Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates

Yarrowia lipolytica is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of Y. lipolytica NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.

Simultaneous Lipid and Carotenoid Production via Rhodotorula paludigena CM33 Using Crude Glycerol as the Main Substrate: Pilot-Scale Experiments

Rhodotorula paludigena CM33 is an oleaginous yeast that has been demonstrated to accumulate substantial quantities of intracellular lipids and carotenoids. In this study, crude glycerol, a by-product of biodiesel production, was used as a carbon source to enhance the accumulation of lipids and carotenoids in the cells. The culture conditions were first optimized using response surface methodology, which revealed that the carotenoid concentration and lipid content improved when the concentration of crude glycerol was 40 g/L. Different fermentation conditions were also investigated: batch, repeated-batch, and fed-batch conditions in a 500 L fermenter. For fed-batch fermentation, the maximum concentrations of biomass, lipids, and carotenoids obtained were 46.32 g/L, 37.65%, and 713.80 mg/L, respectively. A chemical-free carotenoid extraction method was also optimized using high-pressure homogenization and a microfluidizer device. The carotenoids were found to be mostly beta-carotene, which was confirmed by HPLC (high pressure liquid chromatography), LC-MS (liquid chromatography-mass spectrometry), and NMR (nuclear magnetic resonance). The results of this study indicate that crude glycerol can be used as a substrate to produce carotenoids, resulting in enhanced value of this biodiesel by-product.

Comprehensive Exploration of the Growth and Lipid Synthesis Phases of T. oleaginosus Cultures Implementing Design of Experiments and Response Surface Methodology

Trichosporon oleaginosus is an unconventional oleaginous yeast distinguished by its remarkable capacity to accumulate lipids in excess of 70% of its dry weight, particularly when cultivated in nitrogen-restricted conditions with ample carbon sources. A pivotal question that arises pertains to the nutrient dynamics in the culture medium, which give rise to both the excessive lipid content and corresponding lipid concentration. While previous research has predominantly focused on evaluating the impact of the initial carbon-to-nitrogen (C/N) ratio on lipid production, the precise critical thresholds of glucose and ammonium sulfate ((NH4)2SO4) at which growth and intracellular lipid production are either stimulated or impeded remain inadequately defined. This study employs an experimental design and response surface methodology to investigate the complex mechanism of lipid accumulation and its interaction with cellular growth. Application of the aforementioned methodologies resulted in the production of 10.6 g/L of microbial oil in batch cultures under conditions that correspond to a C/N ratio of 76. However, the primary objective is to generate knowledge to facilitate the development of efficient fed-batch cultivation strategies that optimize lipid production exclusively employing inorganic nitrogen sources by finely adjusting carbon and nitrogen levels. The intricate interaction between these levels is comprehensively addressed in the present study, while it is additionally revealed that as glucose levels rise within a non-inhibitory range, lipid-free biomass production decreases while lipid accumulation simultaneously increases. These findings set the stage for further exploration and the potential development of two-stage cultivation approaches, aiming to fully decouple growth and lipid production. This advancement holds the promise of bringing microbial oil production closer to commercial viability.

Hannaella oleicumulans sp. nov. and Hannaella higashiohmiensis sp. nov., two novel oleaginous basidiomycetous yeast species

Three strains of novel oleaginous yeast species were isolated from soil samples collected in Shiga Prefecture, Japan. The sequences of the internal transcribed spacer (ITS) region and the D1/D2 region of the large subunit (LSU) of the rRNA genes indicated that these novel yeast species are members of the genus Hannaella. The results of molecular phylogenetic analysis indicated that strains 38-3 and 8s1 were closely related to Hannaella oryzae. They differed by 10 nucleotide substitutions and one gap (1.77 %) in the D1/D2 region of the LSU of the rRNA genes and by 17-18 nucleotide substitutions and 10-11 gaps (5.45-5.85 %) in the ITS region. Strain 51-4 differed from the type strain of the most closely related species, Hannaella pagnoccae, by 26 nucleotide substitutions (4.46 %) in the D1/D2 region of the LSU of the rRNA genes and by 20 nucleotide substitutions and six gaps (5.42 %) in the ITS region. The names proposed for these previously undescribed species are Hannaella oleicumulans sp. nov. and Hannaella higashiohmiensis sp. nov.

Cellulase mediated stress triggers the mutations of oleaginous yeast Trichosporon cutaneum with super-large spindle morphology and high lipid accumulation

Accumulation of intracellular lipid bodies in oleaginous yeast cells is highly restricted by their natural intracellular space. Here we show a cellulase mediated adaptive evolution with ultra-centrifugation fractionation of oleaginous yeast Trichosporon cutaneum to obtain the favorable cell structure for lipid accumulation. Cellulase was added to the wheat straw hydrolysate during long-term adaptive evolution for disruption of cell wall integrity of T. cutaneum cells. The cellulase, together with ultracentrifugation force, triggered multiple mutations and transcriptional expression changes of the functional genes associated with cell wall integrity and lipid synthesis metabolism. The fractionated mutant T. cutaneum YY52 demonstrated the heavily weakened cell wall and high lipid accumulation by the super-large expanded spindle cells (two orders of magnitude greater than the parental). A record-high lipid production by T. cutaneum YY52 was achieved (55.4 ± 0.5 g L-1 from wheat straw and 58.4 ± 0.1 g L-1 from corn stover). This study not only obtained an oleaginous yeast strain with industrial application potential for lipid production but also provided a new method for generation of mutant cells with high intracellular metabolite accumulation.

Determining mating type and ploidy in Rhodotorula toruloides and its effect on growth on sugars from lignocellulosic biomass

Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33-9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032-0.131 (g/g) and lipid contents were 13.5-53.7% (g/g). Four strains had significantly higher lipid yields and contents. One of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature.

SUMMARY

The yeast Rhodotorula toruloides was used to produce oil using sugars extracted from a bioenergy grass.

Oleaginous Yeast Extracts and Their Possible Effects on Human Health

Four non-conventional oleaginous and pigmented yeast strains of Metschnikowia pulcherrima, Cystofilobasidium infirmominiatum, Phaffia rhodozyma, and Rhodotorula kratochvilovae were used in this study. Complex yeast extracts were prepared and tested for biological activity, safety, and effect on human health. In this paper, we measured the antioxidant activity and antimicrobial effect of yeast biomass as a whole and their extracts to compare the influence of carotenoids and other bioactive substances in the studied biomass. All yeast extracts exhibited a significant dose-dependent antimicrobial effect against both G+ and G- bacteria and had a strong antioxidant effect. No cytotoxicity in the mouse melanoma B16F1 cell line was found in concentrations up to 20% of rehydrated biomass in cell medium. All of the extracts were cytotoxic at a concentration of 5 mg of extract/g of dry biomass. All the pigmented yeast extracts showed some positive results for apoptosis of murine melanoma cell lines and are therefore strong candidates positively effect human health. Red yeast cell biomass is a prospective material with many attractive biological functions and can be used in the food industry, as a pharmaceutical material, or in the feed industry.

Increasing lipid production from Zygosaccharomyces siamensis AP1 in molasses substrate using sequencing batch method

Yeasts are considered potential lipid producers to substitute oil-producing plants. Previous study succeeded in isolating Zygosaccharomyces siamensis AP1 from Indonesia which was able to accumulate 19% lipid. The strain, however, was not optimized for high cell density growth which is required for industry-level. In this study, efforts were made to increase cell density and lipid production of Z. siamensis AP1 using molasses as carbon source and implementing sequencing batch method. The yeast was grown in various combinations of carbon and nitrogen sources. The C:N ratio of the best substrate combination is then optimized. Afterwards, batch and sequencing batch methods were applied in fermentation with various concentrations (20-480 g/L) of molasses. The results show that lipid produced using molasses was slightly higher compared to using glucose, 0.21 g/L and 0.19 g/L respectively, with the same nitrogen source. Combination of molasses and ammonium sulfate with C:N ratio 70:1 gave the highest lipid (0.28 g/L). Sequencing batch able to increase cell density 2.4-fold compared to batch method. This study was the first to report that sequencing batch application with molasses as carbon source can increase lipid production from Z. siamensis. Further study to optimize medium composition for sequencing batch is suggested.

Corrigendum: Oleaginous yeast Rhodotorula toruloides biomass effect on the metabolism of Arctic char (Salvelinus alpinus)

[This corrects the article DOI: 10.3389/fmolb.2022.931946.].

Discovery of Oleaginous Yeast from Mountain Forest Soil in Thailand

As an interesting alternative microbial platform for the sustainable synthesis of oleochemical building blocks and biofuels, oleaginous yeasts are increasing in both quantity and diversity. In this study, oleaginous yeast species from northern Thailand were discovered to add to the topology. A total of 127 yeast strains were isolated from 22 forest soil samples collected from mountainous areas. They were identified by an analysis of the D1/D2 domain of the large subunit rRNA (LSU rRNA) gene sequences to be 13 species. The most frequently isolated species were Lipomyces tetrasporus and Lipomyces starkeyi. Based on the cellular lipid content determination, 78 strains of ten yeast species, and two potential new yeast that which accumulated over 20% of dry biomass, were found to be oleaginous yeast strains. Among the oleaginous species detected, Papiliotrema terrestris and Papiliotrema flavescens have never been reported as oleaginous yeast before. In addition, none of the species in the genera Piskurozyma and Hannaella were found to be oleaginous yeast. L. tetrasporus SWU-NGP 2-5 accumulated the highest lipid content of 74.26% dry biomass, whereas Lipomyces mesembrius SWU-NGP 14-6 revealed the highest lipid quantity at 5.20 ± 0.03 g L-1. The fatty acid profiles of the selected oleaginous yeasts varied depending on the strain and suitability for biodiesel production.

Using gel microdroplets to develop a simple high-throughput screening platform for oleaginous microorganisms

The oleaginous yeast Lipomyces starkeyi is expected to be a new lipid source since this microorganism is capable of accumulating more than 85% lipid per dry cell weight. For effective utilization of oleaginous yeast, mutants with improved lipid production compared to the wild-type have been screened by methods such as single-cell sorting and Percoll density gradient centrifugation. Because these methods need to reculture all mutated oleaginous yeasts together in a flask, it is difficult to evaluate the growth of each individual mutant. Thus, screening for the slow-growing mutants with high-throughput has never been performed by conventional methods. In this study, we developed a high-throughput method using gel microdroplets (GMD). With this method, the growth and lipid production of L. starkeyi can be evaluated simultaneously. L. starkeyi grew in GMD and the size of these microcolonies was evaluated by scattered light. Finally, a mutant with a 10-fold delay in growth compared to the wild-type was obtained. Analysis of genetic information in this mutant could reveal valuable information about critical genes involved in the growth of these microorganisms, which could then be utilized further.

Oleaginous yeast Rhodotorula toruloides biomass effect on the metabolism of Arctic char (Salvelinus alpinus)

Sustainability issues arise when using fish oil and vegetable oils in fish feed production for aquaculture purposes. Microbial production of single cell oil is a potential alternative as a lipid ingredient in the production of fish feed. In this study, we replaced the vegetable oils with the oleaginous yeast R. toruloides biomass in the diet of Arctic char (S. alpinus) and investigated the effects on health and composition. Measurement of fish growth parameters showed a higher liver weight and hepatosomatic index in the experimental group of fish fed partly with yeast biomass compared to a control group fed a diet with vegetable oils. No significant differences in the lipid content of muscle and liver tissues were found. The fatty acid profiles in the muscle of both fish groups were similar while the experimental fish group had a higher amount of monounsaturated fatty acids in the liver. Histology of livers showed no significant difference in the number of lipid droplets. The size of hepatic lipid droplets seemed to be related to liver fat content. Quantification of metabolites in the liver revealed no differences between the fish groups while plasma metabolites involved in energy pathways such as alanine, 3-hydroxybutyrate, creatinine, serine, betaine, and choline were significantly higher in the experimental fish group.

Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

Ultra-centrifugation force in adaptive evolution changes the cell structure of oleaginous yeast Trichosporon cutaneum into a favorable space for lipid accumulation

Microbial lipid production from lignocellulose biomass provides an essential option for sustainable and carbon neutral supply of future aviation fuels, biodiesel, as well as various food and nutrition products. Oleaginous yeast is the major microbial cell factory but its lipid producing performance is far below the requirements of industrial application. Here we show an ultra-centrifugation fractionation in adaptive evolution (UCF) of Trichosporon cutaneum based on the minor cell density difference. The lightest cells with the maximum intracellular lipid content were isolated by ultra-centrifugation fractionation in the long-term adaptive evolution. Significant changes occurred in the cell morphology with a fragile cell wall wrapping and enlarged intracellular space (two orders of magnitude increase in cell size). Complete and coordinate assimilations of all non-glucose sugars derived from lignocellulose were triggered and fluxed into lipid synthesis. Genome mutations and significant transcriptional regulations of the genes responsible for cell structure were identified and experimentally confirmed. The obtained Trichosporon cutaneum MP11 cells achieved a high lipid production of wheat straw, approximately five-folds greater than that of the parental cells. The study provided an effective method for screening the high lipid containing oleaginous yeast cells as well as the intracellular products accumulating cells in general. This article is protected by copyright. All rights reserved.

Expression Profile of Selected Genes Involved in Storage Lipid Synthesis in a Model Oleaginous Yeast Species Yarrowia lipolytica

Yarrowia lipolytica yeast is a model species of the group of oleaginous microorganisms capable of intracellular lipids accumulation in an amount exceeding 20% of the dry mass. Single cell oil biosynthesis can follow one of two biochemical pathways—de novo accumulation of cellular lipids in medium containing non-lipid carbon sources (including saccharides, glycerol) and ex novo microbial oil synthesis which involves fatty acids uptake from the environment. The mRNA expression of selected genes of de novo and ex novo lipid synthesis pathways was analyzed and correlated with the phenotypically observed features. It was proved that the accumulation yield of storage lipids via ex novo pathway was to some extent dependent on the limitation of the nitrogen source in the medium. It was also proposed that the synthesis of intracellular lipids in lipid-rich medium proceeded mainly via ex novo pathway, although the activity of genes encoding the enzymes of the de novo pathway were not completely inhibited at the stage of transcription by fatty acids present in the medium (e.g., ATP-citrate lyase). Molecular markers of two biosynthesis routes has been outlined and a hypothetical connection point between de novo and ex novo route were indicated.

Coq3p relevant residues for protein activity and stability

Coenzyme Q (CoQ) is an essential molecule that consists of a highly substituted benzene ring attached to a polyprenyl tail anchored in the inner mitochondrial membrane. CoQ transfers electrons from NADH dehydrogenase and succinate dehydrogenase complexes toward ubiquinol-cytochrome c reductase, and that allows aerobic growth of cells. In Saccharomyces cerevisiae, the synthesis of CoQ depends on fourteen proteins Coq1p-Co11p, Yah1p, Arh1p, and Hfd1p. Some of these proteins are components of CoQ synthome. Using ab initio molecular modeling and site-directed mutagenesis, we identified the functional residues of the O-methyltransferase Coq3p, which depends on S-adenosylmethionine for catalysis and is necessary for two O-methylation steps required for CoQ maturation. Conserved residues as well as those that coevolved in the protein structure were found to have important roles in respiratory growth, CoQ biosynthesis, and also in the stability of CoQ synthome proteins. Finally, a multiple sequence alignment showed that S. cerevisiae Coq3p has a 45 amino acid residues insertion that is poorly conserved or absent in oleaginous yeast, cells that can store up to 20% of their dry weight as lipids. These results point to the Coq3p structural determinants of its biological and catalytic function and could contribute to the development of lipid-producing yeast for biotechnology.

Increased Lipid Production in Yarrowia lipolytica from Acetate through Metabolic Engineering and Cosubstrate Fermentation

Bioconversion of acetate, a byproduct generated in industrial processes, into microbial lipids using oleaginous yeasts offers a promising alternative for the economic utilization of acetate-containing waste streams. However, high acetate concentrations will inhibit microbial growth and metabolism. In this study, the acetate utilization capability of Yarrowia lipolytica PO1f was successively improved by overexpressing the key enzyme of acetyl-CoA synthetase (ACS), which resulted in an accumulation of 9.2% microbial lipids from acetate in shake flask fermentation. By further overexpressing the second key enzymes of acetyl-CoA carboxylase (ACC1) and fatty acid synthase (FAS) in Y. lipolytica, the lipid content was increased to 25.7% from acetate. Finally, the maximum OD₆₀₀ of 29.2 and a lipid content of 41.7% were obtained with the engineered strain by the adoption of cosubstrate (glycerol and acetate) fed-batch fermentation, which corresponded to an increase of 68 and 95%, respectively. These results presented a promising strategy for economic and efficient microbial lipid production from the waste acetate.

Strains and approaches for genetic crosses in the oleaginous yeast Lipomyces starkeyi

The oleaginous yeast Lipomyces starkeyi is a powerful lipid producer with great industrial potential. Recent studies have reported the isolation of mutant L. starkeyi cells with higher lipid producing capacity. Although genetic engineering strategies have been applied to L. starkeyi, classical genetic approaches are lacking. The development of tools that facilitate genetic crosses in L. starkeyi would not only make it possible to build improved lipid‐producing strains but also facilitate molecular biological analysis of this species. In this study, I report a set of strains and approaches useful for performing genetic crosses with L. starkeyi. The homothallic L. starkeyi reportedly forms an ascus containing two to 20 spores. These spores were resistant to glusulase and could be dissected using a micromanipulator, suggesting that random spore and tetrad (spore dissection) analysis can be adapted for L. starkeyi. Additionally, to isolate a pair of heterothallic strains useful for genetic crosses, the homothallic strain was exposed to UV irradiation, and 10 self‐sterile strains were crossed with one another. One of these combinations, Ls75 and Ls100, sporulated stably. Moreover, to detect genetic recombination, I introduced a different drug resistance marker into each strain and crossed them. The resulting progeny exhibited Mendelian segregation of the resistance markers. Altogether, the work reported here provides a powerful resource for genetic analysis in L. starkeyi.

Tolerance of Trichosporon cutaneum to lignin derived phenolic aldehydes facilitate the cell growth and cellulosic lipid accumulation

Phenolic aldehydes are the major inhibitors from lignocellulose pretreatment. Previous studies show that oleaginous yeasts are difficult to survive in lignocellulosic hydrolysates even after the removal of furan aldehydes and organic acids inhibitors. This study investigated the cell viability, sugar consumption and lipid accumulation of the major oleaginous yeasts including Trichosporon cutaneum, Rhodosporidium toruloides, Rhodotorula glutinis, Yarrowia lipolytica in wheat straw hydrolysate containing only phenolic aldehydes after furan aldehydes and organic acids were selectively degraded by microorganisms. The results confirmed that the existence of residual phenolic aldehydes was the major reason for poor cell growth and metabolism of oleaginous yeasts. Only T. cutaneum demonstrated the higher tolerance by biodegrading phenolic aldehydes and the satisfactory cell growth and lipid production were obtained. This study revealed that T. cutaneum might be one of the promising cell factories for microbial lipid production from lignocellulosic feedstock.

Global Transcriptome Profile of the Oleaginous Yeast Saitozyma podzolica DSM 27192 Cultivated in Glucose and Xylose

Unlike conventional yeasts, several oleaginous yeasts, including Saitozyma podzolica DSM 27192, possess the innate ability to grow and produce biochemicals from plant-derived lignocellulosic components such as hexose and pentose sugars. To elucidate the genetic basis of S. podzolica growth and lipid production on glucose and xylose, we performed comparative temporal transcriptome analysis using RNA-seq method. Approximately 3.4 and 22.2% of the 10,670 expressed genes were differentially (FDR < 0.05, and log2FC > 1.5) expressed under batch and fed batch modes, respectively. Our analysis revealed that a higher number of sugar transporter genes were significantly overrepresented in xylose relative to glucose-grown cultures. Given the low homology between proteins encoded by most of these genes and those of the well-characterised transporters, it is plausible to conclude that S. podzolica possesses a cache of putatively novel sugar transporters. The analysis also suggests that S. podzolica potentially channels carbon flux from xylose via both the non-oxidative pentose phosphate and potentially via the first steps of the Weimberg pathways to yield xylonic acid. However, only the ATP citrate lyase (ACL) gene showed significant upregulation among the essential oleaginous pathway genes under nitrogen limitation in xylose compared to glucose cultivation. Combined, these findings pave the way toward the design of strategies or the engineering of efficient biomass hydrolysate utilization in S. podzolica for the production of various biochemicals.

Two-Stage Fermentation of Lipomyces starkeyi for Production of Microbial Lipids and Biodiesel

The high operating cost is currently a limitation to industrialize microbial lipids production by the yeast Lipomyces starkeyi. To explore economic fermentation technology, the two-stage fermentation of Lipomyces starkeyi using yeast extract peptone dextrose (YPD) medium, orange peel (OP) hydrolysate medium, and their mixed medium were investigated for seven days by monitoring OD₆₀₀ values, pH values, cell growth status, C/N ratios, total carbon concentration, total nitrogen concentration, residual sugar concentration, lipid content, lipid titer, and fatty acids profiles of lipids. The results showed that two-stage fermentation with YPD and 50% YPD + 50% OP medium contributed to lipid accumulation, leading to larger internal lipid droplets in the yeast cells. However, the cells in pure OP hydrolysate grew abnormally, showing skinny and angular shapes. Compared to the one-stage fermentation, the two-stage fermentation enhanced lipid contents by 18.5%, 27.1%, and 21.4% in the flasks with YPD medium, OP medium, and 50%YPD + 50%OP medium, and enhanced the lipid titer by 77.8%, 13.6%, and 63.0%, respectively. The microbial lipids obtained from both one-stage and two-stage fermentation showed no significant difference in fatty acid compositions, which were mainly dominated by palmitic acid (33.36–38.43%) and oleic acid (46.6–48.12%). Hence, a mixture of commercial medium and lignocellulosic biomass hydrolysate could be a promising option to balance the operating cost and lipid production.

Citrate-Mediated Acyl-CoA Synthesis Is Required for the Promotion of Growth and Triacylglycerol Production in Oleaginous Yeast Lipomyces starkeyi

The oleaginous yeast Lipomyces starkeyi is an excellent producer of triacylglycerol (TAG) as a feedstock for biodiesel production. To understand the regulation of TAG synthesis, we attempted to isolate mutants with decreased lipid productivity and analyze the expression of TAG synthesis-related genes in this study. A mutant with greatly decreased lipid productivity, sr22, was obtained by an effective screening method using Percoll density gradient centrifugation. The expression of citrate-mediated acyl-CoA synthesis-related genes (ACL1, ACL2, ACC1, FAS1, and FAS2) was decreased in the sr22 mutant compared with that of the wild-type strain. Together with a notion that L. starkeyi mutants with increased lipid productivities had increased gene expression, there was a correlation between the expression of these genes and TAG synthesis. To clarify the importance of citrate-mediated acyl-CoA synthesis pathway on TAG synthesis, we also constructed a strain with no ATP-citrate lyase responsible for the first reaction of citrate-mediated acyl-CoA synthesis and investigated the importance of ATP-citrate lyase on TAG synthesis. The ATP-citrate lyase was required for the promotion of cell growth and TAG synthesis in a glucose medium. This study may provide opportunities for the development of an efficient TAG synthesis for biodiesel production.

Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement

Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.

Mitochondrial dynamics and degradation in the oleaginous yeast Lipomyces starkeyi

Emerging evidence implicates the vital role of mitochondria in lipid consumption and storage, highlighting the intimate link between energy production and saving. Although formation of giant lipid droplets, which is the key hallmark of the oleaginous yeast Lipomyces starkeyi, appears to be regulated in response to changes in mitochondrial shape and metabolism, technical limitations of genetic manipulation have become an obstacle to uncover the mitochondrial behavior in this nonconventional yeast. Here, we established an L. starkeyi strain stably expressing a fluorescent marker for monitoring mitochondrial morphology and degradation and found that mitochondria are mostly fragmented in L. starkeyi cells under fermentable, nonfermentable, and nitrogen depletion conditions. Notably, a fraction of mitochondria-specific fluorescent signals was localized to the vacuole, a lytic organelle in yeast, indicating degradation of mitochondria in those cells. This possible catabolic event was more predominant in cells under nutrient-poor conditions than that in cells under nutrient-rich conditions, concomitantly with lipid droplet formation. Collectively, our studies provide a new tool to investigate mitochondrial dynamics in L. starkeyi and decipher the potential role of mitochondrial degradation in lipid metabolism.

Nile Red Incubation Time Before Reading Fluorescence Greatly Influences the Yeast Neutral Lipids Quantification

High-throughput screening methodologies to estimate lipid content in oleaginous yeasts use Nile red fluorescence in a given solvent and optimized excitation/emission wavelengths. However, Nile red fluorescence stabilization has been poorly analyzed, and high variability occurs when relative fluorescence is measured immediately or a few minutes after dye addition. The aim of this work was to analyze the fluorescence of Nile red at different incubation times using a variety of solvents and oleaginous/non-oleaginous yeast strains. We showed that fluorescence stabilization occurs between 20 and 30 min, depending on the strain and solvent. Therefore, we suggest that fluorescence measurements should be followed until stabilization, where Relative Fluorescence Units should be considered after stabilization for lipid content estimation.

Analysis of the Yarrowia lipolytica proteome reveals subtle variations in expression levels between lipogenic and non-lipogenic conditions

Oleaginous yeasts have the ability to store greater than 20% of their mass as neutral lipids, in the form of triacylglycerides. The ATP citrate lyase is thought to play a key role in triacylglyceride synthesis, but the relationship between expression levels of this and other related enzymes is not well understood in the role of total lipid accumulation conferring the oleaginous phenotype. We conducted comparative proteomic analyses with the oleaginous yeast, Yarrowia lipolytica, grown in either nitrogen-sufficient rich media or nitrogen-limited minimal media. Total proteins extracted from cells collected during logarithmic and late stationary growth phases were analyzed by 1D liquid chromatography, followed by mass spectroscopy. The ATP citrate lyase enzyme was expressed at similar concentrations in both conditions, in both logarithmic and stationary phase, but many upstream and downstream enzymes showed drastically different expression levels. In non-lipogenic conditions, several pyruvate enzymes were expressed at higher concentration. These enzymes, especially the pyruvate decarboxylase and pyruvate dehydrogenase, may be regulating carbon flux away from central metabolism and reducing the amount of citrate being produced in the mitochondria. While crucial for the oleaginous phenotype, the constitutively expressed ATP citrate lyase appears to cleave citrate in response to carbon flux upstream from other enzymes creating the oleaginous phenotype.

L-asparaginase Production by Leucosporidium scottii in a Bench-Scale Bioreactor With Co-production of Lipids

L-asparaginase (ASNase) is a therapeutical enzyme used for treatment of acute lymphoblastic leukemia. ASNase products available in the market are produced by bacteria and usually present allergic response and important toxicity effects to the patients. Production of ASNase by yeasts could be an alternative to overcome these problems since yeasts have better compatibility with the human system. Recently, it was found that Leucosporidium scottii, a psychrotolerant yeast, produces ASNase. In order to advance the production of ASNase by this yeast, the present study aimed to select suitable process conditions able to maximize the production of this enzyme in a bench-scale bioreactor. Additionally, the accumulation of lipids during the enzyme production process was also determined and quantified. Experiments were carried out with the aim of selecting the most appropriate conditions of initial cell concentration (1.0, 3.5, and 5.6 g L^–1), carbon source (sucrose and glycerol, individually or in mixture) and oxygen transfer rate (k_La in the range of 1.42–123 h^–1) to be used on the production of ASNase by this yeast. Results revealed that the enzyme production increased when using an initial cell concentration of 5.6 g L^–1, mixture of sucrose and glycerol as carbon source, and k_La of 91.72 h^–1. Under these conditions, the enzyme productivity was maximized, reaching 35.11 U L^–1 h^–1, which is already suitable for the development of scale-up studies. Additionally, accumulation of lipids was observed in all the cultivations, corresponding to 2–7 g L^–1 (32–40% of the cell dry mass), with oleic acid (C_18:1) being the predominant compound (50.15%). Since the L-asparaginase biopharmaceuticals on the market are highly priced, the co-production of lipids as a secondary high-value product during the ASNase production, as observed in the present study, is an interesting finding that opens up perspectives to increase the economic feasibility of the enzyme production process.

Inference of Regulatory System for TAG Biosynthesis in Lipomyces starkeyi

Improving the bioproduction ability of efficient host microorganisms is a central aim in bioengineering. To control biosynthesis in living cells, the regulatory system of the whole biosynthetic pathway should be clearly understood. In this study, we applied our network modeling method to infer the regulatory system for triacylglyceride (TAG) biosynthesis in Lipomyces starkeyi, using factor analyses and structural equation modeling to construct a regulatory network model. By factor analysis, we classified 89 TAG biosynthesis-related genes into nine groups, which were considered different regulatory sub-systems. We constructed two different types of regulatory models. One is the regulatory model for oil productivity, and the other is the whole regulatory model for TAG biosynthesis. From the inferred oil productivity regulatory model, the well characterized genes DGA1 and ACL1 were detected as regulatory factors. Furthermore, we also found unknown feedback controls in oil productivity regulation. These regulation models suggest that the regulatory factor induction targets should be selected carefully. Within the whole regulatory model of TAG biosynthesis, some genes were detected as not related to TAG biosynthesis regulation. Using network modeling, we reveal that the regulatory system is helpful for the new era of bioengineering.

Pulsed Electric Field Treatment Promotes Lipid Extraction on Fresh Oleaginous Yeast Saitozyma podzolica DSM 27192

This study reports on the use of pulsed electric field (PEF) as a pre-treatment step to enhance lipid extraction yield using extraction with ethanol-hexane blend on fresh oleaginous yeast Saitozyma podzolica. The yeasts were cultivated on nitrogen-depleted condition and had a lipid content of 26.4 ± 4.6% of dry weight. PEF-treatment was applied on the yeast suspension either directly after harvesting (unwashed route) or after a washing step (washed route) which induced a reduction of conductivity by a factor eight. In both cases, cell concentration was 20 g of biomass per liter of suspension. In the unwashed route, the lipid extraction efficiency increased from 7% (untreated) to 54% thanks to PEF-treatment. In case an additional washing step was added after PEF-treatment, up to 81% of the lipid content could be recovered. The washed route was even more efficient since lipid extraction yields increased from 26% (untreated) to 99% of total lipid. The energy input for the PEF-treatment never exceeded 150 kJ per liter of initial suspension. The best lipid recovery scenario was obtained using pulses of 1 μs, an electric field of 40 kV/cm and it required slightly less than 11 MJ/kg_LIPID. This amount of energy can be further reduced by at least a factor five by optimizing the treatment and especially by increasing the concentration of the treated biomass. The process can be easily up-scaled and does not require any expensive handling of the biomass such as freezing or freeze-drying. These findings demonstrate the potential benefit of PEF-treatment in the downstream processing of oleaginous yeast. From a basic research point of view, the influence of conductivity on PEF energy requirements and extraction yields was examined, and results suggest a higher efficiency of PEF-treatment in terms of energy when treatment is performed at lower conductivity.

Metabolic Engineering of Oleaginous Yeast Yarrowia lipolytica for Overproduction of Fatty Acids

The oleaginous yeast Yarrowia lipolytica has attracted much attention due to its ability to utilize a wide range of substrates to accumulate high lipid content and its flexibility for genetic manipulation. In this study, intracellular lipid metabolism in Y. lipolytica was tailored to produce fatty acid, a renewable oleochemical and precursor for production of advanced biofuels. Two main strategies, including blocking activation and peroxisomal uptake of fatty acids and elimination of biosynthesis of lipids, were employed to reduce fatty acid consumption by the native pathways in Y. lipolytica. Both genetic modifications improved fatty acid production. However, disruption of the genes responsible for assembly of nonpolar lipid molecules including triacylglycerols (TAGs) and steryl esters resulted in the deleterious effects on the cell growth. The gene tesA encoding thioesterase from Escherichia coli was expressed in the strain with disrupted faa genes encoding fatty acyl-CoA synthetases and pxa1 encoding peroxisomal acyl-CoA transporter, and the titer of fatty acids resulted in 2.3 g/L in shake flask culture, representing 11-fold improvement compared with the parent strain. Expressing the native genes encoding acetyl-CoA carboxylase (ACC) and hexokinase also increased fatty acid production, although the improvement was not as significant as that with tesA expression. Saturated fatty acids including palmitic acid (C16:0) and stearic acid (C18:0) increased remarkably in the fatty acid composition of the recombinant bearing tesA compared with the parent strain. The recombinant expressing tesA gene resulted in high lipid content, indicating the great fatty acid producing potential of Y. lipolytica. The results highlight the achievement of fatty acid overproduction without adverse effect on growth of the strain. Results of this study provided insight into the relationship between fatty acid and lipid metabolism in Y. lipolytica, confirming the avenue to reprogram lipid metabolism of this host for overproduction of renewable fatty acids.

Identification of Genes Encoding CENP-A and Heterochromatin Protein 1 of Lipomyces starkeyi and Functional Analysis Using Schizosaccharomyces pombe

Centromeres function as a platform for the assembly of multiple kinetochore proteins and are essential for chromosome segregation. An active centromere is characterized by the presence of a centromere-specific histone H3 variant, CENP-A. Faithful centromeric localization of CENP-A is supported by heterochromatin in almost all eukaryotes; however, heterochromatin proteins have been lost in most Saccharomycotina. Here, identification of CENP-A (CENP-A^L.s.) and heterochromatin protein 1 (Lsw1) in a Saccharomycotina species, the oleaginous yeast Lipomyces starkeyi, is reported. To determine if these proteins are functional, the proteins in S. pombe, a species widely used to study centromeres, were ectopically expressed. CENP-A^L.s. localizes to centromeres and can be replaced with S. pombe CENP-A, indicating that CENP-A^L.s. is a functional centromere-specific protein. Lsw1 binds at heterochromatin regions, and chromatin binding is dependent on methylation of histone H3 at lysine 9. In other species, self-interaction of heterochromatin protein 1 is thought to cause folding of chromatin, triggering transcription repression and heterochromatin formation. Consistent with this, it was found that Lsw1 can self-interact. L. starkeyi chromatin contains the methylation of histone H3 at lysine 9. These results indicated that L. starkeyi has a primitive heterochromatin structure and is an attractive model for analysis of centromere heterochromatin evolution.

Lipid Production from Sugarcane Top Hydrolysate and Crude Glycerol with Rhodosporidiobolus fluvialis using a Two-Stage Batch-Cultivation Strategy with Separate Optimization of Each Stage

Lipids from oleaginous microorganisms, including oleaginous yeasts, are recognized as feedstock for biodiesel production. A production process development of these organisms is necessary to bring lipid feedstock production up to the industrial scale. This study aimed to enhance lipid production of low-cost substrates, namely sugarcane top and biodiesel-derived crude glycerol, by using a two-stage cultivation process with Rhodosporidiobolus fluvialis DMKU-SP314. In the first stage, sugarcane top hydrolysate was used for cell propagation, and in the second stage, cells were suspended in a crude glycerol solution for lipid production. Optimization for high cell mass production in the first stage, and for high lipid production in the second stage, were performed separately using a one-factor-at-a-time methodology together with response surface methodology. Under optimum conditions in the first stage (sugarcane top hydrolysate broth containing; 43.18 g/L total reducing sugars, 2.58 g/L soy bean powder, 0.94 g/L (NH₄)₂SO₄, 0.39 g/L KH₂PO₄ and 2.5 g/L MgSO₄ 7H₂O, pH 6, 200 rpm, 28 °C and 48 h) and second stage (81.54 g/L crude glycerol, pH 5, 180 rpm, 27 °C and 196 h), a high lipid concentration of 15.85 g/L, a high cell mass of 21.07 g/L and a high lipid content of 73.04% dry cell mass were obtained.

Effect of light on carotenoid and lipid production in the oleaginous yeast Rhodosporidium toruloides

The oleaginous yeast Rhodosporodium toruloides is receiving widespread attention as an alternative energy source for biofuels due to its unicellular nature, high growth rate and because it can be fermented on a large-scale. In this study, R. toruloides was cultured under both light and dark conditions in order to understand the light response involved in lipid and carotenoid biosynthesis. Our results from phenotype and gene expression analysis showed that R. toruloides responded to light by producing darker pigmentation with an associated increase in carotenoid production. Whilst there was no observable difference in lipid production, slight changes in the fatty acid composition were recorded. Furthermore, a two-step response was found in three genes (GGPSI, CAR1, and CAR2) under light conditions and the expression of the gene encoding the photoreceptor CRY1 was similarly affected.

Feeding Strategies of Two-Stage Fed-Batch Cultivation Processes for Microbial Lipid Production from Sugarcane Top Hydrolysate and Crude Glycerol by the Oleaginous Red Yeast Rhodosporidiobolus fluvialis

Microbial lipids are able to produce from various raw materials including lignocellulosic biomass by the effective oleaginous microorganisms using different cultivation processes. This study aimed to enhance microbial lipid production from the low-cost substrates namely sugarcane top hydrolysate and crude glycerol by Rhodosporidiobolus fluvialis DMKU-SP314, using two-stage fed-batch cultivation with different feeding strategies in a 3 L stirred-tank fermenter. The effect of two feeding strategies of 147.5 g/L crude glycerol solution was evaluated including pulse feeding at different starting time points (48, 24, and 72 h after initiation of batch operation) and constant feeding at different dilution rates (0.012, 0.020, and 0.033 h-1). The maximum lipid concentration of 23.6 g/L and cell mass of 38.5 g/L were achieved when constant feeding was performed at the dilution rate of 0.012 h-1 after 48 h of batch operation, which represented 1.24-fold and 1.27-fold improvements in the lipid and cell mass concentration, respectively. Whereas, batch cultivation provided 19.1 g/L of lipids and 30.3 g/L of cell mass. The overall lipid productivity increased to 98.4 mg/L/d in the two-stage fed-batch cultivation. This demonstrated that the two-stage fed-batch cultivation with constant feeding strategy has the possibility to apply for large-scale production of lipids by yeast.

Grease Waste as a Reservoir of Lipase-Producing Yeast and Description of Limtongella siamensis gen. nov., sp. nov

A total of 175 yeast isolates were obtained from grease samples. Based on the D1/D2 region of the large subunit (LSU) ribosomal RNA (rRNA) gene analysis, 150 yeast isolates were identified as belonging to 36 described yeast species, whereas 25 isolates required more analysis. Among the described species, Rhodotorula mucilaginosa was the only Basidiomycetous yeast, whereas 149 isolates were identified as belonging to 35 described species of 15 genera in the phylum Ascomycota, and Candida tropicalis was the most abundant species. A study of lipase production indicated that strain DMKU-JMGT1-45 showed volumetric activity of 38.89 ± 9.62 and 155.56 ± 14.70 U/mL when grown in yeast extract malt extract (YM) and YM supplemented with 1% olive oil, respectively. In addition, this strain intracellularly accumulated lipid, of which the fatty acid profile revealed the major fatty acids to be 39.9% oleic acid (C18:1), 27.61% palmitoleic acid (C16:1) and 14.97% palmitic acid (C16:0). A phylogenetic analysis of the combined multi-locus gene sequences showed that the strains DMKU-JMGT1-45^T and DMKU-JMGT4-14 formed a well-separated lineage and could not be assigned to any of the currently recognized genera of the Saccharomycetales. Limtongella siamensis gen. nov., sp. nov. is therefore proposed to accommodate these two strains as members of the order Saccharomycetales.

Optimizing Oleaginous Yeast Cell Factories for Flavonoids and Hydroxylated Flavonoids Biosynthesis

Plants possess myriads of secondary metabolites with a broad spectrum of health-promoting benefits. To date, plant extraction is still the primary route to produce high-value natural products which inherently suffers from economics and scalability issues. Heterologous expression of plant biosynthetic gene clusters in microbial host is considered as a feasible approach to overcoming these limitations. Oleaginous yeast produces a large amount of lipid bodies, the abundant membrane structure and the lipophilic environment provide the ideal environment for the regioselectivity and stereoselectivity of many plant-derived P450 enzymes. In this work, we used modular method to construct, characterize, and optimize the flavonoid pathways in Yarrowia lipolytica. We also evaluated various precursor biosynthetic routes and unleashed the metabolic potential of Y. lipolytica to produce flavonoids and hydroxylated flavonoids. Specifically, we have identified that chalcone synthase (CHS) and cytochrome P450 reductases (CPR) were the bottlenecks of hydroxylated flavonoid production. We determined the optimal gene copy number of CHS and CPR to be 5 and 2, respectively. We further removed precursor pathway limitations by expressing genes associated with chorismate and malonyl-CoA supply. With pH and carbon-nitrogen ratio (C/N) optimization, our engineered strain produced 252.4 mg/L naringenin, 134.2 mg/L eriodictyol, and 110.5 mg/L taxifolin from glucose in shake flasks. Flavonoid and its hydroxylated derivatives are most prominently known as antioxidant and antiaging agents. These findings demonstrate our ability to harness the oleaginous yeast as the microbial workhorse to expand nature's biosynthetic potential, enabling us to bridge the gap between drug discovery and natural product manufacturing.

Achieving a high-density oleaginous yeast culture: Comparison of four processing strategies using Metschnikowia pulcherrima

Microbial lipids have the potential to displace terrestrial oils for fuel, value chemical, and food production, curbing the growth in tropical oil plantations and helping to reduce deforestation. However, commercialization remains elusive partly due to the lack of suitably robust organisms and their low lipid productivity. Extremely high cell densities in oleaginous cultures are needed to increase reaction rates, reduce reactor volume, and facilitate downstream processing. In this investigation, the oleaginous yeast Metschnikowia pulcherrima, a known antimicrobial producer, was cultured using four different processing strategies to achieve high cell densities and gain suitable lipid productivity. In batch mode, the yeast demonstrated lipid contents more than 40% (w/w) under high osmotic pressure. In fed-batch mode, however, high-lipid titers were prevented through inhibition above 70.0 g L^-1 yeast biomass. Highly promising were a semi-continuous and continuous mode with cell recycle where cell densities of up to 122.6 g L^-1 and maximum lipid production rates of 0.37 g L^-1  h^-1 (daily average), a nearly two-fold increase from the batch, were achieved. The findings demonstrate the importance of considering multiple fermentation modes to achieve high-density oleaginous yeast cultures generally and indicate the limitations of processing these organisms under the extreme conditions necessary for economic lipid production.

Utilization of Clarified Butter Sediment Waste as a Feedstock for Cost-Effective Production of Biodiesel

The rising demand and cost of fossil fuels (diesel and gasoline), together with the need for sustainable, alternative, and renewable energy sources have increased the interest for biomass-based fuels such as biodiesel. Among renewable sources of biofuels, biodiesel is particularly attractive as it can be used in conventional diesel engines without any modification. Oleaginous yeasts are excellent oil producers that can grow easily on various types of hydrophilic and hydrophobic waste streams that are used as feedstock for single cell oils and subsequently biodiesel production. In this study, cultivation of Rhodosporidium kratochvilovae on a hydrophobic waste (clarified butter sediment waste medium (CBM)) resulted in considerably high lipid accumulation (70.74% w/w). Maximum cell dry weight and total lipid production were 15.52 g/L and 10.98 g/L, respectively, following cultivation in CBM for 144 h. Neutral lipids were found to accumulate in the lipid bodies of cells, as visualized by BODIPY staining and fluorescence microscopy. Cells grown in CBM showed large and dispersed lipid droplets in the intracellular compartment. The fatty acid profile of biodiesel obtained after transesterification was analyzed by gas chromatography-mass spectrometry (GC–MS), while its quality was determined to comply with ASTM 6751 and EN 14214 international standards. Hence, clarified sediment waste can be exploited as a cost-effective renewable feedstock for biodiesel production.

Improvement of lipid production in oleaginous yeast Rhodosporidium toruloides by ultraviolet mutagenesis

The oleaginous yeast Rhodosporidium toruloides AS 2.1389 is viewed as desirable industrial microorganisms that can accumulate a high content of lipids for biodiesel production. In this study, we attempted to improve lipid accumulation in the yeast Rhodosporidium toruloides by UV irradiation mutagenesis and selection based on lithium chloride tolerance or ethanol-H₂O₂ tolerance. The biomass concentration, lipid yield and glucose consumption of mutant R. toruloides were determined. The transcription levels of lipid accumulation-related genes in the wild-type and mutant strains were also determined. The lithium chloride-tolerant strain R-ZL2 and the ethanol-H₂O₂-resistant strain R-ZY13 were generated by UV mutagenesis. The two mutant strains showed greater lipid productivity and lipid yield compared to the wild type. Transcriptional analysis revealed that IDP1, GPD1 and GND were expressed at significantly higher levels in the two high-lipid-producing mutants. In conclusion, lipid productivity and lipid yield in R. toruloides were successfully improved via UV mutagenesis and selection. We also identified some lipid accumulation-related genes for improving lipid productivity through genetic engineering.

Valorization of Brewers' Spent Grain for the Production of Lipids by Oleaginous Yeast

Brewers’ spent grain (BSG) accounts for 85% of the total amount of by-products generated by the brewing industries. BSG is a lignocellulosic biomass that is rich in proteins, lipids, minerals, and vitamins. In the present study, BSG was subjected to pretreatment by two different methods (microwave assisted alkaline pretreatment and organosolv) and was evaluated for the liberation of glucose and xylose during enzymatic saccharification trials. The highest amount of glucose (46.45 ± 1.43 g/L) and xylose (25.15 ± 1.36 g/L) were observed after enzymatic saccharification of the organosolv pretreated BSG. The glucose and xylose yield for the microwave assisted alkaline pretreated BSG were 34.86 ± 1.27 g/L and 16.54 ± 2.1 g/L, respectively. The hydrolysates from the organosolv pretreated BSG were used as substrate for the cultivation of the oleaginous yeast Rhodosporidium toruloides, aiming to produce microbial lipids. The yeast synthesized as high as 18.44 ± 0.96 g/L of cell dry weight and 10.41 ± 0.34 g/L lipids (lipid content of 56.45 ± 0.76%) when cultivated on BSG hydrolysate with a C/N ratio of 500. The cell dry weight, total lipid concentration and lipid content were higher compared to the results obtained when grown on synthetic media containing glucose, xylose or mixture of glucose and xylose. To the best of our knowledge, this is the first report using hydrolysates of organosolv pretreated BSG for the growth and lipid production of oleaginous yeast in literature. The lipid profile of this oleaginous yeast showed similar fatty acid contents to vegetable oils, which can result in good biodiesel properties of the produced biodiesel.

Multiple Parameters Drive the Efficiency of CRISPR/Cas9-Induced Gene Modifications in Yarrowia lipolytica

Yarrowia lipolytica is an oleaginous yeast of growing industrial interest for biotechnological applications. In the last few years, genome edition has become an easier and more accessible prospect with the world wild spread development of CRISPR/Cas9 technology. In this study, we focused our attention on the production of the two key elements of the CRISPR-Cas9 ribonucleic acid protein complex in this non-conventional yeast. The efficiency of NHEJ-induced knockout was measured by time-course monitoring using multiple parameters flow cytometry, as well as phenotypic and genotypic observations, and linked to nuclease production levels showing that its strong overexpression is unnecessary. Thus, the limiting factor for the generation of a functional ribonucleic acid protein complex clearly resides in guide expression, which was probed by testing different linker lengths between the transfer RNA promoter and the sgRNA. The results highlight a clear deleterious effect of mismatching bases at the 5' end of the target sequence. For the first time in yeast, an investigation of its maturation from the primary transcript was undertaken by sequencing multiple sgRNAs extracted from the host. These data provide insights into of the yeast small RNA processing, from synthesis to maturation, and suggests a pathway for their degradation in Y. lipolytica. Subsequently, a whole-genome sequencing of a modified strain detected no abnormal modification due to off-target effects, confirming CRISPR/Cas9 as a safe strategy for editing Y. lipolytica genome. Finally, the optimized system was used to promote in vivo directed mutagenesis via homology-directed repair with a ssDNA oligonucleotide.

Sugar versus fat: elimination of glycogen storage improves lipid accumulation in Yarrowia lipolytica

Triacylglycerol (TAG) and glycogen are the two major metabolites for carbon storage in most eukaryotic organisms. We investigated the glycogen metabolism of the oleaginous Yarrowia lipolytica and found that this yeast accumulates up to 16% glycogen in its biomass. Assuming that elimination of glycogen synthesis would result in an improvement of lipid accumulation, we characterized and deleted the single gene coding for glycogen synthase, YlGSY1. The mutant was grown under lipogenic conditions with glucose and glycerol as substrates and we obtained up to 60% improvement in TAG accumulation compared to the wild-type strain. Additionally, YlGSY1 was deleted in a background that was already engineered for high lipid accumulation. In this obese background, TAG accumulation was also further increased. The highest lipid content of 52% was found after 3 days of cultivation in nitrogen-limited glycerol medium. Furthermore, we constructed mutants of Y. lipolytica and Saccharomyces cerevisiae that are deleted for both glycogen and TAG synthesis, demonstrating that the ability to store carbon is not essential. Overall, this work showed that glycogen synthesis is a competing pathway for TAG accumulation in oleaginous yeasts and that deletion of the glycogen synthase has beneficial effects on neutral lipid storage.

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.

The fungus Rhodosporidium toruloides can grow on substances extracted from plant matter that is inedible to humans such as corn stalks, wood pulp, and grasses. Under some growth conditions, the fungus can accumulate massive stores of hydrocarbon-rich fats and pigments. A community of scientists and engineers has begun genetically modifying R. toruloides to convert these naturally produced fats and pigments into fuels, chemicals and medicines. These could form sustainable replacements for products made from petroleum or harvested from threatened animal and plant species.

Fungi, plants, animals and other eukaryotes store fat in specialized compartments called lipid droplets. The genes that control the metabolism – the production, use and storage – of fat in lipid bodies have been studied in certain eukaryotes, including species of yeast. However, R. toruloides is only distantly related to the most well-studied of these species. This means that we cannot be certain that a gene will play the same role in R. toruloides as in those species.

To assemble the most comprehensive list possible of the genes in R. toruloides that affect the production, use, or storage of fat in lipid bodies, Coradetti, Pinel et al. constructed a population of hundreds of thousands of mutant fungal strains, each with its own unique DNA ‘barcode’. The effects that mutations in over 6,000 genes had on growth and fat accumulation in these fungi were measured simultaneously in several experiments. This general approach is not new, but technical limitations had, until now, restricted its use in fungi to a few species.

Coradetti, Pinel et al. identified hundreds of genes that affected the ability of R. toruloides to metabolise fat. Many of these genes were related to genes with known roles in fat metabolism in other eukaryotes. Other genes are involved in different cell processes, such as the recycling of waste products in the cell. Their identification adds weight to the view that the links between these cellular processes and fat metabolism are deep and widespread amongst eukaryotes. Finally, some of the genes identified by Coradetti, Pinel et al. are not closely related to any well-studied genes. Further study of these genes could help us to understand why R. toruloides can accumulate much larger amounts of fat than most other fungi.

The methods developed by Coradetti, Pinel et al. should be possible to implement in many species of fungi. As a result these techniques may eventually contribute to the development of new treatments for human fungal diseases, the protection of important food crops, and a deeper understanding of the roles various fungi play in the broader ecosystem.

Lumping kinetics of ABE fermentation wastewater treatment by oleaginous yeast Trichosporon cutaneum

Lumping kinetics models were built for the biological treatment of acetone-butanol-ethanol (ABE) fermentation wastewater by oleaginous yeast Trichosporon cutaneum with different fermentation temperatures. Compared with high temperature (33°C, 306 K) and low temperature (23°C, 296 K), medium temperature (28°C, 301 K) was beneficial for the cell growth and chemical oxygen demand (COD) degradation during the early stage of fermentation but the final yeast biomass and COD removal were influenced little. By lumping method, the materials in the bioconversion network were divided into five lumps (COD, lipid, polysaccharide, other intracellular products, other extracellular products), and the nine rate constants (k₁-k₉) for the models can well explain the bioconversion laws. The Gibbs free energy (G) for this bioconversion was positive, showing that it cannot happen spontaneous, but the existence of yeast can after the chemical equilibrium and make the bioconversion to be possible. Overall, the possibility of using lumping kinetics for elucidating the laws of materials conversion in the biological treatment of ABE fermentation wastewater by T. cutaneum has been initially proved and this method has great potential for further application.

Fast and efficient genetic transformation of oleaginous yeast Rhodosporidium toruloides by using electroporation

Metabolic engineering of Rhodosporidium toruloides, a robust lipid and caroteinoid producer, is of great importance for oleochemicals and carotenoids production. However, the Agrobacterium-mediated gene transformation is tedious and time consuming. Here, we described a fast and efficient genetic transformation of R. toruloides using electroporation with linear DNA fragments, and the process was optimized. The results showed that 2 × 103 transformants can be obtained at 0.7 kV/μg linear DNA by using hygromycin and bleomycin as selection markers after the competent cells pretreated with 25 mM DTT and 100 mM LiAc. Our results would facilitate mutant library construction and metabolic engineering of R. toruloides for production of oleochemicals and carotenoids. We further demonstrated that all transformants arose due to illegitimate integration of transforming DNA fragments by colony PCR.

Sugar versus fat: elimination of glycogen storage improves lipid accumulation in Yarrowia lipolytica

Triacylglycerol (TAG) and glycogen are the two major metabolites for carbon storage in most eukaryotic organisms. We investigated the glycogen metabolism of the oleaginous Yarrowia lipolytica and found that this yeast accumulates up to 16% glycogen in its biomass. Assuming that elimination of glycogen synthesis would result in an improvement of lipid accumulation, we characterized and deleted the single gene coding for glycogen synthase, YlGSY1. The mutant was grown under lipogenic conditions with glucose and glycerol as substrates and we obtained up to 60% improvement in TAG accumulation compared to the wild-type strain. Additionally, YlGSY1 was deleted in a background that was already engineered for high lipid accumulation. In this obese background, TAG accumulation was also further increased. The highest lipid content of 52% was found after 3 days of cultivation in nitrogen-limited glycerol medium. Furthermore, we constructed mutants of Y. lipolytica and Saccharomyces cerevisiae that are deleted for both glycogen and TAG synthesis, demonstrating that the ability to store carbon is not essential. Overall, this work showed that glycogen synthesis is a competing pathway for TAG accumulation in oleaginous yeasts and that deletion of the glycogen synthase has beneficial effects on neutral lipid storage.

New kids on the block: emerging oleaginous yeast of biotechnological importance

There is growing interest in using oleaginous yeast for the production of a variety of fatty acids and fatty acid-derived oleochemicals. This is motivated by natural propensity for high flux through lipid biosynthesis that has naturally evolved, making them a logical starting point for additional genetic engineering to improve titers and productivities. Much of the academic and industrial focus has centered on yeast that have significant genetic engineering tool capabilities, such as Yarrowia lipolytica, and those that have naturally high lipid accumulation, such as Rhodosporidium toruloides and Lipomyces starkeyi; however, there are oleaginous yeast with phenotypes better aligned with typically inhibitory process conditions, such as high salt concentrations and lignocellulosic derived inhibitors. This review addresses the foundational work in characterizing two emerging oleaginous yeast of interest: Debaryomyces hansenii and Trichosporon oleaginosus. We focus on the physiological and metabolic properties of these yeast that make each attractive for bioprocessing of lignocellulose to fuels and chemicals, discuss their respective genetic engineering tools and highlight the critical barriers facing the broader implementation of these oleaginous yeast.

Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica

Nitrogen source is commonly used to control lipid production in industrial fungi. Here we identified regulators of nitrogen catabolite repression in the oleaginous yeast Y. lipolytica to determine how the nitrogen source regulates lipid metabolism. We show that disruption of both activators and repressors of nitrogen catabolite repression leads to increased lipid accumulation via activation of carbon catabolite repression through an as yet uncharacterized method.

Fungi accumulate lipids in a manner dependent on the quantity and quality of the nitrogen source on which they are growing. In the oleaginous yeast Yarrowia lipolytica, growth on a complex source of nitrogen enables rapid growth and limited accumulation of neutral lipids, while growth on a simple nitrogen source promotes lipid accumulation in large lipid droplets. Here we examined the roles of nitrogen catabolite repression and its regulation by GATA zinc finger transcription factors on lipid metabolism in Y. lipolytica. Deletion of the GATA transcription factor genes gzf3 and gzf2 resulted in nitrogen source-specific growth defects and greater accumulation of lipids when the cells were growing on a simple nitrogen source. Deletion of gzf1, which is most similar to activators of genes repressed by nitrogen catabolite repression in filamentous ascomycetes, did not affect growth on the nitrogen sources tested. We examined gene expression of wild-type and GATA transcription factor mutants on simple and complex nitrogen sources and found that expression of enzymes involved in malate metabolism, beta-oxidation, and ammonia utilization are strongly upregulated on a simple nitrogen source. Deletion of gzf3 results in overexpression of genes with GATAA sites in their promoters, suggesting that it acts as a repressor, while gzf2 is required for expression of ammonia utilization genes but does not grossly affect the transcription level of genes predicted to be controlled by nitrogen catabolite repression. Both GATA transcription factor mutants exhibit decreased expression of genes controlled by carbon catabolite repression via the repressor mig1, including genes for beta-oxidation, highlighting the complex interplay between regulation of carbon, nitrogen, and lipid metabolism.

IMPORTANCE Nitrogen source is commonly used to control lipid production in industrial fungi. Here we identified regulators of nitrogen catabolite repression in the oleaginous yeast Y. lipolytica to determine how the nitrogen source regulates lipid metabolism. We show that disruption of both activators and repressors of nitrogen catabolite repression leads to increased lipid accumulation via activation of carbon catabolite repression through an as yet uncharacterized method.

Lipid production by yeasts grown on crude glycerol from biodiesel industry

The main carbon source used for growth by four yeast strains (Yarrowia lipolytica CCMA 0357, Y. lipolytica CCMA 0242, Wickerhamomyces anomalus CCMA 0358, and Cryptococcus humicola CCMA 0346) and their lipid production were evaluated, using different concentrations of crude and pure glycerol and glucose. Whereas crude glycerol (100 g/L) was the main carbon source used by Y. lipolytica CCMA 0357 (nearly 15 g/L consumed at 120 hr) and W. anomalus CCMA 0358 (nearly 45.10 g/L consumed at 48 hr), pure glycerol (150 g/L) was the main one used by C. humicola CCMA 0346 (nearly 130 g/L consumed). On the other hand, Y. lipolytica CCMA 0242 used glucose (100 g/L) as its main source of carbon (nearly 96.48 g/L consumed). Y. lipolytica CCMA 0357 demonstrated the highest lipid production [about 70% (wt/wt)], forming palmitic (45.73% of fatty acid composition), stearic (16.43%), palmitoleic (13.29%), linolenic (10.77%), heptadecanoic (4.07%), and linoleic (14.14%) acids. Linoleic acid, an essential fatty acid, was produced by all four yeast strains but in varying degrees, representing 70.42% of the fatty acid profile of lipids produced by C. humicola CCMA 0346.

Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals

Harnessing lipogenic pathways and rewiring acyl-CoA and acyl-ACP (acyl carrier protein) metabolism in Yarrowia lipolytica hold great potential for cost-efficient production of diesel, gasoline-like fuels, and oleochemicals. Here we assessed various pathway engineering strategies in Y. lipolytica toward developing a yeast biorefinery platform for sustainable production of fuel-like molecules and oleochemicals. Specifically, acyl-CoA/acyl-ACP processing enzymes were targeted to the cytoplasm, peroxisome, or endoplasmic reticulum to generate fatty acid ethyl esters and fatty alkanes with tailored chain length. Activation of endogenous free fatty acids and the subsequent reduction of fatty acyl-CoAs enabled the efficient synthesis of fatty alcohols. Engineering a hybrid fatty acid synthase shifted the free fatty acids to a medium chain-length scale. Manipulation of alternative cytosolic acetyl-CoA pathways partially decoupled lipogenesis from nitrogen starvation and unleashed the lipogenic potential of Y. lipolytica Taken together, the strategies reported here represent promising steps to develop a yeast biorefinery platform that potentially upgrades low-value carbons to high-value fuels and oleochemicals in a sustainable and environmentally friendly manner.