyric and even hexanoic acids. The yeast was then grown on the culture medium derived from the acetogenic fermentation of syngas. Between the two yeast strains tested of the same species, R. toruloides DSM 4444 reached a total VFAs consumption of 69.1 g/L, supplied by successive additions of acids to the reactor, yielding a maximum lipid content of 29.7% w/w cell. The lipid profile obtained in this case, in terms of abundance followed the order C18:1 > C16:0 ≥ C18:0 > C18:2>others; in which the dominant compound (C18:1), represented approximately 50% of the total. This research opens new possibilities in the cultivation of oleaginous yeasts for the production of biofuels and bioproducts from C1 gases.

Combinatorial iterative method for metabolic engineering of Yarrowia lipolytica: Application for betanin biosynthesis

Combinatorial library-based metabolic engineering approaches allow lower cost and faster strain development. We developed a genetic toolbox EXPRESSYALI for combinatorial engineering of the oleaginous yeast Yarrowia lipolytica. The toolbox enables consecutive rounds of engineering, where up to three combinatorially assembled gene expression cassettes can be integrated into each yeast clone per round. The cassettes are integrated into distinct intergenic sites or an open reading frame of a target gene if a simultaneous gene knockout is desired. We demonstrate the application of the toolbox by optimizing the Y. lipolytica to produce the red beet color betanin via six consecutive rounds of genome editing and screening. The library size varied between 24 and 360. Library screening was facilitated by automated color-based colony picking. In the first round, betanin pathway genes were integrated, resulting in betanin titer of around 20 mg/L. Through the following five consecutive rounds, additional biosynthetic genes were integrated, and the precursor supply was optimized, resulting in a titer of 70 mg/L. Three beta-glucosidases were deleted to prevent betanin deglycosylation, which led to a betanin titer of 130 mg/L in a small scale and a titer of 1.4 g/L in fed-batch bioreactors. The EXPRESSYALI toolbox can facilitate metabolic engineering efforts in Y. lipolytica (available via AddGene Cat. Nr. 212682-212704, Addgene kit ID # 1000000245).

Retargeting of heterologous enzymes results in improved β-carotene synthesis in Saccharomyces cerevisiae

AIMS

Carotenoids are a class of hydrophobic substances that are important as food and feed colorants and as antioxidants. The pathway for β-carotene synthesis has been expressed in various yeast species, albeit with rather low yields and titers. The inefficient conversion of phytoene to lycopene is often regarded as a bottleneck in the pathway. In this study, we aimed at the improvement of β-carotene production in Saccharomyces cerevisiae by specifically engineering the enzymatic reactions producing and converting phytoene.

METHODS AND RESULTS

We show that phytoene is stored in intracellular lipid droplets, whereas the enzyme responsible for its conversion, phytoene dehydrogenase, CrtI, is located at the endoplasmic reticulum, like the bifunctional enzyme CrtYB that catalyses the reaction before and after CrtI. To improve the accessibility of phytoene for CrtI and to delay its storage in lipid droplets, we tested the relocation of CrtI and CrtYB to mitochondria. However, only the retargeting of CrtYB resulted in an improvement of the β-carotene content, whereas the mitochondrial variant of CrtI was not functional. Surprisingly, a cytosolic variant of this enzyme, which we obtained through the elimination of its carboxy-terminal membrane anchor, caused an increase in β-carotene accumulation. Overexpression of this CrtI variant in an optimized medium resulted in a strain with a β-carotene content of 79 mg g-1 cell dry weight, corresponding to a 76-fold improvement over the starting strain.

CONCLUSIONS

The retargeting of heterologously expressed pathway enzymes improves β-carotene production in S. cerevisiae, implicating extensive inter-organellar transport phenomena of carotenoid precursors. In addition, strong overexpression of carotenoid biosynthetic enzymes and the optimization of cultivation conditions are required for high contents.

Advanced Fungal Biotechnologies in Accomplishing Sustainable Development Goals (SDGs): What Do We Know and What Comes Next?

The present era has witnessed an unprecedented scenario with extreme climate changes, depleting natural resources and rising global food demands and its widespread societal impact. From providing bio-based resources to fulfilling socio-economic necessities, tackling environmental challenges, and ecosystem restoration, microbes exist as integral members of the ecosystem and influence human lives. Microbes demonstrate remarkable potential to adapt and thrive in climatic variations and extreme niches and promote environmental sustainability. It is important to mention that advances in fungal biotechnologies have opened new avenues and significantly contributed to improving human lives through addressing socio-economic challenges. Microbe-based sustainable innovations would likely contribute to the United Nations sustainable development goals (SDGs) by providing affordable energy (use of agro-industrial waste by microbial conversions), reducing economic burdens/affordable living conditions (new opportunities by the creation of bio-based industries for a sustainable living), tackling climatic changes (use of sustainable alternative fuels for reducing carbon footprints), conserving marine life (production of microbe-based bioplastics for safer marine life) and poverty reduction (microbial products), among other microbe-mediated approaches. The article highlights the emerging trends and future directions into how fungal biotechnologies can provide feasible and sustainable solutions to achieve SDGs and address global issues.

Microbial synthesis of terpenoids for human nutrition - an emerging field with high business potential

Because of their complicated biosynthesis and hydrophobic nature, fermentative production of terpenoids did not play a significant role on a commercial scale until a few years ago. Driven by technological progress in metabolic engineering and process biotechnology, terpene-based food ingredients such as flavors, sweeteners, and vitamins produced by fermentation have now become viable and commercially competitive options. In recent years, several companies have developed microbial platforms for commercial terpene production. Impressive progress has been made in the fermentative production of sesquiterpenes used in flavorings. The development of sweeteners, such as steviol glycosides and mogrosides, and the production of vitamins A and E based on fermentation are also being explored. The production of monoterpenes remains challenging due to their antimicrobial effects.

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.

Broadening the application of Yarrowia lipolytica synthetic biology tools to explore the potential of Yarrowia clade diversity

Yeasts have established themselves as prominent microbial cell factories, and the availability of synthetic biology tools has led to breakthroughs in the rapid development of industrial chassis strains. The selection of a suitable microbial host is critical in metabolic engineering applications, but it has been largely limited to a few well-defined strains. However, there is growing consideration for evaluating strain diversity, as a wide range of specific traits and phenotypes have been reported even within a specific yeast genus or species. Moreover, with the advent of synthetic biology tools, non-type strains can now be easily and swiftly reshaped. The yeast Yarrowia lipolytica has been extensively studied for various applications such as fuels, chemicals, and food. Additionally, other members of the Yarrowia clade are currently being evaluated for their industrial potential. In this study, we demonstrate the versatility of synthetic biology tools originally developed for Y. lipolytica by repurposing them for engineering other yeasts belonging to the Yarrowia clade. Leveraging the Golden Gate Y. lipolytica tool kit, we successfully expressed fluorescent proteins as well as the carotenoid pathway in at least five members of the clade, serving as proof of concept. This research lays the foundation for conducting more comprehensive investigations into the uncharacterized strains within the Yarrowia clade and exploring their potential applications in biotechnology.

Sustainable biorefinery approach by utilizing xylose fraction of lignocellulosic biomass

Lignocellulosic biomass (LCB) has been a lucrative feedstock for developing biochemical products due to its rich organic content, low carbon footprint and abundant accessibility. The recalcitrant nature of this feedstock is a foremost bottleneck. It needs suitable pretreatment techniques to achieve a high yield of sugar fractions such as glucose and xylose with low inhibitory components. Cellulosic sugars are commonly used for the bio-manufacturing process, and the xylose sugar, which is predominant in the hemicellulosic fraction, is rejected as most cell factories lack the five‑carbon metabolic pathways. In the present review, more emphasis was placed on the efficient pretreatment techniques developed for disintegrating LCB and enhancing xylose sugars. Further, the transformation of the xylose to value-added products through chemo-catalytic routes was highlighted. In addition, the review also recapitulates the sustainable production of biochemicals by native xylose assimilating microbes and engineering the metabolic pathway to ameliorate biomanufacturing using xylose as the sole carbon source. Overall, this review will give an edge on the bioprocessing of microbial metabolism for the efficient utilization of xylose in the LCB.

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.

Engineering Yarrowia lipolytica as a Cellulolytic Cell Factory for Production of p-Coumaric Acid from Cellulose and Hemicellulose

De novo biosynthesis of high-value added food additive p-coumaric acid (p-CA) direct from cellulose/hemicellulose is a more sustainable route compared to the chemical route, considering the abundant cellulose/hemicellulose resources. In this study, a novel factory was constructed for the production of p-CA in Yarrowia lipolytica using cellulose/hemicellulose as the sole carbon source. Based on multicopy integration of the TAL gene and reprogramming the shikimic acid pathway, the engineered strain produced 1035.5 ± 67.8 mg/L p-CA using glucose as a carbon source. The strains with overexpression of cellulases and hemicellulases produced 84.3 ± 2.4 and 65.3 ± 4.6 mg/L p-CA, using cellulose (carboxymethyl-cellulose) or hemicellulose (xylan from bagasse) as the carbon source, respectively. This research demonstrated the feasibility of conversion of cost-effective cellulose/hemicellulose into a value-added product and provided a sustainable cellulolytic cell factory for the utilization of cellulose/hemicellulose.

Unlocking the potential of one-carbon gases (CO2, CO) for concomitant bioproduction of β-carotene and lipids

This study investigates the use of a Yarrowia lipolytica strain for the bioconversion of syngas-derived acetic acid into β-carotene and lipids. A two-stage process was employed, starting with the acetogenic fermentation of syngas by Clostridium aceticum, metabolising CO, CO2, H2, to produce acetic acid, which is then utilized by Y. lipolytica for simultaneous lipid and β-carotene synthesis. The research demonstrates that acetic acid concentration plays a pivotal role in modulating lipid profiles and enhancing β-carotene production, with increased acetic acid consumption leading to higher yields of these compounds. This approach showcases the potential of using one-carbon gases as substrates in bioprocesses for generating valuable bioproducts, providing a sustainable and cost-effective alternative to more conventional feedstocks and substrates, such as sugars.

Applications of synthetic yeast consortia for the production of native and non-native chemicals

The application of microbial consortia is a new approach in synthetic biology. Synthetic yeast consortia, simple or complex synthetic mixed cultures, have been used for the production of various metabolites. Cooperation between the members of a consortium and cross-feeding can be applied to create stable microbial communication. These consortia can: consume a variety of substrates, perform more complex functions, produce metabolites in high titer, rate, and yield (TRY), and show higher stability during industrial fermentations. Due to the new research context of synthetic consortia, few yeasts were used to build these consortia, including Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. Here, application of the yeasts for design of synthetic microbial consortia and their advantages and bottlenecks for effective and robust production of valuable metabolites from bioresource, including: cellulose, xylose, glycerol and so on, have been reviewed. Key trends and challenges are also discussed for the future development of synthetic yeast consortia.

Engineering peroxisomal biosynthetic pathways for maximization of triterpene production in Yarrowia lipolytica

Constructing efficient cell factories for product synthesis is frequently hampered by competing pathways and/or insufficient precursor supply. This is particularly evident in the case of triterpenoid biosynthesis in Yarrowia lipolytica, where squalene biosynthesis is tightly coupled to cytosolic biosynthesis of sterols essential for cell viability. Here, we addressed this problem by reconstructing the complete squalene biosynthetic pathway, starting from acetyl-CoA, in the peroxisome, thus harnessing peroxisomal acetyl-CoA pool and sequestering squalene synthesis in this organelle from competing cytosolic reactions. This strategy led to increasing the squalene levels by 1,300-fold relatively to native cytosolic synthesis. Subsequent enhancement of the peroxisomal acetyl-CoA supply by two independent approaches, 1) converting cellular lipid pool to peroxisomal acetyl-CoA and 2) establishing an orthogonal acetyl-CoA shortcut from CO2-derived acetate in the peroxisome, further significantly improved local squalene accumulation. Using these approaches, we constructed squalene-producing strains capable of yielding 32.8 g/L from glucose, and 31.6 g/L from acetate by employing a cofeeding strategy, in bioreactor fermentations. Our findings provide a feasible strategy for protecting intermediate metabolites that can be claimed by multiple reactions by engineering peroxisomes in Y. lipolytica as microfactories for the production of such intermediates and in particular acetyl-CoA-derived metabolites.

Application of New Yarrowia lipolytica Transformants in Production of Citrates and Erythritol from Glycerol

Citric acid and erythritol are obtained on an industrial scale using biotechnological methods. Due to the growing market demand for these products, research is underway to improve the process economics by introducing new microorganisms, in particular of the species Yarrowia lipolytica. The aim of this study was to evaluate transformants of Y. lipolytica for growth and ability to overproduce citric acids and erythritol from glycerol. The transformants were constructed by overexpressing glycerol kinase, methylcitrate synthase and mitochondrial succinate-fumarate transporter in the mutant Wratislavia 1.31. Next, strains were assessed for biosynthesis of citrate (pH 5.5; nitrogen limitation) and erythritol (pH 3.0; high osmotic pressure) from glycerol. Regardless of culture conditions strains, 1.31.GUT1/6 and 1.31.GUT1/6.CIT1/3 exhibited high rates of substrate utilization. Under conditions favoring citrate biosynthesis, both strains produced several percent more citrates, accompanied by higher erythritol production compared to the parental strain. During erythritol biosynthesis, the strain 1.31.GUT1/6.CIT1/3.E34672g obtained as a result of co-expression of all three genes stood out, producing 84.0 g/L of erythritol with yield and productivity of 0.54 g/g and 0.72 g/Lh, respectively, which places it in the group of the highest-ranked producers of erythritol among Y. lipolytica species.

'Mother(Nature) knows best' - hijacking nature-designed transcriptional programs for enhancing stress resistance and protein production in Yarrowia lipolytica; presentation of YaliFunTome database

BACKGROUND

In the era of rationally designed synthetic biology, heterologous metabolites production, and other counter-nature engineering of cellular metabolism, we took a step back and recalled that 'Mother(-Nature) knows best'. While still aiming at synthetic, non-natural outcomes of generating an 'over-production phenotype' we dug into the pre-designed transcriptional programs evolved in our host organism-Yarrowia lipolytica, hoping that some of these fine-tuned orchestrated programs could be hijacked and used. Having an interest in the practical outcomes of the research, we targeted industrially-relevant functionalities-stress resistance and enhanced synthesis of proteins, and gauged them over extensive experimental design's completion.

RESULTS

Technically, the problem was addressed by screening a broad library of over 120 Y. lipolytica strains under 72 combinations of variables through a carefully pre-optimized high-throughput cultivation protocol, which enabled actual phenotype development. The abundance of the transcription program elicitors-transcription factors (TFs), was secured by their overexpression, while challenging the strains with the multitude of conditions was inflicted to impact their activation stratus. The data were subjected to mathematical modeling to increase their informativeness. The amount of the gathered data prompted us to present them in the form of a searchable catalog - the YaliFunTome database ( https://sparrow.up.poznan.pl/tsdatabase/ )-to facilitate the withdrawal of biological sense from numerical data. We succeeded in the identification of TFs that act as omni-boosters of protein synthesis, enhance resistance to limited oxygen availability, and improve protein synthesis capacity under inorganic nitrogen provision.

CONCLUSIONS

All potential users are invited to browse YaliFunTome in the search for homologous TFs and the TF-driven phenotypes of interest.

Multidimensional Optimization of Saccharomyces cerevisiae for Carotenoid Overproduction

Microbial synthesis of carotenoids is a highly desirable alternative to plant extraction and chemical synthesis. In this study, we investigated multidimensional strategies to improve the carotenoid synthesis in the industrial workhorse of Saccharomyces cerevisiae. First, we rewired the yeast central metabolism by optimizing non-oxidative glycolysis pathway for an improved acetyl-CoA supply. Second, we restricted the consumption of farnesyl pyrophosphate (FPP) by the down-regulation of squalene synthase using the PEST degron. Third, we further explored the human lipid binding/transfer protein saposin B (hSapB)-mediated metabolic sink for an enhanced storage of lipophilic carotenoids. Last, the copper-induced GAL expression system was engineered to function in the yeast-peptone-dextrose medium for an increased biomass accumulation. By combining the abovementioned strategies, the final engineered yeast produced 166.79 ± 10.43 mg/l β-carotene in shake flasks, which was nearly 5-fold improvement of the parental carotenoid-producing strain. Together, we envision that multidimensional strategies reported here might be applicable to other hosts for the future industrial development of carotenoid synthesis from renewable feedstocks.

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

Microbial cell factories have shown great potential for industrial production with the benefit of being environmentally friendly and sustainable. Yarrowia lipolytica is a promising and superior non-model host for biomanufacturing due to its cumulated advantages compared to model microorganisms, such as high fluxes of metabolic precursors (acetyl-CoA and malonyl-CoA) and its naturally hydrophobic microenvironment. However, although diverse compounds have been synthesized in Y. lipolytica cell factories, most of the relevant studies have not reached the level of industrialization and commercialization due to a number of remaining challenges, including unbalanced metabolic flux, conflict between cell growth and product synthesis, and cytotoxic effects. Here, various metabolic engineering strategies for solving the challenges are summarized, which is developing fast and extremely conducive to rational design and reconstruction of robust Y. lipolytica cell factories for advanced biomanufacturing. Finally, future engineering efforts for enhancing the production efficiency of this platform strain are highlighted.

Genome Editing, Transcriptional Regulation, and Forward Genetic Screening Using CRISPR-Cas12a Systems in Yarrowia lipolytica

Class II Type V endonucleases have increasingly been adapted to develop sophisticated and easily accessible synthetic biology tools for genome editing, transcriptional regulation, and functional genomic screening in a wide range of organisms. One such endonuclease, Cas12a, presents itself as an attractive alternative to Cas9-based systems. The ability to mature its own guide RNAs (gRNAs) from a single transcript has been leveraged for easy multiplexing, and its lack of requirement of a tracrRNA element, also allows for short gRNA expression cassettes. To extend these functionalities into the industrially relevant oleaginous yeast Yarrowia lipolytica, we developed a set of CRISPR-Cas12a vectors for easy multiplexed gene knockout, repression, and activation. We further extended the utility of this CRISPR-Cas12a system to functional genomic screening by constructing a genome-wide guide library targeting every gene with an eightfold coverage. Pooled CRISPR screens conducted with this library were used to profile Cas12a guide activities and develop a machine learning algorithm that could accurately predict highly efficient Cas12a gRNA. In this protocols chapter, we first present a method by which protein coding genes may be functionally disrupted via indel formation with CRISPR-Cas12a systems. Further, we describe how Cas12a fused to a transcriptional regulator can be used in conjunction with shortened gRNA to achieve transcriptional repression or activation. Finally, we describe the design, cloning, and validation of a genome-wide library as well as a protocol for the execution of a pooled CRISPR screen, to determine guide activity profiles in a genome-wide context in Y. lipolytica. The tools and strategies discussed here expand the list of available synthetic biology tools for facile genome engineering in this industrially important host.

Integrated fermentative process for lipid and β-carotene production from acetogenic syngas fermentation using an engineered oleaginous Yarrowia lipolytica yeast

An engineered Yarrowia lipolytica strain was successfully employed to produce β-carotene and lipids from acetic acid, a product of syngas fermentation by Clostridium aceticum. The strain showed acetic acid tolerance up to concentrations of 20 g/L. Flask experiments yielded a peak lipid content of 33.7 % and β-carotene concentration of 13.6 mg/g under specific nutrient conditions. The study also investigated pH effects on production in bioreactors, revealing optimal lipid and β-carotene contents at pH 6.0, reaching 22.9 % and 44 mg/g, respectively. Lipid profiles were consistent across experiments, with C18:1 being the dominant compound at approximately 50 %. This research underscores a green revolution in bioprocessing, showing how biocatalysts can convert syngas, a potentially polluting byproduct, into valuable β-carotene and lipids with a Y. lipolytica strain.

Sequential bioconversion of C1-gases (CO, CO2, syngas) into lipids, through the carboxylic acid platform, with Clostridium aceticum and Rhodosporidium toruloides

Syngas (CO, CO2, H2) was effectively bioconverted into lipids in a two-stage process. In the first stage, C1-gases were bioconverted into acetic acid by the acetogenic species Clostridium aceticum through the Wood-Ljungdahl metabolic pathway in a stirred tank bioreactor, reaching a maximum acetic acid concentration of 11.5 g/L, with a production rate of 0.05 g/L·h. Throughout this experiment, samples were extracted at different periods, i.e., different concentrations, to be used in the second stage, aiming at the production of lipids from acetic acid. The yeast Rhodosporidium toruloides, inoculated in the acetogenic medium, was able to efficiently accumulate lipids from acetic acid generated in the first stage. The best results, in terms of lipid content, dry biomass, biomass yield (Y(X/S)) and lipid yield (Y(L/S)) were 39.5% g/g dry cell weight, 3 g/L, 0.35 and 0.107, respectively. In terms of abundance, the lipid profile followed the order: C18:1 > C16:0 > C18:2 > C18:0 > Others. Experiments were also performed to determine the toxicity exerted by high concentrations of acetic acid on R. toruloides, resulting in inhibition at initial acid concentrations around 18 g/L leading to a higher lag phase and being lethal to the yeast at initial acetic acid concentrations around 22 g/L and above. This research paves the way for a novel method of growing oleaginous yeasts to produce sustainable biofuels from syngas or C1-pollutant gases.

Metabolic Engineering of Pichia pastoris for High-Level Production of Lycopene

Lycopene is widely used in cosmetics, food, and nutritional supplements. Microbial production of lycopene has been intensively studied. However, few metabolic engineering studies on Pichia pastoris have been aimed at achieving high-yield lycopene production. In this study, the CRISPR/Cpf1-based gene repression system was developed and the gene editing system was optimized, which were applied to improve lycopene production successfully. In addition, the sterol regulatory element-binding protein SREBP (Sre) was used for the regulation of lipid metabolic pathways to promote lycopene overproduction in P. pastoris for the first time. The final engineered strain produced lycopene at 7.24 g/L and 75.48 mg/g DCW in fed-batch fermentation, representing the highest lycopene yield in P. pastoris reported to date. These findings provide effective strategies for extended metabolic engineering assisted by the CRISPR/Cpf1 system and new insights into metabolic engineering through transcriptional regulation of related metabolic pathways to enhance carotenoid production in P. pastoris.

Coproduction of Phase-Separated Carotenoids and β-Farnesene as a Yeast Biomass Valorization Strategy

Valorization, the process whereby waste materials are converted into more valuable products, is rarely practiced in industrial fermentation. We developed a model valorization system whereby Saccharomyces cerevisiae that had previously been engineered to produce high concentrations (>100 g/L) of extracellular β-farnesene was further engineered to simultaneously produce intracellular carotenoids, both products being isoprenoids. Thus, a single fermentation generates two valuable products, namely, β-farnesene in the liquid phase and carotenoids in the solid biomass phase. Initial attempts to produce high levels of canthaxanthin (a ketocarotenoid used extensively in animal feed) in a β-farnesene production strain negatively impacted both biomass growth and β-farnesene production. A refined approach used a promoter titration strategy to reduce β-carotene production to a level that had minimal impact on growth and β-farnesene production in fed-batch fermentations and then engineered the resulting strain to produce canthaxanthin. Further optimization of canthaxanthin coproduction used a bioprospecting approach to identify ketolase enzymes that maximized conversion of β-carotene to canthaxanthin. Finally, we demonstrated that β-carotene is not present in the extracellular β-farnesene at a significant concentration and that which is present can be removed by a simple distillation, indicating that β-farnesene (the primary fermentation product) purity is unaffected by coproduction of carotenoids.

The apocarotenoid production in microbial biofactories: An overview

Carotenoids are a vast group of natural pigments that come in a variety of colors ranging from red to orange. Apocarotenoids are derived from these carotenoids, which are hormones, pigments, retinoids, and volatiles employed in the textiles, cosmetics, pharmaceutical, and food industries. Due to the high commercial value and poor natural host abundance, they are significantly undersupplied. Microbes like Saccharomyces cerevisiae and Escherichia coli act as heterologous hosts for apocarotenoid production. This article briefly reviews categories of apocarotenoids, their biosynthetic pathway commencing from the MVA and MEP, its significance, the tool enzymes for apocarotenoid biosynthesis like CCDs, their biotechnological production in microbial factories, and future perspectives.

Microbial production of nutraceuticals: Metabolic engineering interventions in phenolic compounds, poly unsaturated fatty acids and carotenoids synthesis

Nutraceuticals have attained substantial attention due to their health-boosting or disease-prevention characteristics. Growing awareness about the potential of nutraceuticals for the prevention and management of diseases affecting human has led to an increase in the market value of nutraceuticals in several billion dollars. Nevertheless, limitations in supply and isolation complications from plants, animals or fungi, limit the large-scale production of nutraceuticals. Microbial engineering at metabolic level has been proved as an environment friendly substitute for the chemical synthesis of nutraceuticals. Extensively used microbial systems such as E. coli and S. cerevisiae have been modified as versatile cell factories for the synthesis of diverse nutraceuticals. This review describes current interventions in metabolic engineering for synthesising some of the therapeutically important nutraceuticals (phenolic compounds, polyunsaturated fatty acids and carotenoids). We focus on the interventions in enhancing product yield through engineering at gene level or pathway level.

Concomitant Production of Erythritol and β-Carotene by Engineered Yarrowia lipolytica

While the expansion of the erythritol production industry has resulted in unprecedented production of yeast cells, it also suffers from a lack of effective utilization. β-Carotene is a value-added compound that can be synthesized by engineered Yarrowia lipolytica. Here, we first evaluated the production performance of erythritol-producing yeast strains under two different morphologies and then successfully constructed a chassis with yeast-like morphology by deleting Mhy1 and Cla4 genes. Subsequently, β-carotene synthesis pathway genes, CarRA and CarB from Blakeslea trispora, were introduced to construct the β-carotene and erythritol coproducing Y. lipolytica strain ylmcc. The rate-limiting genes GGS1 and tHMG1 were overexpressed to increase the β-carotene yield by 45.32-fold compared with the strain ylmcc. However, increased β-carotene accumulation led to prolonged fermentation time; therefore, transporter engineering through overexpression of YTH1 and YTH3 genes was used to alleviate fermentation delays. Using batch fermentation in a 3 L bioreactor, this engineered Y. lipolytica strain produced erythritol with production, yield, and productivity values of 171 g/L, 0.56 g/g glucose, and 2.38 g/(L·h), respectively, with a concomitant β-carotene yield of 47.36 ± 0.06 mg/g DCW. The approach presented here improves the value of erythritol-producing cells and offers a low-cost technique to obtain hydrophobic terpenoids.

Combining Metabolic Engineering and Lipid Droplet Storage Engineering for Improved α-Bisabolene Production in Yarrowia Lipolytica

Bisabolene is a bioactive sesquiterpene with a wide range of applications in food, cosmetics, medicine, and aviation fuels. Microbial production offers a green, efficient, and sustainable alternative. In this study, we focused on improving the titers of α-bisabolene in Yarrowia lipolytica by applying two strategies, (i) optimizing the metabolic flux of α-bisabolene biosynthetic pathway and (ii) sequestering α-bisabolene in lipid droplet, thus alleviating its inherent toxicity to host cells. We showed that overexpression of DGA1 and OLE1 to increase lipid content and unsaturated fatty acid levels was essential for boosting the α-bisabolene synthesis when supplemented with auxiliary carbon sources. The final engineered strain Po1gαB10 produced 1954.3 mg/L α-bisabolene from the waste cooking oil under shake flask fermentation, which was 96-fold higher than the control strain Po1gαB0. At the time of writing, our study represents the highest reported α-bisabolene titer in the engineered Y. lipolytica cell factory. This work describes novel strategies to improve the bioproduction of α-bisabolene that potentially may be applicable for other high-value terpene products.

Compound K Production: Achievements and Perspectives

Compound K (CK) is one of the major metabolites found in mammalian blood and organs following oral administration of Panax plants. CK, also known as minor ginsenoside, can be absorbed in the systemic circulation. It has garnered significant attention in healthcare and medical products due to its pharmacological activities, such as antioxidation, anticancer, antiproliferation, antidiabetics, neuroprotection, and anti-atherogenic activities. However, CK is not found in natural ginseng plants but in traditional chemical synthesis, which uses toxic solvents and leads to environmental pollution during the harvest process. Moreover, enzymatic reactions are impractical for industrial CK production due to low yield and high costs. Although CK could be generated from major ginsenosides, most ginsenosides, including protopanaxatriol-oleanane and ocotillol-type, are not converted into CK by catalyzing β-glucosidase. Therefore, microbial cell systems have been used as a promising solution, providing a safe and efficient approach to CK production. This review provides a summary of various approaches for the production of CK, including chemical and enzymatic reactions, biotransformation by the human intestinal bacteria and endophytes as well as engineered microbes. Moreover, the approaches for CK production have been discussed to improve the productivity of target compounds.

Transcription factors enhancing synthesis of recombinant proteins and resistance to stress in Yarrowia lipolytica

Resistance to environmental stress and synthesis of recombinant proteins (r-Prots) are both complex, strongly interconnected biological traits relying on orchestrated contribution of multiple genes. This, in turn, makes their engineering a challenging task. One of the possible strategies is to modify the operation of transcription factors (TFs) associated with these complex traits. The aim of this study was to examine the potential implications of selected five TFs (HSF1-YALI0E13948g, GZF1-YALI0D20482g, CRF1-YALI0B08206g, SKN7-YALI0D14520g, and YAP-like-YALI0D07744g) in stress resistance and/or r-Prot synthesis in Yarrowia lipolytica. The selected TFs were over-expressed or deleted (OE/KO) in a host strain synthesizing a reporter r-Prot. The strains were subjected to phenotype screening under different environmental conditions (pH, oxygen availability, temperature, and osmolality), and the obtained data processing was assisted by mathematical modeling. The results demonstrated that growth and the r-Prot yields under specific conditions can be significantly increased or decreased due to the TFs' engineering. Environmental factors "awakening" individual TFs were indicated, and their contribution was mathematically described. For example, OE of Yap-like TF was proven to alleviate growth retardation under high pH, while Gzf1 and Hsf1 were shown to serve as universal enhancers of r-Prot production in Y. lipolytica. On the other hand, KO of SKN7 and HSF1 disabled growth under hyperosmotic stress. This research demonstrates the usefulness of the TFs engineering approach in the manipulation of complex traits and evidences newly identified functions of the studied TFs. KEY POINTS: • Function and implication in complex traits of 5 TFs in Y. lipolytica were studied. • Gzf1 and Hsf1 are the universal r-Prots synthesis enhancers in Y. lipolytica. • Yap-like TF's activity is pH-dependent; Skn7 and Hsf1 act in osmostress response.

Industrially Important Fungal Carotenoids: Advancements in Biotechnological Production and Extraction

Carotenoids are lipid-soluble compounds that are present in nature, including plants and microorganisms such as fungi, certain bacteria, and algae. In fungi, they are widely present in almost all taxonomic classifications. Fungal carotenoids have gained special attention due to their biochemistry and the genetics of their synthetic pathway. The antioxidant potential of carotenoids may help fungi survive longer in their natural environment. Carotenoids may be produced in greater quantities using biotechnological methods than by chemical synthesis or plant extraction. The initial focus of this review is on industrially important carotenoids in the most advanced fungal and yeast strains, with a brief description of their taxonomic classification. Biotechnology has long been regarded as the most suitable alternative way of producing natural pigment from microbes due to their immense capacity to accumulate these pigments. So, this review mainly presents the recent progress in the genetic modification of native and non-native producers to modify the carotenoid biosynthetic pathway for enhanced carotenoid production, as well as factors affecting carotenoid biosynthesis in fungal strains and yeast, and proposes various extraction methods to obtain high yields of carotenoids in an attempt to find suitable greener extraction methods. Finally, a brief description of the challenges regarding the commercialization of these fungal carotenoids and the solution is also given.

Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll

Xanthophyll is an oxidated version of carotenoid. It presents significant value to the pharmaceutical, food, and cosmetic industries due to its specific antioxidant activity and variety of colors. Chemical processing and conventional extraction from natural organisms are still the main sources of xanthophyll. However, the current industrial production model can no longer meet the demand for human health care, reducing petrochemical energy consumption and green sustainable development. With the swift development of genetic metabolic engineering, xanthophyll synthesis by the metabolic engineering of model microorganisms shows great application potential. At present, compared to carotenes such as lycopene and β-carotene, xanthophyll has a relatively low production in engineering microorganisms due to its stronger inherent antioxidation, relatively high polarity, and longer metabolic pathway. This review comprehensively summarized the progress in xanthophyll synthesis by the metabolic engineering of model microorganisms, described strategies to improve xanthophyll production in detail, and proposed the current challenges and future efforts needed to build commercialized xanthophyll-producing microorganisms.

Focus and Insights into the Synthetic Biology-Mediated Chassis of Economically Important Fungi for the Production of High-Value Metabolites

Substantial progress has been achieved and knowledge gaps addressed in synthetic biology-mediated engineering of biological organisms to produce high-value metabolites. Bio-based products from fungi are extensively explored in the present era, attributed to their emerging importance in the industrial sector, healthcare, and food applications. The edible group of fungi and multiple fungal strains defines attractive biological resources for high-value metabolites comprising food additives, pigments, dyes, industrial chemicals, and antibiotics, including other compounds. In this direction, synthetic biology-mediated genetic chassis of fungal strains to enhance/add value to novel chemical entities of biological origin is opening new avenues in fungal biotechnology. While substantial success has been achieved in the genetic manipulation of economically viable fungi (including Saccharomyces cerevisiae) in the production of metabolites of socio-economic relevance, knowledge gaps/obstacles in fungal biology and engineering need to be remedied for complete exploitation of valuable fungal strains. Herein, the thematic article discusses the novel attributes of bio-based products from fungi and the creation of high-value engineered fungal strains to promote yield, bio-functionality, and value-addition of the metabolites of socio-economic value. Efforts have been made to discuss the existing limitations in fungal chassis and how the advances in synthetic biology provide a plausible solution.

Simultaneous Production of Cellulase and β-Carotene in the Filamentous Fungus Trichoderma reesei

β-Carotene is an indispensable additive in beverage, cosmetic, feed, and pharmaceutical production. The fermentation industry annually generates abundant waste mycelia from Trichoderma reesei (T. reesei), a pivotal industrial strain for cellulase and heterologous protein production. In this study, we constructed a T. reesei cell factory for β-carotene production for the first time. Four key enzymes, CarRP, CarB, GGS1/CrtE, and HMG1, were overexpressed in T. reesei. The concentrations of medium components, including tryptone and glucose, were optimized. The modified strain accumulated β-carotene at a titer of 218.8 mg/L in flask culture. We achieved cellulase production (FPase, 22.33 IU/mL) with the concomitant production of β-carotene (286.63 mg/L) from T. reesei in a jar. Overall, this study offers a novel and unique approach to address the costly waste mycelium management process using T. reesei industrial strains that simultaneously produce proteins and carotenoids.

Research progress of engineering microbial cell factories for pigment production

Pigments are widely used in people's daily life, such as food additives, cosmetics, pharmaceuticals, textiles, etc. In recent years, the natural pigments produced by microorganisms have attracted increased attention because these processes cannot be affected by seasons like the plant extraction methods, and can also avoid the environmental pollution problems caused by chemical synthesis. Synthetic biology and metabolic engineering have been used to construct and optimize metabolic pathways for production of natural pigments in cellular factories. Building microbial cell factories for synthesis of natural pigments has many advantages, including well-defined genetic background of the strains, high-density and rapid culture of cells, etc. Until now, the technical means about engineering microbial cell factories for pigment production and metabolic regulation processes have not been systematically analyzed and summarized. Therefore, the studies about construction, modification and regulation of synthetic pathways for microbial synthesis of pigments in recent years have been reviewed, aiming to provide an up-to-date summary of engineering strategies for microbial synthesis of natural pigments including carotenoids, melanins, riboflavins, azomycetes and quinones. This review should provide new ideas for further improving microbial production of natural pigments in the future.

A review of synthetic biology tools in Yarrowia lipolytica

Yarrowia lipolytica is a non-conventional oleaginous yeast with great potential for industrial production. Y. lipolytica has a high propensity for flux through tricarboxylic acid cycle intermediates. Therefore, this host is currently being developed as a workhorse, and is rapidly emerging in biotechnology fields, especially for industrial chemical production, whole-cell bioconversion, and the treatment and recycling of industrial waste. In recent studies, Y. lipolytica has been rewritten and introduced with non-native metabolites of certain compounds of interest owing to the advancement in synthetic biology tools. In this review, we collate recent progress to present a detailed and insightful summary of the major developments in synthetic biology tools and techniques for Y. lipolytica, including promoters, terminators, selection markers, autonomously replicating sequences, DNA assembly techniques, genome editing techniques, and subcellular organelle engineering. This comprehensive overview would be a useful resource for future genetic engineering studies to improve the yield of desired metabolic products in Y. lipolytica.