Production of the carotenoids lycopene, beta-carotene, and astaxanthin in the food yeast Candida utilis

Last Decade Insights in Exploiting Marine Microorganisms as Sources of New Bioactive Natural Products

Marine microorganisms have emerged as prolific sources of bioactive natural products, offering a large chemical diversity and a broad spectrum of biological activities. Over the past decade, significant progress has been made in discovering and characterizing these compounds, pushed by technological innovations in genomics, metabolomics, and bioinformatics. Furthermore, innovative isolation and cultivation approaches have improved the isolation of rare and difficult-to-culture marine microbes, leading to the identification of novel secondary metabolites. Advances in synthetic biology and metabolic engineering have further optimized natural product yields and the generation of novel compounds with improved bioactive properties. This review highlights key developments in the exploitation of marine bacteria, fungi, and microalgae for the discovery of novel natural products with potential applications in diverse fields, underscoring the immense potential of marine microorganisms in the growing Blue Economy sector.

Characterization of cotton stalk as a lignocellulosic feedstock for single-cell protein production

Cotton stalk, an important by-product of cotton farming, is challenging in lignocellulosic feedstock application due to the limited understanding of their compositional and lignin structural characteristics. This study elucidates the composition of lignocellulose components and fundamental lignin structural features of cotton stalk. Lignocellulosic hydrolysates were prepared from various cotton stalk parts and used for single-cell protein production. As a proof of concept, cotton stalk hydrolysates were successfully converted into single-cell protein using the superior microbial host, Candida utilis ACCC20060, owing to its favorable sugar consumption efficiency and high protein quality. The highest SCP concentration of 5.74 g/L was obtained, yielding 0.23 g/g from the lignocellulose-derived sugars released from cotton stalk roots. This study provides valuable references for cotton stalk utilization toward lignocellulosic feedstock application and introduces a promising microbial host for single-cell protein production from such feedstocks.

Phytochemical Content of Malus floribunda: In Vitro and Molecular Docking Studies

Malus floribunda Siebold ex Van Houtte is a plant planted for landscaping, and its sour and red fruits have been seen to be frequently used in the treatment of diabetes, making vinegar marmalade, and producing natural food dyes. Apart from these usage areas of this plant, it is aimed at determining the phytochemical content. For this purpose, plant parts (fruit, leaf, and branch) were examined. The antioxidant capacity (vitamins A, E, and C, lycopene, beta-carotene, total phenolic and flavonoid amounts, and DPPH radical scavenging effect), antimicrobial activity (agar well diffusion method, minimum inhibitory concentration-MIC), and GC-MS contents of plant parts were determined. High-performance liquid chromatography (HPLC), spectrophotometers, and gas chromatography/mass spectroscopy (GC-MS) methods were used in the study. It was determined that M. floribunda fruit is rich in lycopene, beta-carotene, and antioxidant vitamins and contains many biomolecules. In addition, it was concluded that the extracts of different parts of the plant have antimicrobial activity. This study has revealed the idea that this plant, whose phytochemical, antioxidant, and antimicrobial content has been determined, can be used as a bioactive substance equivalent to antibiotics in medicine, the food industry, and human nutrition. In addition, it is expected that the study will contribute to the plant literature. Molecular docking studies were performed to evaluate the binding interactions between the compound and human peroxiredoxin 5 and S. aureus. Both in vitro and in silico results indicated that synthesized extracts could act as potent antioxidant and antimicrobial agents.

Arts, cultural heritage, sciences, and micro-/bio-/technology: Impact of biomaterials and biocolorants from antiquity till today!

Nature has inspired and provided humans with ideas, concepts, and thoughts on design, art, and performance for millennia. From early societies when humankind often took shelter in caves, until today, many materials and colorants to express feelings or communicate with one another were derived from plants, animals, or microbes. In this manuscript, an overview of these natural products used in the creation of art is given, from paintings on rocks to fashionable dresses made from bacterial cellulose. Besides offering many examples of art works, the origin and application of various biomaterials and colorants are discussed. While many facets of our daily lives have changed over millennia, one certainty has been that humans have an intrinsic need to conceptualize and create to express themselves. Driven by technological advances in the past decades and in the light of global warming, new and often more sustainable materials and colorants have been discovered and implemented. The impact of art on human societies remains relevant and powerful.

ONE-SENTENCE SUMMARY

This manuscript discusses the use of biomaterials and biocolorants in art from a historical perspective, spanning 37,000 bc until today.

Development of CRISPR/Cas9-Based Genome Editing Tools for Polyploid Yeast Cyberlindnera jadinii and Its Application in Engineering Heterologous Steroid-Producing Strains

In this study, a suite of efficient CRISPR/Cas9 tools was developed to overcome the genetic manipulation challenges posed by the polyploid genome of industrial yeast Cyberlindnera jadinii. The developed CRISPR/Cas9 system can achieve a 100% single-gene knockdown efficiency in strain NBRC0988. Moreover, the integration of a single exogenous gene into the target locus using a 50 bp homology arm achieved near-100% efficiency. The efficiency of simultaneous integration of three genes into the chromosome is strongly influenced by the length of the homology arm, with the highest integration efficiency of 62.5% obtained when selecting a homology arm of about 500 bp. By utilizing the CRISPR/Cas system, this study demonstrated the potential of C. jadinii in producing heterologous sterols. Through shake-flask fermentation, the engineered strains produced 92.1 and 81.8 mg/L of campesterol and cholesterol, respectively. Furthermore, the production levels of these two sterols were further enhanced through high-cell-density fed-batch fermentation in a 5 L bioreactor. The highest titer of campesterol reached 807 mg/L [biomass OD600 = 294, productivity of 6.73 mg/(L·h)]. The titer of cholesterol reached 1.52 g/L [biomass OD600 = 380, productivity of 9.06 mg/(L·h)], marking the first gram-scale production of steroidal compounds in C. jadinii.

Natural Pigments Production and Their Application in Food, Health and Other Industries

In addition to fulfilling their function of giving color, many natural pigments are known as interesting bioactive compounds with potential health benefits. These compounds have various applications. In recent times, in the food industry, there has been a spread of natural pigment application in many fields, such as pharmacology and toxicology, in the textile and printing industry and in the dairy and fish industry, with almost all major natural pigment classes being used in at least one sector of the food industry. In this scenario, the cost-effective benefits for the industry will be welcome, but they will be obscured by the benefits for people. Obtaining easily usable, non-toxic, eco-sustainable, cheap and biodegradable pigments represents the future in which researchers should invest.

Yeast Carotenoids: Cost-Effective Fermentation Strategies for Health Care Applications

Carotenoid production from oleaginous red yeast has been considered as a safe alternative to chemically synthesized carotenoids commonly used in the food industry, since plant-based carotenoids are expensive and an irregular source for obtaining pigments. This is a summative review on the factors affecting carotenoid production, cost-effective production strategies using various inexpensive feedstock, metabolic engineering, and strain improvisation. The review specially highlights the various potential applications of carotenoids as anti-microbial, anti-viral, antioxidant, anti-cancerous, anti-malarial agents, etc. The importance of such natural and easily available resources for prevention, evasion, or cure of emerging diseases and their plausible nutraceutical effect demands exhaustive research in this area.

Advances in the synthesis of three typical tetraterpenoids including β-carotene, lycopene and astaxanthin

Carotenoids are natural pigments that widely exist in nature. Due to their excellent antioxidant, anticancer and anti-inflammatory properties, carotenoids are commonly used in food, medicine, cosmetic and other fields. At present, natural carotenoids are mainly extracted from plants, algae and microorganisms. With the rapid development of metabolic engineering and molecular biology as well as the continuous in-depth study of carotenoids synthesis pathways, industrial microorganisms have showed promising applications in the synthesis of carotenoids. In this review, we introduced the properties of several carotenoids and their biosynthetic metabolism process. Then, the microorganisms synthesizing carotenoids through the natural and non-natural pathways and the extraction methods of carotenoids were summarized and compared. Meanwhile, the influence of substrates on the carotenoids production was also listed. The methods and strategies for achieving high carotenoid production are categorized to help with future research.

Carotenoids and Their Biosynthesis in Fungi

Carotenoids represent a class of pigmented terpenoids. They are distributed in all taxonomic groups of fungi. Most of the fungal carotenoids differ in their chemical structures to those from other organisms. The general function of carotenoids in heterotrophic organisms is protection as antioxidants against reactive oxygen species generated by photosensitized reactions. Furthermore, carotenoids are metabolized to apocarotenoids by oxidative cleavage. This review presents the current knowledge on fungal-specific carotenoids, their occurrence in different taxonomic groups, and their biosynthesis and conversion into trisporic acids. The outline of the different pathways was focused on the reactions and genes involved in not only the known pathways, but also suggested the possible mechanisms of reactions, which may occur in several non-characterized pathways in different fungi. Finally, efforts and strategies for genetic engineering to enhance or establish pathways for the production of various carotenoids in carotenogenic or non-carotenogenic yeasts were highlighted, addressing the most-advanced producers of each engineered yeast, which offered the highest biotechnological potentials as production systems.

Biotechnological advances for improving natural pigment production: a state-of-the-art review

In current years, natural pigments are facing a fast-growing global market due to the increase of people's awareness of health and the discovery of novel pharmacological effects of various natural pigments, e.g., carotenoids, flavonoids, and curcuminoids. However, the traditional production approaches are source-dependent and generally subject to the low contents of target pigment compounds. In order to scale-up industrial production, many efforts have been devoted to increasing pigment production from natural producers, via development of both in vitro plant cell/tissue culture systems, as well as optimization of microbial cultivation approaches. Moreover, synthetic biology has opened the door for heterologous biosynthesis of pigments via design and re-construction of novel biological modules as well as biological systems in bio-platforms. In this review, the innovative methods and strategies for optimization and engineering of both native and heterologous producers of natural pigments are comprehensively summarized. Current progress in the production of several representative high-value natural pigments is also presented; and the remaining challenges and future perspectives are discussed.

Bacterial and fungal communities of traditional fermented Chinese soybean paste (Doujiang) and their properties

Soybean paste (Doujiang) is one of the traditional fermented foods from China, fermented by various microorganisms. However, the microflora of Doujiang keeps little known. In this study, the microbial communities of seven kinds of representative Doujiang samples were investigated by both culture-independent and culture-dependent methods. We found that core OTUs among seven Doujiang samples were mainly from Bacillus, Pseudomonas, Candida, and Aspergillus according to Illumina sequencing. Every type of Doujiang sample harbored a different composition of microbial community. Doujiang LSJ and LBJ had the highest bacterial and fungal richness and diversity, respectively. The structure of microbial community was remarkably correlated with Doujiang properties-pH, and the content of total protein, soluble protein, amino acid, and total sugar (p < .05). Bacillus spp. were most frequently isolated bacterial species. Fungi of Monascus, Candida, and Aspergillus were also isolated. Eleven microbial strains showed high protease activities to degrade corn proteins, which can form obvious transparent hydrolytic circles in corn gluten meal medium plates. Therefore, microbial communities were supposed to tightly connect to Doujiang type and properties. It is possible to apply potential protein-degrading microbial strains to corn byproducts for protein production in the future study.

Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii

Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii.

Reprogramming microorganisms for the biosynthesis of astaxanthin via metabolic engineering

There is an increasing demand for astaxanthin in food, feed, cosmetics and pharmaceutical applications because of its superior anti-oxidative and coloring properties. However, naturally produced astaxanthin is expensive, mainly due to low productivity and limited sources. Reprogramming of microorganisms for astaxanthin production via metabolic engineering is a promising strategy. We primarily focus on the application of synthetic biology, enzyme engineering and metabolic engineering in enhancing the synthesis and accumulation of astaxanthin in microorganisms in this review. We also discuss the biosynthetic pathways of astaxanthin within natural producers, and summarize the achievements and challenges in reprogramming microorganisms for enhancing astaxanthin production. This review illuminates recent biotechnological advances in microbial production of astaxanthin. Future perspectives on utilization of new technologies for boosting microbial astaxanthin production are also discussed.

Turning a green alga red: engineering astaxanthin biosynthesis by intragenic pseudogene revival in Chlamydomonas reinhardtii

The green alga Chlamydomonas reinhardtii does not synthesize high-value ketocarotenoids like canthaxanthin and astaxanthin; however, a β-carotene ketolase (CrBKT) can be found in its genome. CrBKT is poorly expressed, contains a long C-terminal extension not found in homologues and likely represents a pseudogene in this alga. Here, we used synthetic redesign of this gene to enable its constitutive overexpression from the nuclear genome of C. reinhardtii. Overexpression of the optimized CrBKT extended native carotenoid biosynthesis to generate ketocarotenoids in the algal host causing noticeable changes the green algal colour to reddish-brown. We found that up to 50% of native carotenoids could be converted into astaxanthin and more than 70% into other ketocarotenoids by robust CrBKT overexpression. Modification of the carotenoid metabolism did not impair growth or biomass productivity of C. reinhardtii, even at high light intensities. Under different growth conditions, the best performing CrBKT overexpression strain was found to reach ketocarotenoid productivities up to 4.3 mg/L/day. Astaxanthin productivity in engineered C. reinhardtii shown here might be competitive with that reported for Haematococcus lacustris (formerly pluvialis) which is currently the main organism cultivated for industrial astaxanthin production. In addition, the extractability and bio-accessibility of these pigments were much higher in cell wall-deficient C. reinhardtii than the resting cysts of H. lacustris. Engineered C. reinhardtii strains could thus be a promising alternative to natural astaxanthin producing algal strains and may open the possibility of other tailor-made pigments from this host.

Structures of Astaxanthin and Their Consequences for Therapeutic Application

Reactive oxygen species (ROS) are continuously generated as a by-product of normal aerobic metabolism. Elevated ROS formation leads to potential damage of biological structures and is implicated in various diseases. Astaxanthin, a xanthophyll carotenoid, is a secondary metabolite responsible for the red-orange color of a number of marine animals and microorganisms. There is mounting evidence that astaxanthin has powerful antioxidant, anti-inflammatory, and antiapoptotic activities. Hence, its consumption can result in various health benefits, with potential for therapeutic application. Astaxanthin contains both a hydroxyl and a keto group, and this unique structure plays important roles in neutralizing ROS. The molecule quenches harmful singlet oxygen, scavenges peroxyl and hydroxyl radicals and converts them into more stable compounds, prevents the formation of free radicals, and inhibits the autoxidation chain reaction. It also acts as a metal chelator and converts metal prooxidants into harmless molecules. However, like many other carotenoids, astaxanthin is affected by the environmental conditions, e.g., pH, heat, or exposure to light. It is hence susceptible to structural modification, i.e., via isomerization, aggregation, or esterification, which alters its physiochemical properties. Here, we provide a concise overview of the distribution of astaxanthin in tissues, and astaxanthin structures, and their role in tackling singlet oxygen and free radicals. We highlight the effect of structural modification of astaxanthin molecules on the bioavailability and biological activity. These studies suggested that astaxanthin would be a promising dietary supplement for health applications.

Engineered Microbes for Pigment Production Using Waste Biomass

Agri-food waste biomass is the most abundant organic waste and has high valorisation potential for sustainable bioproducts development. These wastes are not only recyclable in nature but are also rich sources of bioactive carbohydrates, peptides, pigments, polyphenols, vitamins, natural antioxidants, etc. Bioconversion of agri-food waste to value-added products is very important towards zero waste and circular economy concepts. To reduce the environmental burden, food researchers are seeking strategies to utilize this waste for microbial pigments production and further biotechnological exploitation in functional foods or value-added products. Microbes are valuable sources for a range of bioactive molecules, including microbial pigments production through fermentation and/or utilisation of waste. Here, we have reviewed some of the recent advancements made in important bioengineering technologies to develop engineered microbial systems for enhanced pigments production using agri-food wastes biomass/by-products as substrates in a sustainable way.

The ploidy determination of the biotechnologically important yeast Candida utilis

Yeast Candida utilis is considered to be a potentially advantageous expression system for production of recombinant proteins utilizable for industrial and pharmaceutical purposes. As the scientific literature is not consistent in the ploidy of this yeast, in this work, we focused on resolving the problem via several methods such as the copy number determination of maltase gene by multiplex PCR, measuring α-glucosidase activity, the characterization of maltase gene copy number in deletion mutants using qPCR and flow cytometry. In context with the published data and results obtained in this study about the copy number of the maltase gene on C. utilis genome, we attempted to hypothesise and made conclusion about the ploidy of C. utilis. The results of this work, besides the biotechnological aspect, contribute to the elementary knowledge of C. utilis. The exact information about the ploidy or more specifically about the copy number of appropriate gene is essential for expression cassette dosage determination integrated into the chromosome of the host. In this study, we come to the conclusion that the maltase gene is present in C. utilis genome in four alleles, and in combination with flow cytometry, published information and the published genome sequences, the observations support the theory about tetraploidy of C. utilis.

Enhanced Lycopene Production in Escherichia coli by Expression of Two MEP Pathway Enzymes from Vibrio sp. Dhg

Microbial production is a promising method that can overcome major limitations in conventional methods of lycopene production, such as low yields and variations in product quality. Significant efforts have been made to improve lycopene production by engineering either the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway or mevalonate (MVA) pathway in microorganisms. To further improve lycopene production, it is critical to utilize metabolic enzymes with high specific activities. Two enzymes, 1-deoxy-d-xylulose-5-phosphate synthase (Dxs) and farnesyl diphosphate synthase (IspA), are required in lycopene production using MEP pathway. Here, we evaluated the activities of Dxs and IspA of Vibrio sp. dhg, a newly isolated and fast-growing microorganism. Considering that the MEP pathway is closely related to the cell membrane and electron transport chain, the activities of the two enzymes of Vibrio sp. dhg were expected to be higher than the enzymes of Escherichia coli. We found that Dxs and IspA in Vibrio sp. dhg exhibited 1.08-fold and 1.38-fold higher catalytic efficiencies, respectively. Consequently, the heterologous overexpression improved the specific lycopene production by 1.88-fold. Our findings could be widely utilized to enhance production of lycopene and other carotenoids.

Redirection of the Glycolytic Flux Enhances Isoprenoid Production in Saccharomyces cerevisiae

Sufficient supply of reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a prerequisite of the overproduction of isoprenoids and related bioproducts in Saccharomyces cerevisiae. Although S. cerevisiae highly depends on the oxidative pentose phosphate (PP) pathway to produce NADPH, its metabolic flux toward the oxidative PP pathway is limited due to the rigid glycolysis flux. To maximize NADPH supply for the isoprenoid production in yeast, upper glycolytic metabolic fluxes are reduced by introducing mutations into phosphofructokinase (PFK) along with overexpression of ZWF1 encoding glucose-6-phosphate (G6P) dehydrogenase. The PFK mutations (Pfk1 S724D and Pfk2 S718D) result in less glycerol production and more accumulation of G6P, which is a gateway metabolite toward the oxidative PP pathway. When combined with the PFK mutations, overexpression of ZWF1 caused substantial increases of [NADPH]/[NADP⁺ ] ratios whereas the effect of ZWF1 overexpression alone in the wild-type strain is not noticeable. Also, the introduction of ZWF1 overexpression and the PFK mutations into engineered yeast overexpressing acetyl-CoA C-acetyltransferase (ERG10), truncated HMG-CoA reductase isozyme 1 (tHMG1), and amorphadiene synthase (ADS) leads to a titer of 497 mg L^-1 of amorphadiene (3.7-fold over the parental strain). These results suggest that perturbation of upper glycolytic fluxes, in addition to ZWF1 overexpression, is necessary for efficient NADPH supply through the oxidative PP pathway and enhanced production of isoprenoids by engineered S. cerevisiae.

Microbial Pigments in the Food Industry-Challenges and the Way Forward

Developing new colors for the food industry is challenging, as colorants need to be compatible with a food flavors, safety, and nutritional value, and which ultimately have a minimal impact on the price of the product. In addition, food colorants should preferably be natural rather than synthetic compounds. Micro-organisms already produce industrially useful natural colorants such as carotenoids and anthocyanins. Microbial food colorants can be produced at scale at relatively low costs. This review highlights the significance of color in the food industry, why there is a need to shift to natural food colors compared to synthetic ones and how using microbial pigments as food colorants, instead of colors from other natural sources, is a preferable option. We also summarize the microbial derived food colorants currently used and discuss their classification based on their chemical structure. Finally, we discuss the challenges faced by the use and development of food grade microbial pigments and how to deal with these challenges, using advanced techniques including metabolic engineering and nanotechnology.

Insights into the role of bacteria in vitamin A biosynthesis: Future research opportunities

Significant efforts have been made to address the hidden hunger challenges due to iron, zinc, iodine, and vitamin A since the beginning of the 21st century. Prioritizing the vitamin A deficiency (VAD) disorders, many countries are looking for viable alternative strategies such as biofortification. One of the leading causes of VAD is the poor bioconversion of β-carotene into retinoids. This review is focused on the opportunities of bacterial biosynthesis of retinoids, in particular, through the gut microbiota. The proposed hypothesis starts with the premise that an animal can able to store and timely convert carotenoids into retinoids in the liver and intestinal tissues. This theory is experimental with many scientific insights. The syntrophic metabolism, potential crosstalk of bile acids, lipocalins and lipopolysaccharides of gut microbiota are reported to contribute significantly to the retinoid biosynthesis. The gut bacteria respond to these kinds of factors by genetic restructuring driven mainly by events like horizontal gene transfer. A phylogenetic analysis of β-carotene 15, 15'-mono (di) oxygenase enzymes among a selected group of prokaryotes and eukaryotes was carried out to validate the hypotheses. Shedding light on the probiotic strategies through non-genetically modified organism such as gut bacteria capable of synthesizing vitamin A would address the VAD disorders.

Selected Methods of Extracting Carotenoids, Characterization, and Health Concerns: A Review

Carotenoids are the most powerful nutrients (medicine) on earth due to their potent antioxidant properties. The ability of these tetraterpenoids in obviating human chronic ailments like cancer, cardiovascular disease, osteoporosis, and diabetes has drawn public attention toward these novel compounds. Conventionally, carotenoids have been extracted from plant materials and agro-industrial byproduct using different solvents, but these procedures result in contaminating the target compound (carotenoids) with extraction solvents. Furthermore, some utilized solvents are not safe and hence are harmful to the environment. This has attracted criticism from consumers, ecologists, environmentalists, and public health workers. However, there is clear consumer preference for carotenoids from natural origin without traces of extracting solvent. Therefore, this review seeks to discuss methods for higher recovery of pure carotenoids without contamination from a solvent. Methods such as enzyme-based extraction, supercritical fluid extraction, microwave-assisted extraction, Soxhlet extraction, ultrasonic extraction, and postextraction treatment (saponification) are discussed. Merits and demerits of these methods along with health concerns during intake of carotenoids were also considered.

Lycopene Production by Mated Fermentation of Blakeslea trispora

Lycopene is a carotenoid mainly present in red-colored fruits and vegetables. Its value in the pharmaceutical and food industry is linked to its benefits for the human health, including properties against cancer and cardiovascular diseases, and its use as a food colorant. Lycopene can be produced either by synthetic or natural means, but there is a preference for the second, since it is considered a more eco-friendly and less harmful process. Among natural methods for obtaining lycopene, microbial fermentation is a good alternative to extraction from plants that naturally contain lycopene, since it implies obtaining higher and more specific amounts of this carotenoid. This chapter describes lycopene production by fermentation of the fungus Blakeslea trispora, a naturally carotenoid producer, at 30 L scale. This procedure involves separated growth of the two sexual mating types of B. trispora during the vegetative stages and the use of a lycopene cyclase inhibitor to achieve lycopene accumulation during the production stage.

Discovery of Several Novel Targets that Enhance β-Carotene Production in Saccharomyces cerevisiae

β-Carotene is the precursor of vitamin A, and also exhibits multiple pharmaceutical functions by itself. In comparison to chemical synthesis, the production of β-carotene in microbes by metabolic engineering strategy is relatively inexpensive. Identifying genes enhancing β-carotene production in microbes is important for engineering a strain of producing higher yields of β-carotene. Most of previous efforts in identifying the gene targets have focused on the isoprenoid pathway where the β-carotene biosynthesis belongs. However, due to the complex interactions between metabolic fluxes, seemingly irrelevant genes that are outside the isoprenoid pathway might also affect β-carotene biosynthesis. To this end, here we provided an example that several novel gene targets, which are outside the isoprenoid pathway, have improving effects on β-carotene synthesis in yeast cells, when they were over-expressed. Among these targets, the class E protein of the vacuolar protein-sorting pathway (Did2) led to the highest improvement in β-carotene yields, which was 2.1-fold to that of the corresponding control. This improvement was further explained by the observation that the overexpression of the DID2 gene generally boosted the transcriptions of β-carotene pathway genes. The mechanism by which the other targets improve the production of β-carotene is discussed.

Microbial processing of fruit and vegetable wastes into potential biocommodities: a review

The review focuses on some of the high value-end biocommodities, such as fermented beverages, single-cell proteins, single-cell oils, biocolors, flavors, fragrances, polysaccharides, biopesticides, plant growth regulators, bioethanol, biogas and biohydrogen, developed from the microbial processing of fruit and vegetable wastes. Microbial detoxification of fruit and vegetable processing effluents is briefly described. The advances in genetic engineering of microorganisms for enhanced yield of the above-mentioned biocommodities are elucidated with selected examples. The bottleneck in commercialization, integrated approach for improved production, techno-economical feasibility and real-life uses of some of these biocommodities, as well as research gaps and future directions are discussed.

Iterative integration of multiple-copy pathway genes in Yarrowia lipolytica for heterologous β-carotene production

β-Carotene is a terpenoid molecule with high hydrophobicity that is often used as an additive in foods and feed. Previous work has demonstrated the heterologous biosynthesis of β-carotene from an intrinsic high flux of acetyl-CoA in 12 steps through 11 genes in Yarrowia lipolytica. Here, an efficient biosynthetic pathway capable of producing 100-fold more β-carotene than the baseline construct was generated using strong promoters and multiple gene copies for each of the 12 steps. Using fed-batch fermentation with an optimized medium, the engineered pathway could produce 4g/L β-carotene, which was stored in lipid droplets within engineered Y. lipolytica cells. Expansion of these cells for squalene production also demonstrated that Y. lipolytica could be an industrially relevant platform for hydrophobic terpenoid production.

Microbial production strategies and applications of lycopene and other terpenoids

Terpenoids are a large class of compounds that have far-reaching applications and economic value, particularly those most commonly found in plants; however, the extraction and synthesis of these compounds is often expensive and technically challenging. Recent advances in microbial metabolic engineering comprise a breakthrough that may enable the efficient, cost-effective production of these limited natural resources. Via the engineering of safe, industrial microorganisms that encode product-specific enzymes, and even entire metabolic pathways of interest, microbial-derived semisynthetic terpenoids may soon replace plant-derived terpenoids as the primary source of these valuable compounds. Indeed, the recent metabolic engineering of an Escherichia coli strain that produces the precursor to lycopene, a commercially and medically important compound, with higher yields than those in tomato plants serves as a successful example. Here, we review the recent developments in the metabolic engineering of microbes for the production of certain terpenoid compounds, particularly lycopene, which has been increasingly used in pharmaceuticals, nutritional supplements, and cosmetics. Furthermore, we summarize the metabolic engineering strategies used to achieve successful microbial production of some similar compounds. Based on this overview, there is a reason to believe that metabolic engineering comprises an optimal approach for increasing the production of lycopene and other terpenoids.

Development of GRAS strains for nutraceutical production using systems and synthetic biology approaches: advances and prospects

Nutraceuticals are food substances with medical and health benefits for humans. Limited by complicated procedures, high cost, low yield, insufficient raw materials, resource waste, and environment pollution, chemical synthesis and extraction are being replaced by microbial synthesis of nutraceuticals. Many microbial strains that are generally regarded as safe (GRAS) have been identified and developed for the synthesis of nutraceuticals, and significant nutraceutical production by these strains has been achieved. In this review, we systematically summarize recent advances in nutraceutical research in terms of physiological effects on health, potential applications, drawbacks of traditional production processes, characteristics of production strains, and progress in microbial fermentation. Recent advances in systems and synthetic biology techniques have enabled comprehensive understanding of GRAS strains and its wider applications. Thus, these microbial strains are promising cell factories for the commercial production of nutraceuticals.

Engineered biosynthesis of natural products in heterologous hosts

Natural products produced by microorganisms and plants are a major resource of antibacterial and anticancer drugs as well as industrially useful compounds. However, the native producers often suffer from low productivity and titers. Here we summarize the recent applications of heterologous biosynthesis for the production of several important classes of natural products such as terpenoids, flavonoids, alkaloids, and polyketides. In addition, we will discuss the new tools and strategies at multi-scale levels including gene, pathway, genome and community levels for highly efficient heterologous biosynthesis of natural products.

Toward a photosynthetic microbial platform for terpenoid engineering

Plant terpenoids are among the most diverse group of naturally-occurring organic compounds known, and several are used in contemporary consumer products. Terpene synthase enzymes catalyze complex rearrangements of carbon skeleton precursors to yield thousands of unique chemical structures that range in size from the simplest five carbon isoprene unit to the long polymers of rubber. Such chemical diversity has established plant terpenoids as valuable commodity chemicals with applications in the pharmaceutical, neutraceutical, cosmetic, and food industries. More recently, terpenoids have received attention as a renewable alternative to petroleum-derived fuels and as the building blocks of synthetic biopolymers. However, the current plant- and petrochemical-based supplies of commodity terpenoids have major limitations. Photosynthetic microorganisms provide an opportunity to generate terpenoids in a renewable manner, employing a single consolidated host organism that is able to use solar energy, H2O and CO2 as the primary inputs for terpenoid biosynthesis. Advances in synthetic biology have seen important breakthroughs in microbial terpenoid engineering, traditionally via fermentative pathways in yeast and Escherichia coli. This review draws on the knowledge obtained from heterotrophic microbial engineering to propose strategies for the development of microbial photosynthetic platforms for industrial terpenoid production. The importance of utilizing the wealth of genetic information provided by nature to unravel the regulatory mechanisms of terpenoid biosynthesis is highlighted.

Microbial biosynthesis of medicinally important plant secondary metabolites

Secondary metabolites derived from plants are a valuable source of pharmaceuticals, nutraceuticals, and cosmetics. To harness the potential of these natural products, reliable methods must be developed for their rapid and sustainable resupply. Microbial production of plant secondary metabolites through the heterologous expression of plant biosynthetic genes represents one such solution. This highlight focuses on recent advances in the microbial biosynthesis of plant secondary metabolites including terpenoids, flavonoids, and alkaloids as well as providing a brief insight into the current limitations and future prospects.

Synthetic biology and metabolic engineering for marine carotenoids: new opportunities and future prospects

Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations.

Efficient production of lycopene in Saccharomyces cerevisiae by expression of synthetic crt genes from a plasmid harboring the ADH2 promoter

Lycopene is an effective antioxidant proposed as a possible treatment for some cancers and other degenerative human conditions. This study aims at generation of a yeast strain (Saccharomyces cerevisiae) of efficient productivity of lycopene by overexpressing synthetic genes derived from crtE, crtB and crtI genes of Erwinia uredovora. These synthetic genes were constructed in accordance with the preferred codon usage in S. cerevisiae but with no changes in amino acid sequences of the gene products. S. cerevisiae cells were transformed with these synthetic crt genes, whose expression was regulated by the ADH2 promoter, which is de-repressed upon glucose depletion. The RT-PCR and Western blotting analyses indicated that the synthetic crt genes were efficiently transcribed and translated in crt-transformed S. cerevisiae cells. The highest level of lycopene in one of the transformed lines was 3.3mglycopene/g dry cell weight, which is higher than the previously reported levels of lycopene in other microorganisms transformed with the three genes. These results suggest the excellence of using the synthetic crt genes and the ADH2 promoter in generation of recombinant S. cerevisiae that produces a high level of lycopene. The level of ergosterol was reversely correlated to that of lycopene in crt-transformed S. cerevisiae cells, suggesting that two pathways for lycopene and ergosterol syntheses compete for the use of farnesyl diphosphate.

Reconstruction of the carotenoid biosynthetic pathway of Cronobacter sakazakii BAA894 in Escherichia coli

Cronobacter sakazakii could form yellow-pigmented colonies. However, the chemical structure and the biosynthetic pathway of the yellow pigments have not been identified. In this study, the yellow pigments of C. sakazakii BAA894 were purified and analyzed. The major components of the yellow pigments were confirmed as zeaxanthin-monoglycoside and zeaxanthin-diglycoside. A gene cluster containing seven genes responsible for the yellow pigmentation in C. sakazakii BAA894 was identified. The seven genes of C. sakazakii BAA894 or parts of them were reconstructed in a heterologous host Escherichia coli DH5α. The pigments formed in these E. coli strains were isolated and analyzed by thin layer chromatography, UV-visible spectroscopy, high performance liquid chromatography, and electron spray ionization-mass spectrometry. These redesigned E. coli strains could produce different carotenoids. E. coli strain expressing all the seven genes could produce zeaxanthin-monoglycoside and zeaxanthin-diglycoside; E. coli strains expressing parts of the seven genes could produce lycopene, β-carotene, cryptoxanthin or zeaxanthin. This study identified the gene cluster responsible for the yellow pigmentation in C. sakazakii BAA894.

Biotechnological production of carotenoids by yeasts: an overview

Nowadays, carotenoids are valuable molecules in different industries such as chemical, pharmaceutical, poultry, food and cosmetics. These pigments not only can act as vitamin A precursors, but also they have coloring and antioxidant properties, which have attracted the attention of the industries and researchers. The carotenoid production through chemical synthesis or extraction from plants is limited by low yields that results in high production costs. This leads to research of microbial production of carotenoids, as an alternative that has shown better yields than other aforementioned. In addition, the microbial production of carotenoids could be a better option about costs, looking for alternatives like the use of low-cost substrates as agro-industrials wastes. Yeasts have demonstrated to be carotenoid producer showing an important growing capacity in several agro-industrial wastes producing high levels of carotenoids. Agro-industrial wastes provide carbon and nitrogen source necessary, and others elements to carry out the microbial metabolism diminishing the production costs and avoiding pollution from these agro-industrial wastes to the environmental. Herein, we discuss the general and applied concepts regarding yeasts carotenoid production and the factors influencing carotenogenesis using agro-industrial wastes as low-cost substrates.

Production of lycopene in the non-carotenoid-producing yeast Yarrowia lipolytica

The codon-optimized genes crtB and crtI of Pantoea ananatis were expressed in Yarrowia lipolytica under the control of the TEF1 promoter of Y. lipolytica. Additionally, the rate-limiting genes for isoprenoid biosynthesis in Y. lipolytica, GGS1 and HMG1, were overexpressed to increase the production of lycopene. All of the genes were also expressed in a Y. lipolytica strain with POX1 to POX6 and GUT2 deleted, which led to an increase in the size of lipid bodies and a further increase in lycopene production. Lycopene is located mainly within lipid bodies, and increased lipid body formation leads to an increase in the lycopene storage capacity of Y. lipolytica. Growth-limiting conditions increase the specific lycopene content. Finally, a yield of 16 mg g(-1) (dry cell weight) was reached in fed-batch cultures, which is the highest value reported so far for a eukaryotic host.