Evaluation of lipid production from xylose and glucose/xylose mixed sugar in various oleaginous yeasts and improvement of lipid production by UV mutagenesis

Engineering oleaginous red yeasts as versatile chassis for the production of oleochemicals and valuable compounds: Current advances and perspectives

Enabling the transition towards a future circular bioeconomy based on industrial biomanufacturing necessitates the development of efficient and versatile microbial platforms for sustainable chemical and fuel production. Recently, there has been growing interest in engineering non-model microbes as superior biomanufacturing platforms due to their broad substrate range and high resistance to stress conditions. Among these non-conventional microbes, red yeasts belonging to the genus Rhodotorula have emerged as promising industrial chassis for the production of specialty chemicals such as oleochemicals, organic acids, fatty acid derivatives, terpenoids, and other valuable compounds. Advancements in genetic and metabolic engineering techniques, coupled with systems biology analysis, have significantly enhanced the production capacity of red yeasts. These developments have also expanded the range of substrates and products that can be utilized or synthesized by these yeast species. This review comprehensively examines the current efforts and recent progress made in red yeast research. It encompasses the exploration of available substrates, systems analysis using multi-omics data, establishment of genome-scale models, development of efficient molecular tools, identification of genetic elements, and engineering approaches for the production of various industrially relevant bioproducts. Furthermore, strategies to improve substrate conversion and product formation both with systematic and synthetic biology approaches are discussed, along with future directions and perspectives in improving red yeasts as more versatile biotechnological chassis in contributing to a circular bioeconomy. The review aims to provide insights and directions for further research in this rapidly evolving field. Ultimately, harnessing the capabilities of red yeasts will play a crucial role in paving the way towards next-generation sustainable bioeconomy.

Sustainable biorefinery approach by utilizing xylose fraction of lignocellulosic biomass

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

Transcriptomic profiling of an evolved Yarrowia lipolytica strain: tackling hexanoic acid fermentation to increase lipid production from short-chain fatty acids

BACKGROUND

Short-chain fatty acids (SCFAs) are cost-effective carbon sources for an affordable production of lipids. Hexanoic acid, the acid with the longest carbon chain in the SCFAs pool, is produced in anaerobic fermentation of organic residues and its use is very challenging, even inhibiting oleaginous yeasts growth.

RESULTS

In this investigation, an adaptive laboratory evolution (ALE) was performed to improve Yarrowia lipolytica ACA DC 50109 tolerance to high hexanoic acid concentrations. Following ALE, the transcriptomic analysis revealed several genetic adaptations that improved the assimilation of this carbon source in the evolved strain compared to the wild type (WT). Indeed, the evolved strain presented a high expression of the up-regulated gene YALI0 E16016g, which codes for FAT1 and is related to lipid droplets formation and responsible for mobilizing long-chain acids within the cell. Strikingly, acetic acid and other carbohydrate transporters were over-expressed in the WT strain.

CONCLUSIONS

A more tolerant yeast strain able to attain higher lipid content under the presence of high concentrations of hexanoic acid has been obtained. Results provided novel information regarding the assimilation of hexanoic acid in yeasts.

Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates

Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log₂ fold change| ≥ 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose.

LsSpt23p is a regulator of triacylglycerol synthesis in the oleaginous yeast Lipomyces starkeyi

The oleaginous yeast Lipomyces starkeyi has considerable potential in industrial application, since it can accumulate a large amount of triacylglycerol (TAG), which is produced from sugars under nitrogen limitation condition. However, the regulation of lipogenesis in L. starkeyi has not been investigated in depth. In this study, we compared the genome sequences of wild-type and mutants with increased TAG productivity, and identified a regulatory protein, LsSpt23p, which contributes to the regulation of TAG synthesis in L. starkeyi. L. starkeyi mutants overexpressing LsSPT23 had increased TAG productivity compared with the wild-type strain. Quantitative real-time PCR analysis showed that LsSpt23p upregulated the expression of GPD1, which encodes glycerol 3-phosphate dehydrogenase; the Kennedy pathway genes SCT1, SLC1, PAH1, DGA1, and DGA2; the citrate-mediated acyl-CoA synthesis pathway-related genes ACL1, ACL2, ACC1, FAS1, and FAS2; and OLE1, which encodes ∆9 fatty acid desaturase. Chromatin immunoprecipitation-quantitative PCR assays indicated that LsSpt23p acts as a direct regulator of SLC1 and PAH1, all the citrate-mediated acyl-CoA synthesis pathway-related genes, and OLE1. These results indicate that LsSpt23p regulates TAG synthesis. Phosphatidic acid is a common substrate of phosphatidic acid phosphohydrolase, which is used for TAG synthesis, and phosphatidate cytidylyltransferase 1 for phospholipid synthesis in the Kennedy pathway. LsSpt23p directly regulated PAH1 but did not affect the expression of CDS1, suggesting that the preferred route of carbon is the Pah1p-mediated TAG synthesis pathway under nitrogen limitation condition. The present study contributes to understanding the regulation of TAG synthesis, and will be valuable in future improvement of TAG productivity in oleaginous yeasts. KEY POINTS: LsSpt23p was identified as a positive regulator of TAG biosynthesis LsSPT23 overexpression enhanced TAG biosynthesis gene expression and TAG production LsSPT23_M1108T overexpression mutant showed fivefold higher TAG production than control.

Phosphate limitation as crucial factor to enhance yeast lipid production from short-chain fatty acids

Microbial lipids for chemical synthesis are commonly obtained from sugar-based substrates which in most cases is not economically viable. As a low-cost carbon source, short-chain fatty acids (SCFAs) that can be obtained from food wastes offer an interesting alternative for achieving an affordable lipid production process. In this study, SCFAs were employed to accumulate lipids using Yarrowia lipolytica ACA DC 50109. For this purpose, different amounts of SCFAs, sulfate, phosphate and carbon: phosphate ratios were used in both synthetic and real SCFAs-rich media. Although sulfate limitation did not increase lipid accumulation, phosphate limitation was proved to be an optimal strategy for increasing lipid content and lipid yields in both synthetic and real media, reaching a lipid productivity up to 8.95 g/L h. Remarkably, the highest lipid yield (0.30 g/g) was achieved under phosphate absence condition (0 g/L). This fact demonstrated the suitability of using low-phosphate concentrations to boost lipid production from SCFAs.

Degradation of Ochratoxin A by a UV-Mutated Aspergillus niger Strain

Ochratoxin A (OTA) is a mycotoxin that can contaminate a wide range of crops such as grains and grapes. In this study, a novel fungal mutant strain (FS-UV-21) with a high OTA degradation rate (74.5%) was obtained from Aspergillus niger irradiated with ultraviolet light (15 W for 20 min). The effect of pH, temperature, and inoculation concentration on the degradation of OTA by FS-UV-21 was investigated, and the results revealed that the detoxification effect was optimal (89.4%) at a pH of 8 and a temperature of 30 °C. Ultra-performance liquid chromatography-tandem mass spectrometry was used to characterize the degraded products of OTA, and the main degraded product was ochratoxin α. Triple quadrupole-linear ion trap-mass spectrometry combined with LightSight software was used to analyze the biotransformation pathway of OTA in FS-UV-21, to trace the degraded products, and to identify the main metabolite, P1 (C19H18ClNO6, m/z 404). After the FS-UV-21 strain was treated with OTA, the HepG2 cellular toxicity of the degradation products was significantly reduced. For the real sample, FS-UV-21 was used to remove OTA from wheat bran contaminated by mycotoxins through fermentation, resulting in the degradation of 59.8% of OTA in wheat bran. Therefore, FS-UV-21 can be applied to the degradation of OTA in agricultural products and food.

A review on contemporary approaches in enhancing the innate lipid content of yeast cell

For the past few decades, industrialization has made a huge environmental hazard to the world with its waste. The approach of waste to wealth in the recent era has made many Eco-economical suggestions for the industries. The valuable products in biorefinery aspects of the eco-economical suggestions include; energy products, high-value drugs and novel materials. Bio-lipids are found to be the major influencing eco-economical products in the process. Production of bio-lipid from microbial sources has paved the way for future research on lipid-bioproducts. The yeast cell is a unique organism with a large unicellular structure capable of accumulating a high amount of lipids. It constitutes 90% of neutral lipids. Various strategies enhance the lipid profile of yeast cells: usage of oleaginous yeast, usage of low cost (or) alternative substrates, developing stress conditions in the growth medium, using genetically modified yeast, altering metabolic pathways of yeast and by using the symbiotic cultures of yeast with other microbes. The metabolic alterations of lipid pathways such as lipid biosynthesis, lipid elongation, lipid accumulation and lipid degradation have been a striking feature of research in lipid-based microbial work. The lipid-bioproducts have also made a strong footprint in the history of alternative energy products. It includes partial acyl glycerol, oleochemicals, phospholipids and biofuels. This report comprises the recent approaches carried out in the yeast cell for enhancing its lipid content. The limitations, challenges and future scope of individual strategies were also highlighted in this article.

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.

Rhodotorula toruloides: an ideal microbial cell factory to produce oleochemicals, carotenoids, and other products

Requirement of clean energy sources urges us to find substitutes for fossil fuels. Microorganisms provide an option to produce feedstock for biofuel production by utilizing inexpensive, renewable biomass. Rhodotorula toruloides (Rhodosporidium toruloides), a non-conventional oleaginous yeast, can accumulate intracellular lipids (single cell oil, SCO) more than 70% of its cell dry weight. At present, the SCO-based biodiesel is not a price-competitive fuel to the petroleum diesel. Many efforts are made to cut the cost of SCO by strengthening the performance of genetically modified R. toruloides strains and by valorization of low-cost biomass, including crude glycerol, lignocellulosic hydrolysates, food and agro waste, wastewater, and volatile fatty acids. Besides, optimization of fermentation and SCO recovery processes are carefully studied as well. Recently, new R. toruloides strains are developed via metabolic engineering and synthetic biology methods to produce value-added chemicals, such as sesquiterpenes, fatty acid esters, fatty alcohols, carotenoids, and building block chemicals. This review summarizes recent advances in the main aspects of R. toruloides studies, namely, construction of strains with new traits, valorization of low-cost biomass, process detection and optimization, and product recovery. In general, R. toruloides is a promising microbial cell factory for production of biochemicals.

Optimising nutrients in the culture medium of Rhodosporidium toruloides enhances lipids production

Rhodosporidium toruloides is a useful oleaginous yeast, but lipids production is affected by various factors including nutrients in the culture medium. Herein, the R-ZL2 high-yield mutant strain was used to investigate the effects of different carbon sources (sucrose, glucose, xylose), nitrogen sources (ammonium sulphate, ammonium nitrate), and C/N ratio on lipids production capacity, get the following conclusion (1) Compared with glucose and xylose, sucrose was a superior carbon source for lipids production; (2) When using ammonium sulphate as the nitrogen source, a C/N ratio of 200:1 achieved the highest biomass, lipids production and lipids content (10.7 g/L, 6.32 g/L and 59%, respectively), and lipids produced under different C/N conditions have potential for biodiesel production (except for C/N = 40 and C/N = 80); (3) When using ammonium nitrate as the nitrogen source, a C/N ratio of 200:1 achieved the highest biomass, lipids production and lipids content (12.1 g/L, 8.25 g/L and 65%, respectively), and lipids produced under different C/N ratio conditions have potential for biodiesel production. Thus, a combination of sucrose and ammonium nitrate was optimal for the lipid accumulation in R-ZL2. The findings will lay a foundation for further improving lipids yields.

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.

Yeasts of the Blastobotrys genus are promising platform for lipid-based fuels and oleochemicals production

Strains of the yeast genus Blastobotrys (subphylum Saccharomycotina) represent a valuable biotechnological resource for basic biochemistry research, single-cell protein, and heterologous protein production processes. Species of this genus are dimorphic, non-pathogenic, thermotolerant, and can assimilate a variety of hydrophilic and hydrophobic substrates. These can constitute a single-cell oil platform in an emerging bio-based economy as oleaginous traits have been discovered recently. However, the regulatory network of lipogenesis in these yeasts is poorly understood. To keep pace with the growing market demands for lipid-derived products, it is critical to understand the lipid biosynthesis in these unconventional yeasts to pinpoint what governs the preferential channelling of carbon flux into lipids instead of the competing pathways. This review summarizes information relevant to the regulation of lipid metabolic pathways and prospects of metabolic engineering in Blastobotrys yeasts for their application in food, feed, and beyond, particularly for fatty acid-based fuels and oleochemicals. KEY POINTS: • The production of biolipids by heterotrophic yeasts is reviewed. • Summary of information concerning lipid metabolism regulation is highlighted. • Special focus on the importance of diacylglycerol acyltransferases encoding genes in improving lipid production is made.

Transcriptomic and metabolomic profiling of a Rhodotorula color mutant to improve its lipid productivity in fed-batch fermentation

Lipids produced by oleaginous microorganisms enrich the supply of feedstock for bio-fuel. In this study, a mutant (Mut) obtained by UV-nitrosoguanidine mutagenesis turned its colony color from orange-red to light-yellow and showed higher lipid productivity at 37 °C than the original strain Rhodotorula sp. U13N3 (Rht) in the glycerol medium. The metabolic changes between Mut and Rht in batch fermentation were investigated by transcriptomic and metabolomic profiling at the biomass accumulation (30 h) and lipid production (96 h) stages. The average base number in each strain was 5.80 × 10⁹ ± 0.38 × 10⁹ bp (mean ± SD) with 62.43% ± 0.13% GC ratio, and 7499 unigenes were assembled after Illumina sequencing. Moreover, 33 metabolites were quantified by ¹H NMR-based profiling. The multi-omics results demonstrated that Mut showed increased glycerol transport and utilization capabilities especially at the first stage (30 h). Then the carbon flux shifted from the TCA cycle to lipid production (96 h). The increased lipid productivity of Mut was partially attributed to the down-regulation of mannitol biosynthesis. However, the mechanism for color change was elusive. At 96 h, the low level of cytosol glycerol probably restricted the lipid production. As a result, supplementation of glycerol in fed-batch fermentation remarkably improved the biomass, lipid production, and lipid content to 34.60 g/L, 25.72 g/L, and 74.3% (w/w dcw), respectively. The cell morphology implied that excessively prolonging the fermentation time was detrimental to the final lipid yield due to cell breakage. In conclusion, the Rhodotorula mutant provided a candidate strain for lipid production with glycerol as the carbon source.

Isolation and characterization of Lipomyces starkeyi mutants with greatly increased lipid productivity following UV irradiation

The oleaginous yeast Lipomyces starkeyi is an intriguing lipid producer that can produce triacylglycerol (TAG), a feedstock for biodiesel production. We previously reported that the L. starkeyi mutant E15 with high levels of TAG production compared with the wild-type was efficiently obtained using Percoll density gradient centrifugation. However, considering its use for biodiesel production, it is necessary to further improve the lipid productivity of the mutant. In this study, we aimed to obtain mutants with better lipid productivity than E15, evaluate its lipid productivity, and analyze lipid synthesis-related gene expression in the wild-type and mutant strains. The mutants E15-11, E15-15, and E15-25 exhibiting higher lipid productivity than E15 were efficiently isolated from cells exposed to ultraviolet light using Percoll density gradient centrifugation. They exhibited approximately 4.5-fold higher lipid productivity than the wild-type on day 3. The obtained mutants did not exhibit significantly different fatty acid profiles than the wild-type and E15 mutant strains. E15-11, E15-15, and E15-25 exhibited higher expression of acyl-CoA synthesis- and Kennedy pathway-related genes than the wild-type and E15 mutant strains. Activation of the pentose phosphate pathway, which supplies NADPH, was also observed. These results suggested that the increased expression of acyl-CoA synthesis- and Kennedy pathway-related genes plays a vital role in lipid productivity in the oleaginous yeast L. starkeyi.

Lignocellulosic Biomass as a Substrate for Oleaginous Microorganisms: A Review

Microorganisms capable of accumulating lipids in high percentages, known as oleaginous microorganisms, have been widely studied as an alternative for producing oleochemicals and biofuels. Microbial lipid, so-called Single Cell Oil (SCO), production depends on several growth parameters, including the nature of the carbon substrate, which must be efficiently taken up and converted into storage lipid. On the other hand, substrates considered for large scale applications must be abundant and of low acquisition cost. Among others, lignocellulosic biomass is a promising renewable substrate containing high percentages of assimilable sugars (hexoses and pentoses). However, it is also highly recalcitrant, and therefore it requires specific pretreatments in order to release its assimilable components. The main drawback of lignocellulose pretreatment is the generation of several by-products that can inhibit the microbial metabolism. In this review, we discuss the main aspects related to the cultivation of oleaginous microorganisms using lignocellulosic biomass as substrate, hoping to contribute to the development of a sustainable process for SCO production in the near future.

Characterization of two sugar transporters responsible for efficient xylose uptake in an oleaginous yeast Candida tropicalis SY005

Microbial conversion of lignocellulosic feedstock to the target bioproduct requires efficient assimilation of its constituent sugars, a large part of which comprises of glucose and xylose. This study aims to identify and characterize sugar transporters capable of xylose uptake in an oleaginous strain of the industrially relevant yeast Candida tropicalis. In silico database mining resulted in two sugar transporter proteins- CtStp1 and CtStp2, containing conserved amino acid residues and motifs that have been previously reported to be involved in xylose transport in other organisms. Several softwares predicted the likelihood of 10-12 transmembrane (TM) helices to be present in both the Stps, while molecular modelling showed 12 TM helices that were organized into a typical structure found in the major facilitator superfamily of transporters. Docking with different sugars also predicted favorable interactions. Heterologous expression in a Saccharomyces cerevisiae strain harboring functional xylose metabolic genes validated the broad substrate specificity of the two Stps. Each transporter supported prominent growth of recombinant S. cerevisiae strains on six sugars including xylose at various concentrations. Expression of CtSTP1 and CtSTP2 along with the xylose metabolic genes in yeast transformants grown in presence of xylose was confirmed by transcript detection. Growth curve and sugar consumption profiles revealed uptake of both glucose and xylose simultaneously by the recombinant yeast strains, though CtStp1 showed relatively less effect of glucose repression in mixed sugars and was a better transporter of xylose than CtStp2. Such glucose-xylose utilizing efficient transporters can be effective tools for developing co-fermenting yeasts through genetic engineering in future, with noteworthy applications in renewable biomass utilization.

Patterns of Lignocellulosic Sugar Assimilation and Lipid Production by Newly Isolated Yeast Strains From Chilean Valdivian Forest

Three yeast strains were isolated from decaying wood of Chilean Valdivian forest and identified as Meyerozyma guilliermondii, Scheffersomyces coipomensis, and Sugiyamaella paludigena. These strains were able to efficiently grow on the major monomers contained in Pinus spp. and Eucalyptus spp. wood that includes glucose (Glc), xylose (Xyl), and mannose (Man), showing at 28 °C higher uptake rates for Man, and in some cases for Glc, than for Xyl, used as single carbon sources. Nevertheless, in cultures performed on sugar mixtures, the strains displayed a notable preference for Glc. Additionally, in sugar mixtures, the absence of regulatory mechanisms in sugar assimilation (e.g., catabolic repression) was observed and documented when the activities of several enzymes involved in sugar assimilation (i.e., phosphoglucose isomerase, phosphomannose isomerase, and xylulokinase) were determined. The activity of the key enzymes involved in the onset of lipid accumulation (i.e., NAD⁺-ICDH) and in fatty acid (FA) biosynthesis (i.e., ATP:CL) indicated a significant accumulation of storage lipids (i.e., up to 24%, w/w) containing oleic and palmitic acids as the major components. The present paper is the first report on the potential of M. guilliermondii, S. coipomensis, and S. paludigena as oleaginous yeasts. We conclude that the new isolates, being able to simultaneously assimilate the major lignocellulosic sugars and efficiently convert them into oily biomass, present a biotechnological potential which deserve further investigation.

Harnessing the Power of Mutagenesis and Adaptive Laboratory Evolution for High Lipid Production by Oleaginous Microalgae and Yeasts

Oleaginous microalgae and yeasts represent promising candidates for large-scale production of lipids, which can be utilized for production of drop-in biofuels, nutraceuticals, pigments, and cosmetics. However, low lipid productivity and costly downstream processing continue to hamper the commercial deployment of oleaginous microorganisms. Strain improvement can play an essential role in the development of such industrial microorganisms by increasing lipid production and hence reducing production costs. The main means of strain improvement are random mutagenesis, adaptive laboratory evolution (ALE), and rational genetic engineering. Among these, random mutagenesis and ALE are straight forward, low-cost, and do not require thorough knowledge of the microorganism’s genetic composition. This paper reviews available mutagenesis and ALE techniques and screening methods to effectively select for oleaginous microalgae and yeasts with enhanced lipid yield and understand the alterations caused to metabolic pathways, which could subsequently serve as the basis for further targeted genetic engineering.

Combining genetically-encoded biosensors with high throughput strain screening to maximize erythritol production in Yarrowia lipolytica

Erythritol is an important sweetener ingredient and chemical precursor for synthesizing materials with phase transition behavior. Commercial erythritol is primarily produced by industrial fermentation. Further strain engineering necessitates the development of high throughput screening method for rapid detection and screening of mutant strain libraries. In this work, we took advantage of the erythritol-responsive transcription factor EryD, and constructed a sensor-regulator system for rapid screening and characterization of erythritol overproducers. We configured the optimal architecture of the EryD sensor-regulator construct with improved sensitivity, specificity and dynamic response range. Coupled with mutagenesis and strain screening based on biosensors, we rapidly screened and characterized a strain library containing 1152 mutants derived from combined UV and ARTP mutagenesis, in a relatively short period of time (1 week). The optimal strain produced more than 148 g/L erythritol in bench-top reactors. This work provides a reference for other metabolic engineering researchers to develop industrially-relevant strains. The reported framework enables us to rapidly improve strain performance and engineer efficient microbial cell factories for industrial applications.

Comparative evaluation of different carbon sources supply on simultaneous production of lipid and carotene of Rhodotorula glutinis with irradiation and the assessment of key gene transcription

To investigate the feasibility of simultaneously enhancing lipid and carotene production by irradiation with different carbon sources, a strategy by controlling the carbon sources supply were selected to culture Rhodotorula glutinis under the irradiation condition. The results demonstrated that the irradiation indeed enhanced cell growth, lipid and carotene production with different carbon sources supply. Besides, the fatty acids profiling as revealed by more unsaturated fatty acids (mainly C16:1, C18:2 and C18:3) and less saturated fatty acids (C18:0, C22:0 and C24:0) were found during the process of irradiation. Compared with the control, the increase of the transcription levels in genes connected with substrates assimilation, lipid production and carotene accumulation were observed under the irradiation condition. The results suggest the possibility of using irradiation as an effective strategy to increase the production of both lipid and carotene with the controlled carbon sources supply.

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.

Species disparity response to mutagenesis of marine yeasts for the potential production of biodiesel

BACKGROUND

Among the third-generation biodiesel feed stock, oleaginous marine yeasts are the least studied microorganisms for such purpose.

RESULTS

Wild strains yeasts were isolated from various Tunisian marine sources including fish waste (Candida tenuis CtTun15, Debaryomyces hansenii DhTun2015, Trichosporon asahii TaTun15 and Yarrowia lipolytica YlTun15) and seawater (Rhodotorula mucilaginosa RmTun15). Following incubation with ethyl methanesulfonate (EMS: 75 mM) for various periods of time (T15, T30, T45, T60 min), the cell viability of these strains responded differentially according to yeast species. For instance, mutated CtTun15 did not survive after 30 min of EMS treatment; higher resistances were observed in DhTun2015 (45 min), in YlTun15, RmTun15 and in TaTun15 (60 min) but with significant decreased cell viabilities (survival rate: 6.02, 3.16, 11.22, 11.58, 7.70%, respectively). For all surviving mutated strains, the optima of biomass and lipid yields were detected after 96 h in YPD culture; but derived from strains submitted to different period of EMS incubation. In most mutated strains, the maximum biomass (BP) and lipid (LP) productivities coincided and were observed after 30 min of EMS incubation. Only CtTun15 showed different optima of BP and LP (after 30 min and 15 min, respectively). The fatty acids (FA) compositions considered essential in the prediction of biodiesel criteria; were highly affected by EMS mutagenesis. Essentially, 30- and 45-min EMS incubation induced the highest levels of PUFA and MUFA in YlTun15, RmTun15 and TaTun15 with non-significant differences in the different times. However, CtTun15 and DhTun2015 mutant strains responded differently, with the highest levels of MUFA observed following 15 and 45 min; and that of PUFA after 30 and 45 min, respectively.

CONCLUSION

The methyl-esterification of FA from the three mutated yeast strains (30 min-YlTun15, RmTun15 and TaTun15) yielded biodiesel with physical proprieties consistent with the International Standard System. However, investigations are needed for up-scaling biodiesel production.

Multi-Factorial-Guided Media Optimization for Enhanced Biomass and Lipid Formation by the Oleaginous Yeast Cutaneotrichosporon oleaginosus

The non-conventional, oleaginous yeast Cutaneotrichosporon oleaginosus is flagged as an industrial cell factory for generation of oleochemicals and biofuels due to its substrate flexibility and high triglyceride yields. In this study, we employed a computational Response Surface Methodology to guide and streamline the experimental media optimization matrix with 12 nitrogen and 10 carbon sources in order to provide for high biomass and lipid accumulation toward an industrially relevant fermentation process. The resulting data provide new insights into C. oleaginosus physiology under variable nutritional states. Accordingly, the lipid content % (lipid weight/yeast dry weight) is controlled by a defined interplay between carbon and nitrogen. In our experimental setup, the highest biomass (18.4 ± 2.20 g/L) and lipid yield (9 ± 0.34 g/L; 49.74 ± 5.16% g lipid weight/g yeast dry cell weight) were obtained with lactose and yeast extract as carbon and nitrogen sources at an elemental weight ratio of 120:1, respectively. Interestingly, with ammonium salts as a N-source, the intracellularly accumulated triglycerides increasingly contain saturated fatty acids, which provides a new route to generate tailored fatty acid profiles for specific oleochemicals or food applications. Our data indicate that a metabolic ceiling for lipid accumulation in C. oleaginosus is obtained with the correct carbon and nitrogen source mixture.

Microbial conversion of xylose into useful bioproducts

Microorganisms can produce a number of different bioproducts from the sugars in plant biomass. One challenge is devising processes that utilize all of the sugars in lignocellulosic hydrolysates. D-xylose is the second most abundant sugar in these hydrolysates. The microbial conversion of D-xylose to ethanol has been studied extensively; only recently, however, has conversion to bioproducts other than ethanol been explored. Moreover, in the case of yeast, D-xylose may provide a better feedstock for the production of bioproducts other than ethanol, because the relevant pathways are not subject to glucose-dependent repression. In this review, we discuss how different microorganisms are being used to produce novel bioproducts from D-xylose. We also discuss how D-xylose could be potentially used instead of glucose for the production of value-added bioproducts.