Increased torulene accumulation in red yeast Sporidiobolus pararoseus NGR as stress response to high salt conditions

Research progress on carotenoid production by Rhodosporidium toruloides

Carotenoids are natural lipophilic pigments, which have been proven to provide significant health benefits to humans, relying on their capacity to efficiently scavenge singlet oxygen and peroxyl radicals as antioxidants. Strains belonging to the genus Rhodosporidium represent a heterogeneous group known for a number of phenotypic traits including accumulation of carotenoids and lipids and tolerance to heavy metals and oxidative stress. As a representative of these yeasts, Rhodosporidium toruloides naturally produces carotenoids with high antioxidant activity and grows on a wide variety of carbon sources. As a result, R. toruloides is a promising host for the efficient production of more value-added lipophilic compound carotenoids, e.g., torulene and torularhodin. This review provides a comprehensive summary of the research progress on carotenoid biosynthesis in R. toruloides, focusing on the understanding of biosynthetic pathways and the regulation of key enzymes and genes involved in the process. Moreover, the relationship between the accumulation of carotenoids and lipid biosynthesis, as well as the stress from diverse abiotic factors, has also been discussed for the first time. Finally, several feasible strategies have been proposed to promote carotenoid production by R. toruloides. It is possible that R. toruloides may become a critical strain in the production of carotenoids or high-value terpenoids by genetic technologies and optimal fermentation processes. KEY POINTS: • Biosynthetic pathway and its regulation of carotenoids in Rhodosporidium toruloides were concluded • Stimulation of abiotic factors for carotenoid biosynthesis in R. toruloides was summarized • Feasible strategies for increasing carotenoid production by R. toruloides were proposed.

Research advancements in the maintenance mechanism of Sporidiobolus pararoseus enhancing the quality of soy sauce during fermentation

Soy sauce is a traditional condiment that undergoes microbial fermentation of various ingredients to achieve its desired color, scent, and flavor. Sporidiobolus pararoseus, which is a type of Rhodocerevisiae, shows promising potential as a source of lipids, carotenoids, and enzymes that can enrich the taste and color of soy sauce. However, there is currently a lack of systematic and comprehensive studies on the functions and mechanisms of action of S. pararoseus during soy sauce fermentation. In this review, it is well established that S. pararoseus produces lipids that are abundant in unsaturated fatty acids, particularly oleic acid, as well as various carotenoids, such as β-carotene, torulene, and torularhodin. These pigments are synthesized through the mevalonic acid pathway and possess remarkable antioxidant properties, acting as natural colorants. The synthesis of carotenoids is stimulated by high salt concentrations, which induces oxidative stress caused by NaCl. This stress further activates crucial enzymes involved in carotenoid production, ultimately leading to pigment formation. Moreover, S. pararoseus can produce high-quality enzymes that aid in the efficient utilization of soy sauce substrates during fermentation. Furthermore, this review focused on the impact of S. pararoseus on the color and quality of soy sauce and comprehensively analyzed its characteristics and ingredients. Thus, this review serves as a basis for screening high-quality oleaginous red yeast strains and improving the quality of industrial soy sauce production through the wide application of S. pararoseus.

Molecular Basis of Yeasts Antimicrobial Activity-Developing Innovative Strategies for Biomedicine and Biocontrol

In the context of the growing concern regarding the appearance and spread of emerging pathogens with high resistance to chemically synthetized biocides, the development of new agents for crops and human protection has become an emergency. In this context, the yeasts present a huge potential as eco-friendly agents due to their widespread nature in various habitats and to their wide range of antagonistic mechanisms. The present review focuses on some of the major yeast antimicrobial mechanisms, their molecular basis and practical applications in biocontrol and biomedicine. The synthesis of killer toxins, encoded by dsRNA virus-like particles, dsDNA plasmids or chromosomal genes, is encountered in a wide range of yeast species from nature and industry and can affect the development of phytopathogenic fungi and other yeast strains, as well as human pathogenic bacteria. The group of the "red yeasts" is gaining more interest over the last years, not only as natural producers of carotenoids and rhodotorulic acid with active role in cell protection against the oxidative stress, but also due to their ability to inhibit the growth of pathogenic yeasts, fungi and bacteria using these compounds and the mechanism of competition for nutritive substrate. Finally, the biosurfactants produced by yeasts characterized by high stability, specificity and biodegrability have proven abilities to inhibit phytopathogenic fungi growth and mycelia formation and to act as efficient antibacterial and antibiofilm formation agents for biomedicine. In conclusion, the antimicrobial activity of yeasts represents a direction of research with numerous possibilities of bioeconomic valorization as innovative strategies to combat pathogenic microorganisms.

The Property of a Key Amino Acid Determines the Function of Farnesyl Pyrophosphate Synthase in Sporobolomyces pararoseus NGR

Farnesyl pyrophosphate synthase (FPPS) catalyzes the synthesis of C15 farnesyl diphosphate (FPP) from C5 dimethylallyl diphosphate (DMAPP) and two or three C5 isopentenyl diphosphates (IPPs). FPP is an important precursor for the synthesis of isoprenoids and is involved in multiple metabolic pathways. Here, farnesyl pyrophosphate synthase from Sporobolomyces pararoseus NGR (SpFPPS) was isolated and expressed by the prokaryotic expression system. The SpFPPS full-length genomic DNA and cDNA are 1566 bp and 1053 bp, respectively. This gene encodes a 350-amino acid protein with a predicted molecular mass of 40.33 kDa and a molecular weight of 58.03 kDa (40.33 kDa + 17.7 kDa), as detected by SDS-PAGE. The function of SpFPPS was identified by induction, purification, protein concentration and in vitro enzymatic activity experiments. Structural analysis showed that Y90 was essential for chain termination and changing the substrate scope. Site-directed mutation of Y90 to the smaller side-chain amino acids alanine (A) and lysine (K) showed in vitro that wt-SpFPPS catalyzed the condensation of the substrate DMAPP or geranyl diphosphate (GPP) with IPP at apparent saturation to synthesize FPP as the sole product and that the mutant protein SpFPPS-Y90A synthesized FPP and C20 geranylgeranyl diphosphate (GGPP), while SpFPPS-Y90K hydrolyzed the substrate GGPP. Our results showed that FPPS in S. pararoseus encodes the SpFPPS protein and that the amino acid substitution at Y90 changed the distribution of SpFPPS-catalyzed products. This provides a baseline for potentially regulating SpFPPS downstream products and improving the carotenoid biosynthesis pathway.

Two at once: simultaneous increased production of astaxanthin and mycosporines in a single batch culture using a Phaffia rhodozyma mutant strain

Phaffia rhodozyma is a basidiomycetous yeast characterized by its production of the carotenoid pigment astaxanthin, which holds high commercial value for its significance in aquaculture, cosmetics and as nutraceutics, and the UV-B-absorbing compound mycosporine-glutaminol-glucoside (MGG), which is of great biotechnological relevance for its incorporation into natural sunscreens. However, the industrial exploitation has been limited to the production of astaxanthin in small quantities. On the other hand, the accumulation of MGG in P. rhodozyma was recently reported and could add value to the simultaneous production of both metabolites. In this work, we obtain a mutant strain that overproduces both compounds, furthermore we determined how the accumulation of each is affected by the carbon-to-nitrogen ratio and six biotic and abiotic factors. The mutant obtained produces 159% more astaxanthin (470.1 μg g-1) and 220% more MGG (57.9 mg g-1) than the parental strain (295.8 μg g-1 and 26.2 mg g-1 respectively). Furthermore, we establish that the carotenoids accumulate during the exponential growth phase while MGG accumulates during the stationary phase. The carbon-to-nitrogen ratio affects each metabolite differently, high ratios favoring carotenoid accumulation while low ratios favoring MGG accumulation. Finally, the accumulation of both metabolites is stimulated only by photosynthetically active radiation and low concentrations of hydrogen peroxide. The mutant strain obtained is the first hyper-productive mutant capable of accumulating high concentrations of MGG and astaxanthin described to date. The characterization of how both compounds accumulate during growth and the factors that stimulate their accumulation, are the first steps toward the future commercial exploitation of strains for the simultaneous production of two biotechnologically important metabolites.

Cellular Stress Impact on Yeast Activity in Biotechnological Processes-A Short Overview

The importance of Saccharomyces cerevisiae yeast cells is known worldwide, as they are the most used microorganisms in biotechnology for bioethanol and biofuel production. Also, they are analyzed and studied for their similar internal biochemical processes to human cells, for a better understanding of cell aging and response to cell stressors. The special ability of S. cerevisiae cells to develop in both aerobic and anaerobic conditions makes this microorganism a viable model to study the transformations and the way in which cellular metabolism is directed to face the stress conditions due to environmental changes. Thus, this review will emphasize the effects of oxidative, ethanol, and osmotic stress and also the physiological and genetic response of stress mitigation in yeast cells.

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.

Integrative analysis of genomic and metabolomic data reveals key metabolic pathways involved in lipid and carotenoid biosynthesis in oleaginous red yeast Rhodosporidiobolus odoratus XQR

Rhodosporidiobolus odoratus, one of the oleaginous red yeasts, is gaining biotechnological importance for their ability to produce microbial lipids and carotenoids. However, to date, the genomic resource underling lipid and carotenoid biosynthesis in R. odoratus has not been reported. Here, we reported the first genome assembly of R. odoratus using a combination of PacBio and Illumina techniques. The final genome assembly is 23.74 Mb in size, containing 52 scaffolds with a N50 length of 1200,460 bp and a GC content of 56.90%. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment showed that our assembly contains 94.23% of Basidiomycota universal single-copy orthologs. The genome was predicted to contain 4986 protein-coding genes, 4967 of which were functionally annotated. Metabolomic profiling identified 574 lipids, 3 carotenoids, and 208 volatile organic compounds synthesized by R. odoratus. Integrative analysis of genomics and metabolomics provides insights into the biosynthesis of lipid, carotenoid, and other bioactive compounds in R. odoratus. Collectively, the results presented herein greatly enhance our understanding of R. odoratus in lipids and carotenoids biosynthesis, and thus further accelerate its fundamental molecular investigations and biotechnological applications.

Functional verification and characterization of a type-III geranylgeranyl diphosphate synthase gene from Sporobolomyces pararoseus NGR

Carotenoids, a group of natural pigments, have strong antioxidant properties and act as precursors to vitamin A, which have garnered attention from industry and researchers. Sporobolomyces pararoseus represents a hyper-producer of carotenoids, mainly including β-carotene, torulene, and torularhodin. Geranylgeranyl diphosphate synthase (GGPPS) is regarded as a key enzyme in the carotenoid biosynthesis pathway. However, the precise nature of the gene encoding GGPPS in S. pararoseus has not been reported yet. Here, we cloned a cDNA copy of the GGPPS protein-encoding gene crtE from S. pararoseus NGR. The crtE full-length genomic DNA and cDNA are 1,722 and 1,134 bp, respectively, which consist of 9 exons and 8 introns. This gene encodes 377 amino acids protein with a predicted molecular mass of 42.59 kDa and a PI of 5.66. Identification of the crtE gene encoding a functional GGPPS was performed using heterologous complementation detection in Escherichia coli. In vitro enzymatic activity experiments showed that CrtE utilized farnesyl diphosphate (FPP) as an allylic substrate for the condensation reaction with isopentenyl diphosphate (IPP), generating more of the unique product GGPP compared to other allylic substrates. The predicted CrtE 3D-model was analyzed in comparison with yeast GGPPS. The condensation reaction occurs in the cavity of the subunit, and three bulky amino acids (Tyr110, Phe111, and His141) below the cavity prevent further extension of the product. Our findings provide a new source of genes for carotenoid genetic engineering.

Microbial torularhodin – a comprehensive review

The demand for food, feed, cosmeceutical, and nutraceutical supplements/additives from natural sources has been rapidly increasing, with expectations for a faster expansion than the growth of the global markets in the coming years. In this framework, a particular interest is given to carotenoids due to their outstanding antioxidant activities, particularly the xanthophylls class. Torularhodin is one of these carotenoids that stands out for its multifunctional role as: antioxidant, anticancer and antimicrobial, yet its commercial potential is still unexplored. Although most xanthophylls can be naturally found in: microbial, plant and animal sources, torularhodin is only produced by microbial species, especially red oleaginous yeast. The microbial production of xanthophylls has many advantages as compared to other natural sources, such as: the need for low production area, easier extraction, high yields (at optimum operating conditions), and low (or no) seasonal, climatic, and geographic variation dependency. Due to the importance of natural products and their relevance to the market, this review provides a comprehensive overview of the: properties, characteristics and potential health benefits of torularhodin. Moreover, the most promising developments in both upstream and downstream processing to obtain this colorant from microbial sources are considered. For this purpose, the main microorganisms used for torularhodin production are firstly reviewed, including biosynthesis pathway and torularhodin properties. Following, an overall analysis of the processing aspects related with its: extraction, separation and purification is provided. Lastly, current status and future trends of torularhodin-based processes and products such as therapeutic agents or biomaterials are discussed, indicating promising directions toward biorefinery and circular economy.

Biosynthesis, evolution and ecology of microbial terpenoids

Covering: through June 2021Terpenoids are the largest class of natural products recognised to date. While mostly known to humans as bioactive plant metabolites and part of essential oils, structurally diverse terpenoids are increasingly reported to be produced by microorganisms. For many of the compounds biological functions are yet unknown, but during the past years significant insights have been obtained for the role of terpenoids in microbial chemical ecology. Their functions include stress alleviation, maintenance of cell membrane integrity, photoprotection, attraction or repulsion of organisms, host growth promotion and defense. In this review we discuss the current knowledge of the biosynthesis and evolution of microbial terpenoids, and their ecological and biological roles in aquatic and terrestrial environments. Perspectives on their biotechnological applications, knowledge gaps and questions for future studies are discussed.

Carotenoids from fungi and microalgae: A review on their recent production, extraction, and developments

The demand for carotenoids from natural sources obtained by biological extraction methods is increasing with the development of biotechnology and the continued awareness of food safety. Natural plant-derived carotenoids have a relatively high production cost and are affected by the season, while microbial-derived carotenoids are favored due to their natural, high-efficiency, low production cost, and ease of industrialization. This article reviewed the following aspects of natural carotenoids derived from microorganisms: (1) the structures and properties of main carotenoids; (2) fungal and microalgal sources of the main carotenoids; (3) influencing factors and modes of improvement for carotenoids production; (4) efficient extraction methods for carotenoids; and (5) the commercial value of carotenoids. This review provided a reference and guidance for the development of natural carotenoids derived from microorganisms.

Transcriptomic and Metabolomic Analyses Provide Insights into the Enhancement of Torulene and Torularhodin Production in Rhodotorula glutinis ZHK under Moderate Salt Conditions

Carotenoids are a group of tetraterpene pigments widely used in the food, pharmaceutical, and cosmetic industries. Torulene, torularhodin, and β-carotene, three principal carotenoids synthesized by Rhodotorula glutinis ZHK, possess strong health-promoting properties such as antioxidant, provitamin A, and antitumor. Here, the effect of different salt conditions on carotenoids production of R. glutinisZHK was investigated. The results showed that the total carotenoids were significantly enhanced in 0.5 M (3.91 mg/L) and 0.75 M (5.41 mg/L) NaCl treatments than that in 1.0 M (0.35 mg/L) and control (1.42 mg/L) after 120 h of cultivation. Of which, the increase in torulene and torularhodin production acts as the main contributor to the enhancement of total carotenoids. Transcriptome profiling revealed that salt stress efficiently promotes the gene expression of crtI, which could explain the molecular mechanisms of the enhanced torulene and torularhodin production under salt stress. Further experiments indicated that torulene and torularhodin play an important role in quenching excrescent reactive oxygen species induced by salt stress. Together, the present study reports an effective strategy for simultaneously improving torulene and torularhodin production in R. glutinis ZHK.

Genomics and lipidomics analysis of the biotechnologically important oleaginous red yeast Rhodotorula glutinis ZHK provides new insights into its lipid and carotenoid metabolism

Background

Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. glutinis is the formation of intracellular lipid droplets full of carotenoids. However, the basic genomic features that underlie the biosynthesis of these valuable compounds in R. glutinis have not been fully documented. To reveal the biotechnological potential of R. glutinis, the genomics and lipidomics analysis was performed through the Next-Generation Sequencing and HPLC-MS-based metabolomics technologies.

Results

Here, we firstly assemble the genome of R. glutinis ZHK into 21.8 Mb, containing 30 scaffolds and 6774 predicted genes with a N50 length of 14, 66,672 bp and GC content of 67.8%. Genome completeness assessment (BUSCO alignment: 95.3%) indicated the genome assembly with a high-quality features. According to the functional annotation of the genome, we predicted several key genes involved in lipids and carotenoids metabolism as well as certain industrial enzymes biosynthesis. Comparative genomics results suggested that most of orthologous genes have underwent the strong purifying selection within the five Rhodotorula species, especially genes responsible for carotenoids biosynthesis. Furthermore, a total of 982 lipids were identified using the lipidomics approaches, mainly including triacylglycerols, diacylglyceryltrimethylhomo-ser and phosphatidylethanolamine.

Conclusion

Using whole genome shotgun sequencing, we comprehensively analyzed the genome of R. glutinis and predicted several key genes involved in lipids and carotenoids metabolism. By performing comparative genomic analysis, we show that most of the ortholog genes have undergone strong purifying selection within the five Rhodotorula species. Furthermore, we identified 982 lipid species using lipidomic approaches. These results provided valuable resources to further advance biotechnological applications of R .glutinis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07244-z.

Metabolomics integrated with transcriptomics: assessing the central metabolism of marine red yeast Sporobolomyces pararoseus under salinity stress

Salinity stress is one of the most serious environmental issues in agricultural regions worldwide. Excess salinity inhibits root growth of various crops, and results in reductions of yield. It is of crucial to understand the molecular mechanisms mediating salinity stress responses for enhancing crops' salt tolerance. Marine red yeast Sporobolomyces pararoseus should have evolved some unique salt-tolerant mechanism, because they long-term live in high-salt ecosystems. However, little research has conducted so far by considering S. pararoseus as model microorganisms to study salt-tolerant mechanisms. Here, we successfully integrated metabolomics with transcriptomic profiles of S. pararoseus in response to salinity stress. Screening of metabolite features with untargeted metabolic profiling, we characterized 4862 compounds from the LC-MS/MS-based datasets. The integrated results showed that amino acid metabolism, carbohydrate metabolism, and lipid metabolism is significantly enriched in response to salt stress. Co-expression network analysis showed that 28 genes and 8 metabolites play an important role in the response of S. pararoseus, which provides valuable clues for subsequent validation. Together, the results provide valuable information for assessing the central metabolism of mediating salt responses in S. pararoseus and offer inventories of target genes for salt tolerance improvement via genetic engineering.

Evaluation of olive mill waste as substrate for carotenoid production by Rhodotorula mucilaginosa

The “alperujo” is a waste from the olive oil industry with great potential for valorization. It has a high organic load, with the presence of valuable compounds such as biophenols and sugars. The use of this waste can be thought of as a biorefinery from which different compounds of high added value can be obtained, whether they are present in the “alperujo” such as biophenols or can be generated from the “alperujo”. Therefore, the production of carotenoids by Rhodotorula mucilaginosa was evaluated using the liquid fraction of ‘alperujo’ (Alperujo Water, AW) or an aqueous extract (AE) of “alperujo” at different concentrations (5, 10, 20 and 30% w/V) as substrates. The AEs had an acidic pH, a total sugar concentration ranging from 1.6 to 7.6 g/L, a polyphenols content from 0.4 to 2.9 g/L and a significant amount of proteins (0.5–3 g/L). AW is similar in composition as 30% AE, but with a higher amount of total sugars. Rh. mucilaginosa was able to grow at the different mediums with consumption of glucose and fructose, a reduction in protein content and alkalinization of the medium. Maximum total carotenoid production (7.3 ± 0.6 mg/L) was achieved at AW, while the specific production was higher when the yeast grew at AW or at 30% AE (0.78 ± 0.06 and 0.73 ± 0.10 mg/g of biomass, respectively). Torulene and torularhodin were the main carotenoids produced. Polyphenol content did not change; thus, it is still possible to recover these compounds after producing carotenoids. These results demonstrate the feasibility of using alperujo-based mediums as cheap substrates to produce torularhodin and torulene and to include this bioprocess as a step in an integral approach for alperujo valorization.

Effects of carbon sources on the removal of ammonium, nitrite and nitrate nitrogen by the red yeast Sporidiobolus pararoseus Y1

Heterotrophic nitrification and aerobic denitrification (HN-AD), which is primarily performed by bacteria rather than fungi, is an attractive approach for nitrogen removal. In this study, a red yeast, Sporidiobolus pararoseus Y1, was isolated and shown to exhibit optimal growth and nitrogen removal efficiency on glucose, followed by citrate, sucrose, acetate and starch. The nitrogen removal efficiency increased with increasing initial concentrations of NH₄⁺-N, NO₂^--N and NO₃^--N from 14 to 140 mg·L^-1. At an initial nitrogen concentration of 140 mg·L^-1, the maximum removal efficiencies of NH₄⁺-N, NO₂^--N and NO₃^--N were 98.67%, 97.13% and 83.51% after 72 h incubation, while those of corresponding total nitrogen were 88.89%, 81.31% and 70.18%, respectively. The nitrification (amoA) and denitrification genes (nirK and napA) were amplified from Y1. These results suggest that yeast are also capable of HN-AD, which can be used to remove nitrogen in wastewater systems.

Carotenoids and lipid production from Rhodosporidium toruloides cultured in tea waste hydrolysate

BACKGROUND

In this study, renewable tea waste hydrolysate was used as a sole carbon source for carotenoids and lipid production. A novel Rhodosporidium toruloides mutant strain, RM18, was isolated through atmospheric and room-temperature plasma mutagenesis and continuous domestication in tea waste hydrolysate from R. toruloides ACCC20341.

RESULTS

RM18 produced a larger biomass and more carotenoids and α-linolenic acid compared with the control strain cultured in tea waste hydrolysate. The highest yields of torularhodin (481.92 μg/g DCW) and torulene (501 μg/g DCW) from RM18 cultured in tea waste hydrolysate were 12.86- and 1.5-fold higher, respectively, than that of the control strain. In addition, α-linolenic acid production from RM18 in TWH accounted for 5.5% of total lipids, which was 1.58 times more than that of the control strain. Transcriptomic profiling indicated that enhanced central metabolism and terpene biosynthesis led to improved carotenoids production, whereas aromatic amino acid synthesis and DNA damage checkpoint and sensing were probably relevant to tea waste hydrolysate tolerance.

CONCLUSION

Tea waste is suitable for the hydrolysis of microbial cell culture mediums. The R. toruloides mutant RM18 showed considerable carotenoids and lipid production cultured in tea waste hydrolysate, which makes it viable for industrial applications.

Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting

BACKGROUND

Sporobolomyces pararoseus is regarded as an oleaginous red yeast, which synthesizes numerous valuable compounds with wide industrial usages. This species hold biotechnological interests in biodiesel, food and cosmetics industries. Moreover, the ballistospores-shooting promotes the colonizing of S. pararoseus in most terrestrial and marine ecosystems. However, very little is known about the basic genomic features of S. pararoseus. To assess the biotechnological potential and ballistospores-shooting mechanism of S. pararoseus on genome-scale, the whole genome sequencing was performed by next-generation sequencing technology.

RESULTS

Here, we used Illumina Hiseq platform to firstly assemble S. pararoseus genome into 20.9 Mb containing 54 scaffolds and 5963 predicted genes with a N50 length of 2,038,020 bp and GC content of 47.59%. Genome completeness (BUSCO alignment: 95.4%) and RNA-seq analysis (expressed genes: 98.68%) indicated the high-quality features of the current genome. Through the annotation information of the genome, we screened many key genes involved in carotenoids, lipids, carbohydrate metabolism and signal transduction pathways. A phylogenetic assessment suggested that the evolutionary trajectory of the order Sporidiobolales species was evolved from genus Sporobolomyces to Rhodotorula through the mediator Rhodosporidiobolus. Compared to the lacking ballistospores Rhodotorula toruloides and Saccharomyces cerevisiae, we found genes enriched for spore germination and sugar metabolism. These genes might be responsible for the ballistospores-shooting in S. pararoseus NGR.

CONCLUSION

These results greatly advance our understanding of S. pararoseus NGR in biotechnological potential and ballistospores-shooting, which help further research of genetic manipulation, metabolic engineering as well as its evolutionary direction.

Effect of exogenous stress factors on the biosynthesis of carotenoids and lipids by Rhodotorula yeast strains in media containing agro-industrial waste

In this study, we aimed to determine the effect of exogenous stress factors (sodium chloride as osmotic stressor, hydrogen peroxide as an inducer of oxidative stress, white light irradiation, and low temperature) on the biosynthesis of carotenoids and lipids by red yeast (Rhodotorula glutinis, R. mucilaginosa, and R. gracilis) during cultivation in media containing potato wastewater and glycerol. According to our results, the yeast were able to grow and biosynthesize lipids and carotenoids in the presence of the applied stress factors. Low temperature caused an increase in the biosynthesis of intracellular lipids and carotenoids. R. gracilis synthesized lipids (21.1 g/100 g_d.w.) and carotenoids (360.4 µg/g_d.w.) in greater quantities than that of other strains. Under these conditions, there was also an increase in the content of unsaturated fatty acids, especially linoleic and linolenic acids. The highest percentage of polyunsaturated fatty acid (PUFA) (30.4%) was synthesized by the R. gracilis yeast after cultivation at 20°C. Their quantity was 2.5-fold greater than that of the biomass grown in control conditions. The contribution of individual carotenoid fractions depended both on the yeast strain and the culture conditions. Induction of osmotic stress and low temperature intensified the biosynthesis of β-carotene (up to 73.9% of the total carotenoid content). In oxidative stress conditions, yeast synthesized torulene (up to 82.2%) more efficiently than under other conditions, whereas white light irradiation increased the production of torularhodin (up to 20.0%).

Increased torulene production by the red yeast, Sporidiobolus pararoseus, using citrus juice

Response surface methodology was applied to maximize the yield and production of carotenoids by Sporidiobolus pararoseus WZ012 using citrus juice. A high concentration of yeast extract and citrus juice favored carotenoid production and biomass concentration, respectively. Under optimal conditions, a more than 51 percent (from 860 to 1300 µg/g) and 62 percent (from 17.05 to 27.66 mg/L) respective enhancement in intracellular and total carotenoid production was achieved. Finally, this process was successfully upscaled in a 5-L fermentor. A comparison of the carotenoid distributions revealed that torulene (61.3%) was the dominant carotenoid when using the citrus based medium, while the main carotenoid was β-carotene (62.5%) when using the glucose medium. The present work provides an alternative method to produce high-value products derived from waste and low-grade citrus.

Comparative transcriptome analysis revealed the improved β-carotene production in Sporidiobolus pararoseus yellow mutant MuY9

Carotenoids are ubiquitous constituents of living organisms. These structurally diverse pigments have received considerable attention due to their biotechnological applications and potential beneficial effects on human health. In this study, we characterized an over-producing β-carotene mutant of Sporidiobolus pararoseus, obtained by ultraviolet mutagenesis, named MuY9. We compared the transcriptome between the wild-type and MuY9. A total of 348 differential expressed genes (DEGs) were found, and only one DEG crtYB is involved in carotenoid biosynthesis. The overproduction of β-carotene in MuY9 should be attributed to the up-regulation of crtYB. Functional identification of crtYB was performed using heterologous complementation in Escherichia coli. Our findings indicate that the enzymatic conversions of geranylgeranyl pyrophosphate to phytoene, as well as lycopene to β-carotene, are catalyzed by this CrtYB. Furthermore, our insights into the crtYB gene should facilitate a more detailed understanding of the carotenogenic pathway in S. pararoseus, and advance the development of the genetic engineering for the bio-production of carotenoids.

Lipid and Carotenoid Production by Rhodotorula glutinis with a Combined Cultivation Mode of Nitrogen, Sulfur, and Aluminium Stress

Torulene is a promising pink pigment, produced only by yeasts and fungi, and its production is still in a developing stage due to the low production rate. Accordingly, this study focuses on maximizing torulene production by Rhodotorula glutinis using shaken flask fermentation. The effect of different nitrogen sources, and C/N and C/S ratios on lipid and carotenoid production by R. glutinis was studied using 60 g/L glucose. The largest cells filled with golden fluorescence lipid bodies were observed using fluorescence microscopy when peptone was used as a nitrogen source. The highest total pigment (0.947 mg/L) and carotenoid relative productivity (Car-RP) (89.04 µg/g) were obtained at C/N 146 and C/S 120, and with ammonium sulfate as a nitrogen source, with 62% torulene domination using High Performance Liquid Chromatography (HPLC) for identification. Under a high C/N ratio, regardless of the C/S ratio, the carotenoid synthesis rate decreased after three days while the lipid synthesis rate kept increasing to the sixth day. Interestingly, after adding 0.7 mM Al2(SO4)3 to the optimized medium, the total pigment and Car-RP (2.2 mg/L and 212.9 µg/g) sharply increased, producing around 2.16 mg/L torulene (98%) with around 50% decrease in lipid yield. This is the first report on the role of Al2(SO4)3 for enhancing torulene production under lipogenesis condition, which could be used as a potential tool for torulene production.

Salt stress increases carotenoid production of Sporidiobolus pararoseus NGR via torulene biosynthetic pathway

Carotenoids represent a diverse class of aliphatic C40 molecules with a variety of applications in the food and pharmaceutical industries. Sporidiobolus pararoseus NGR produces various carotenoids, including torulene, torularhodin and β-carotene. Salt stress significantly increases the torulene accumulation of S. pararoseus NGR. However, little is known, about the molecular mechanisms underlying the increased torulene biosynthesis. In this work, we investigated the effects of NaCl treatment on the contents of carotenoids (both qualitatively and quantitatively) and transcriptome. A total of 12.3 Gb of clean bases were generated in six cDNA libraries. These bases were de novo assembled into 9,533 unigenes with an average length of 1,654 nt and N50 of 2,371 nt. Transcriptome analysis revealed that of 3,849 differential expressed genes (DEGs) in response to salt stress, 2,019 were up-regulated, and 1,830 were down-regulated. Among these DEGs, we identified three carotenogenic genes crtE, crtYB, and crtI. In addition, fourteen candidate genes were predicted to participate in the conversion from torulene to torularhodin. Our findings should provide insights into the mechanisms of carotenoid biosynthesis and salt-tolerance of S. pararoseus NGR.

Development of an Improved Carotenoid Extraction Method to Characterize the Carotenoid Composition under Oxidative Stress and Cold Temperature in the Rock Inhabiting Fungus Knufia petricola A95

Black yeasts are a highly specified group of fungi, which are characterized by a high resistance against stress factors. There are several factors enabling the cells to survive harsh environmental conditions. One aspect is the pigmentation, the melanin black yeasts often display a highly diverse carotenoid spectrum. Determination and characterization of carotenoids depend on an efficient extraction and separation, especially for black yeast, which is characterized by thick cell walls. Therefore, specific protocols are needed to ensure reliable analyses regarding stress responses in these fungi. Here we present both. First, we present a method to extract and analyze carotenoids and secondly we present the unusual carotenoid composition of the black yeast Knufia petricola A95. Mechanical treatment combined with an acetonitrile extraction gave us very good extraction rates with a high reproducibility. The presented extraction and elution protocol separates the main carotenoids (7) in K. petricola A95 and can be extended for the detection of additional carotenoids in other species. K. petricola A95 displays an unusual carotenoid composition, with mainly didehydrolycopene, torulene, and lycopene. The pigment composition varied in dependency to oxidative stress but remained relatively constant if the cells were cultivated under low temperature. Future experiments have to be carried out to determine if didehydrolycopene functions as a protective agent itself or if it serves as a precursor for antioxidative pigments like torulene and torularhodin, which could be produced after induction under stress conditions. Black yeasts are a promising source for carotenoid production and other substances. To unravel the potential of these fungi, new methods and studies are needed. The established protocol allows the determination of carotenoid composition in black yeasts.

Comprehensive Description of Fusarium graminearum Pigments and Related Compounds

Several studies have explored in depth the biochemistry and genetics of the pigments present in Fusarium graminearum, but there is a need to discuss their relationship with the mold's observable surface color pattern variation throughout its lifecycle. Furthermore, they require basic cataloguing, including a description of their major features known so far. Colors are a viable alternative to size measurement in growth studies. When grown on yeast extract agar (YEA) at 25 °C, F. graminearum initially exhibits a whitish mycelium, developing into a yellow-orange mold by the sixth day and then turning into wine-red. The colors are likely due to accumulation of the golden yellow polyketide aurofusarin and the red rubrofusarin, but the carotenoid neurosporaxanthin also possibly plays a major role in the yellow or orange coloration. Torulene might contribute to red tones, but it perhaps ends up being converted into neurosporaxanthin. Culmorin is also present, but it does not contribute to the color, though it was initially isolated in pigment studies. Additionally, there is the 5-deoxybostrycoidin-based melanin, but it mostly occurs in the teleomorph's perithecium. There is still a need to chemically quantify the pigments throughout the lifecycle, and analyze their relationships and how much each impacts F. graminearum's surface color.

Torulene and torularhodin: "new" fungal carotenoids for industry?

Torulene and torularhodin represent the group of carotenoids and are synthesized by yeasts and fungi. The most important producers of these two compounds include yeasts of Rhodotorula and Sporobolomyces genera. The first reports confirming the presence of torulene and torularhodin in the cells of microorganisms date to the 1930s and 1940s; however, only in the past few years, the number of works describing the properties of these compounds increased. These compounds have strong anti-oxidative and anti-microbial properties, and thus may be successfully used as food, feedstock, and cosmetics additives. In addition, tests performed on rats and mice showed that both torulene and torularhodin have anti-cancerous properties. In order to commercialize the production of these two carotenoids, it is necessary to obtain highly efficient yeast strains, for example, via mutagenization and optimization of cultivation conditions. Further studies on the activity of torulene and torularhodin on the human body are also needed.