Identification of a xylose reductase gene in the xylose metabolic pathway of Kluyveromyces marxianus NBRC1777

Genome mining of an endophytic natural yeast isolate Rhodotorula sp. Y090 and production of the potent antioxidant ergothioneine

Endophytic yeast strains are promising sources of various valuable bioactive compounds. However, studies on endophytic strains derived from lichen samples remain limited. In this study, we isolated and characterized Rhodotorula sp. Y090 from a Usnea longissima lichen sample, and investigated its biosynthetic potential. Genome mining revealed distinct genetic features that differed from its closest relative strain R. graminis WP1. Ergothioneine (EGT) is a potent antioxidant and rare sulfur-containing histidine derivative. However, so far, the EGT biosynthetic enzymes by natural yeast strains have been limitedly studied. In this study, combining genome mining and transcriptomic analysis, genes encoding the potential enzymes for the production of EGT and xylose utilization were identified in Rhodotorula sp. Y090. Further studies demonstrated that Rhodotorula sp. Y090 was capable of producing EGT using xylose, glucose, glycerol, or sucrose as the sole carbon source, and the highest titer reached 363.6 mg/L in shake flask culture, which is significantly higher than that of the most reported levels in the other natural yeasts. Rhodotorula sp. Y090 also exhibited a good ability of EGT export, which could facilitate cost-effective production. These findings suggest that the lichen-derived endophytic yeast Rhodotorula sp. Y090 represents a promising natural candidate for bio-production of the potent antioxidant.

Engineering thermotolerant Kluyveromyces marxianus strains for resveratrol production by simultaneous saccharification and fermentation of whole slurry corn cob

The microbial biosynthesis of the antioxidant compound resveratrol offers an eco-friendly and sustainable alternative to chemical synthesis or plant extraction. Here, we showed that Kluyveromyces marxianus strains produce p-coumaric acid, a key precursor of resveratrol, with higher titres achieved under increased agitation conditions. Through further strain engineering, resveratrol production was achieved using glucose, xylose, and/or ethanol as substrates. Xylose emerged as the most favourable carbon source for resveratrol production, with ethanol supplementation during xylose culture resulting in increased resveratrol titres by limiting the accumulation of the by-product xylitol. At 37 ◦C, resveratrol production from corn cob hydrolysate and whole slurry substantially increased the yield of resveratrol per sugar, reaching titres of up to 69.26 mg/L. This work shows, for the first time, resveratrol production by K. marxianus and from corn cob whole slurry, establishing foundations for the development of an integrated sustainable process for resveratrol production from lignocellulosic materials.

Stress-Driven Production of γ-Aminobutyric Acid Using Non-Conventional Yeast Strains Kluyveromyces marxianus JMY140K and Metschnikowia reukaufii JMY075

γ-Aminobutyric acid (GABA) is a valuable amino acid widely used in food, healthcare, and agriculture. GABA bioproduction by budding yeasts has been commonly reported, but related studies using non-conventional yeasts remain limited. In this study, two non-conventional natural yeast strains, namely, Kluyveromyces marxianus JMY140K and Metschnikowia reukaufii JMY075, were identified as promising GABA producers, and M. reukaufii JMY075 was discovered to be a GABA producer. Enhanced GABA production was observed in the two yeast strains under stress conditions, including high temperature and high ethanol and acetic acid levels. In particular, K. marxianus JMY140K showed 7.93 times higher GABA titers under thermal stress than that of the control. External stress conditions significantly influenced the GABA production of these two yeast strains. The culture filtrate of K. marxianus JMY140K also showed promising activities in human skin cells. In addition, K. marxianus JMY140K could also produce GABA using rice straw hydrolysate, which indicated that it has the potential to produce GABA using renewable biomass. Our studies provide insight for further enhancing the GABA production of natural yeasts and promoting its biotechnology applications.

Lignocellulosic xylitol production from corncob using engineered Kluyveromycesmarxianus

Xylitol production from lignocellulose hydrolysate is a sustainable and environment-friendly process. In this study, a systematic process of converting corncob waste into xylitol is described. First, the corncobs are hydrolyzed with acid to a hydrolysate. Second, Kluyveromyces marxianus YZJQ016 derived from K. marxianus YZJ074, constructed by overexpressing ScGAL2-N376F from Saccharomyces cerevisiae, CtXYL1 from Candida tropicalis, and KmZWF1 from K. marxianus, produces xylitol from the hydrolysate. A total of ten xylose reductase genes were evaluated, and CtXYL1 proved best by showing the highest catalytic activity under the control of the KmGAPDH promoter. A 5 L fermenter at 42°C produced 105.22 g/L xylitol using K. marxianus YZJQ016—the highest production reported to date from corncob hydrolysate. Finally, for crystallization of the xylitol, the best conditions were 50% (v/v) methanol as an antisolvent, at 25°C, with purity and yield of 99%–100% and 74%, respectively—the highest yield reported to date.

Deletion of NGG1 in a recombinant Saccharomyces cerevisiae improved xylose utilization and affected transcription of genes related to amino acid metabolism

Production of biofuels and biochemicals from xylose using yeast cell factory is of great interest for lignocellulosic biorefinery. Our previous studies revealed that a natural yeast isolate Saccharomyces cerevisiae YB-2625 has superior xylose-fermenting ability. Through integrative omics analysis, NGG1, which encodes a transcription regulator as well as a subunit of chromatin modifying histone acetyltransferase complexes was revealed to regulate xylose metabolism. Deletion of NGG1 in S. cerevisiae YRH396h, which is the haploid version of the recombinant yeast using S. cerevisiae YB-2625 as the host strain, improved xylose consumption by 28.6%. Comparative transcriptome analysis revealed that NGG1 deletion down-regulated genes related to mitochondrial function, TCA cycle, ATP biosynthesis, respiration, as well as NADH generation. In addition, the NGG1 deletion mutant also showed transcriptional changes in amino acid biosynthesis genes. Further analysis of intracellular amino acid content confirmed the effect of NGG1 on amino acid accumulation during xylose utilization. Our results indicated that NGG1 is one of the core nodes for coordinated regulation of carbon and nitrogen metabolism in the recombinant S. cerevisiae. This work reveals novel function of Ngg1p in yeast metabolism and provides basis for developing robust yeast strains to produce ethanol and biochemicals using lignocellulosic biomass.

Kluyveromyces marxianus as a microbial cell factory for lignocellulosic biomass valorisation

The non-conventional yeast Kluyveromyces marxianus is widely used for several biotechnological applications, mainly due to its thermotolerance, high growth rate, and ability to metabolise a wide range of sugars. These cell traits are strategic for lignocellulosic biomass valorisation and strain diversity prompts the development of robust chassis, either with improved tolerance to lignocellulosic inhibitors or ethanol. This review summarises bioethanol and value-added chemicals production by K. marxianus from different lignocellulosic biomasses. Moreover, metabolic engineering and process optimization strategies developed to expand K. marxianus potential are also compiled, as well as studies reporting cell mechanisms to cope with lignocellulosic-derived inhibitors. The main lignocellulosic-based products are bioethanol, representing 71% of the reports, and xylitol, representing 17% of the reports. K. marxianus also proved to be a good chassis for lactic acid and volatile compounds production from lignocellulosic biomass, although the literature on this matter is still scarce. The increasing advances in genome editing tools and process optimization strategies will widen the K. marxianus-based portfolio products.

Establishment of Kluyveromyces marxianus as a Microbial Cell Factory for Lignocellulosic Processes: Production of High Value Furan Derivatives

The establishment of lignocellulosic biorefineries is dependent on microorganisms being able to cope with the stressful conditions resulting from the release of inhibitory compounds during biomass processing. The yeast Kluyveromyces marxianus has been explored as an alternative microbial factory due to its thermotolerance and ability to natively metabolize xylose. The lignocellulose-derived inhibitors furfural and 5-hydroxymethylfurfural (HMF) are considered promising building-block platforms that can be converted into a wide variety of high-value derivatives. Here, several K. marxianus strains, isolated from cocoa fermentation, were evaluated for xylose consumption and tolerance towards acetic acid, furfural, and HMF. The potential of this yeast to reduce furfural and HMF at high inhibitory loads was disclosed and characterized. Our results associated HMF reduction with NADPH while furfural-reducing activity was higher with NADH. In addition, furans' inhibitory effect was higher when combined with xylose consumption. The furan derivatives produced by K. marxianus in different conditions were identified. Furthermore, one selected isolate was efficiently used as a whole-cell biocatalyst to convert furfural and HMF into their derivatives, furfuryl alcohol and 2,5-bis(hydroxymethyl)furan (BHMF), with high yields and productivities. These results validate K. marxianus as a promising microbial platform in lignocellulosic biorefineries.

The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels

Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.

Glycerol uptake and synthesis systems contribute to the osmotic tolerance of Kluyveromyces marxianus

The accumulation of glycerol is essential for yeast viability upon hyperosmotic stress. In this study, the STL1 homolog KmSTL1, encoding a putative glycerol transporter contributing to cell osmo-tolerance, was identified in Kluyveromyces marxianus NBRC1777. We constructed the KmSTL1, KmGPD1, and KmFPS1 single-deletion mutants and the KmSTL1/KmGPD1 and KmSTL1/KmFPS1 double-deletion mutants of K. marxianus. Deletion of KmSTL1 or KmGPD1 resulted in K. marxianus cell sensitization to hyperosmotic stress, whereas deletion of KmFPS1 improved stress tolerance. The expression of KmSTL1 was osmotically induced, whereas that of KmFPS1 was osmotically inhibited. The expression of KmGPD1 was constitutive and continuous in the ΔKmSTL1 mutant strain but inhibited in the ΔKmFPS1 mutant strain due to feedback suppression by glycerol. In summary, our findings indicated that K. marxianus would increase glycerol synthesis by increasing GPD1 expression, increase glycerol import from the extracellular environment by increasing STL1 expression, and reduce glycerol efflux by reducing FPS1 expression under hyperosmotic stress.

Functional analysis of PGI1 and ZWF1 in thermotolerant yeast Kluyveromyces marxianus

Glycolysis and the pentose phosphate pathway (PPP) are two basic metabolic pathways that are simultaneously present in yeasts. As the main pathway in most species, the glycolysis provides ATP and NADH for cell metabolism while PPP, as a complementary pathway, supplies NADPH. In this study, the performance of Kluyveromyces marxianus using glycolysis or PPP were studied through the disruption of PGI1 or ZWF1 gene, respectively. K. marxianus using glycolysis as the only pathway showed higher ethanol production ability than that of the Kluyveromyces lactis zwf1Δ mutant; K. marxianus using only PPP showed more robustness than that of Saccharomyces cerevisiae pgi1Δ mutant. Additionally, K. marxianus pgi1Δ strain accumulated much more intracellular NADPH than the wild type strain and co-utilized glucose and xylose more effectively. These findings suggest that phosphoglucose isomerase participates in the regulation of the repression of glucose on xylose utilization in K. marxianus. The NADPH/NADP⁺ ratio, dependent on the activity of the PPP, regulated the expression of multiple genes related to NADPH metabolism in K. marxianus (including NDE1, NDE2, GLR1, and GDP1). Since K. marxianus is considered a promising host in industrial biotechnology to produce renewable chemicals from plant biomass feedstocks, our research showed the potential of the thermotolerant K. marxianus to produce NADP(H)-dependent chemical synthesis from multiple feedstocks. KEY POINTS: • The function of PGI1 and ZWF1 in K. marxianus has been analyzed in this study. • K. marxianus zwf1Δ strain produced ethanol but with decreased productivity. • K. marxianus pgi1Δ strain grew with glucose and accumulated NADPH. • K. marxianus pgi1Δ strain released glucose repression on xylose utilization.

Valorization of apple pomace using bio-based technology for the production of xylitol and 2G ethanol

Apple pomace was studied as a raw material for the production of xylitol and 2G ethanol, since this agroindustrial residue has a high concentration of carbohydrate macromolecules, but is still poorly studied for the production of fermentation bioproducts, such as polyols. The dry biomass was subjected to dilute-acid hydrolysis with H₂SO₄ to obtain the hemicellulosic hydrolysate, which was concentrated, detoxified and fermented. The hydrolyzate after characterization was submitted to submerged fermentations, which were carried out in Erlenmeyer flasks using, separately, the yeasts Candida guilliermondii and Kluyveromyces marxianus. High cellulose (32.62%) and hemicellulose (23.60%) contents were found in this biomass, and the chemical hydrolysis yielded appreciable quantities of fermentable sugars, especially xylose. Both yeasts were able to metabolize xylose, but Candida guilliermondii produced only xylitol (9.35 g L^-1 in 96 h), while K. marxianus produced ethanol as the main product (10.47 g L^-1 in 24 h) and xylitol as byproduct (9.10 g L^-1 xylitol in 96 h). Maximum activities of xylose reductase and xylitol dehydrogenase were verified after 24 h of fermentation with C. guilliermondii (0.23 and 0.53 U/mg_prot, respectively) and with K. marxianus (0.08 e 0.08 U/mg_prot, respectively). Apple pomace has shown potential as a raw material for the fermentation process, and the development of a biotechnological platform for the integrated use of both the hemicellulosic and cellulosic fraction could add value to this residue and the apple production chain.

A unique xylose reductase from Thermomyces lanuginosus: Effect of lignocellulosic substrates and inhibitors and applicability in lignocellulosic bioconversion

In this study, the xylose reductase gene (XRTL) from Thermomyces lanuginosus SSBP was expressed in Pichia pastoris GS115 and Saccharomyces cerevisiae Y294. The purified 39.2 kDa monomeric enzyme was optimally active at pH 6.5 and 50 °C and showed activity over a wide range of temperatures (30-70 °C) and pH (4.0-9.0), with a half-life of 1386 min at 50 °C. The enzyme preferred NADPH as cofactor and showed broad substrate specificity. The enzyme was inhibited by Cu²⁺, Fe²⁺ and Zn²⁺, while ferulic acid was found to be the most potent lignocellulosic inhibitor. Recombinant S. cerevisiae with the XRTL gene showed 34% higher xylitol production than the control strain. XRTL can therefore be used in a cell-free xylitol production process or as part of a pathway for utilization of xylose from lignocellulosic waste.

Release of glucose repression on xylose utilization in Kluyveromyces marxianus to enhance glucose-xylose co-utilization and xylitol production from corncob hydrolysate

BACKGROUND

Lignocellulosic biomass is one of the most abundant materials for biochemicals production. However, efficient co-utilization of glucose and xylose from the lignocellulosic biomass is a challenge due to the glucose repression in microorganisms. Kluyveromyces marxianus is a thermotolerant and efficient xylose-utilizing yeast. To realize the glucose-xylose co-utilization, analyzing the glucose repression of xylose utilization in K. marxianus is necessary. In addition, a glucose-xylose co-utilization platform strain will facilitate the construction of lignocellulosic biomass-utilizing strains.

RESULTS

Through gene disruption, hexokinase 1 (KmHXK1) and sucrose non-fermenting 1 (KmSNF1) were proved to be involved in the glucose repression of xylose utilization while disruption of the downstream genes of cyclic AMP-protein kinase A (cAMP-PKA) signaling pathway or sucrose non-fermenting 3 (SNF3) glucose-sensing pathway did not alleviate the repression. Furthermore, disruption of the gene of multicopy inhibitor of GAL gene expression (KmMIG1) alleviated the glucose repression on some nonglucose sugars (galactose, sucrose, and raffinose) but still kept glucose repression of xylose utilization. Real-time PCR analysis of the xylose utilization related genes transcription confirmed these results, and besides, revealed that xylitol dehydrogenase gene (KmXYL2) was the critical gene for xylose utilization and stringently regulated by glucose repression. Many other genes of candidate targets interacting with SNF1 were also evaluated by disruption, but none proved to be the key regulator in the pathway of the glucose repression on xylose utilization. Therefore, there may exist other signaling pathway(s) for glucose repression on xylose consumption. Based on these results, a thermotolerant xylose-glucose co-consumption platform strain of K. marxianus was constructed. Then, exogenous xylose reductase and xylose-specific transporter genes were overexpressed in the platform strain to obtain YHY013. The YHY013 could efficiently co-utilized the glucose and xylose from corncob hydrolysate or xylose mother liquor for xylitol production (> 100 g/L) even with inexpensive organic nitrogen sources.

CONCLUSIONS

The analysis of the glucose repression in K. marxianus laid the foundation for construction of the glucose-xylose co-utilizing platform strain. The efficient xylitol production strain further verified the potential of the platform strain in exploitation of lignocellulosic biomass.

Efficient l-lactic acid production from corncob residue using metabolically engineered thermo-tolerant yeast

Lactic acid is an important industrial product and the production from inexpensive and renewable lignocellulose can reduce the cost and environmental pollution. In this study, a Kluyveromyces marxianus strain which produced lactic acid efficiently from corncob was constructed. Firstly, two of six different lactate dehydrogenases, which from Plasmodium falciparum and Bacillus subtilis, respectively, were proved to be effective for l-lactic acid production. Then, five single genetic modifications were conducted. The overexpression of Saccharomyces cerevisiae proton-coupled monocarboxylate transporter, K. marxianus 6-phosphofructokinase, or disruption of K. marxianus putative d-lactate dehydrogenase enhanced the l-lactic acid accumulation. Finally, the strain YKX071, obtained via combination of above effective genetic engineering, produced 103.00 g/L l-lactic acid at 42 °C with optical purity of 99.5% from corncob residue via simultaneous saccharification and co-fermentation. This study first developed an effective platform for high optical purity l-lactic acid production from lignocellulose using yeast with inexpensive nitrogen sources.

Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1-2

BACKGROUND

Efficient bioconversion of lignocellulosic biomass to bioethanol is one of key challenges in the situation of increasing bioethanol demand. The ethanologenic microbes for such conversion are required to possess abilities of utilization of various sugars including xylose and arabinose in lignocellulosic biomass. As required additional characteristics, there are a weak or no glucose repression that allows cells to simultaneously utilize various sugars together with glucose and thermotolerance for fermentation at high temperatures, which has several advantages including reduction of cooling cost. Spathaspora passalidarum ATCC MYA-4345, a type strains, isolated previously have mainly of these abilities or characteristics but its thermotolerance is not so strong and its glucose repression on xylose utilization is revealed.

RESULTS

Newly isolated S. passalidarum CMUWF1-2 was found to have a high ability to produce ethanol from various sugars included in lignocellulosic biomass at high temperatures. The strain achieved ethanol yields of 0.43 g, 0.40 g and 0.20 g ethanol/g xylose at 30 °C, 37 °C and 40 °C, respectively. Interestingly, no significant glucose repression was observed in experiments with mixed sugars, being consistent with the strong resistance to 2-deoxyglucose, and antimycin A showed no effect on its growth in xylose medium. Moreover, the strain was tolerant to glucose and ethanol at concentrations up to 35.0% (w/v) and 8.0% (v/v), respectively.

CONCLUSIONS

S. passalidarum CMUWF1-2 was shown to achieve efficient production of ethanol from various sugars and a high ethanol yield from xylose with little accumulation of xylitol. The strain also exhibited stress-resistance including thermotolerance and no detectable glucose repression as beneficial characteristics. Therefore, S. passalidarum CMUWF1-2 has remarkable potential for conversion of lignocellulosic biomass to bioethanol.

Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism

The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modified K. marxianus. Pairs of substrates (lactose, glucose, inulin, xylose) and products (ethanol, acetate, lactate, glycerol, ethyl acetate, succinate, glutamate, phenylethanol and phenylalanine) are examined by various modelling and optimisation methods. Our model reveals the organism's potential for industrial application and metabolic engineering. Modelling results imply that the aeration regime can be used as a tool to optimise product yield and flux distribution in K. marxianus. Also rebalancing NADH and NADPH utilisation can be used to improve the efficiency of substrate conversion. Xylose is identified as a biotechnologically promising substrate for K. marxianus.

Engineered Kluyveromyces marxianus for pyruvate production at elevated temperature with simultaneous consumption of xylose and glucose

Xylose and glucose from lignocellulose are sustainable sources for production of pyruvate, which is the starting material for the synthesis of many drugs and agrochemicals. In this study, the pyruvate decarboxylase gene (KmPDC1) and glycerol-3-phosphate dehydrogenase gene (KmGPD1) of Kluyveromyces marxianus YZJ051 were disrupted to prevent ethanol and glycerol accumulation. The deficient growth of PDC disruption was rescued by overexpressing mutant KmMTH1-ΔT. Then pentose phosphate pathway and xylitol dehydrogenase SsXYL2-ARS genes were overexpressed to obtain strain YZB053 which produced pyruvate with xylose other than glucose. It produced 24.62g/L pyruvate from 80g/L xylose with productivity of 0.51g/L/h at 42°C. Then, xylose-specific transporter ScGAL2-N376F was overexpressed to obtain strain YZB058, which simultaneously consumed 40g/L glucose and 20g/L xylose and produced 29.21g/L pyruvate with productivity of 0.81g/L/h at 42°C. Therefore, a platform for pyruvate production from glucose and xylose at elevated temperature was developed.

Identification and characterization of d-arabinose reductase and d-arabinose transporters from Pichia stipitis

d-xylose and l-arabinose are the major constituents of plant lignocelluloses, and the related fungal metabolic pathways have been extensively examined. Although Pichia stipitis CBS 6054 grows using d-arabinose as the sole carbon source, the hypothetical pathway has not yet been clarified at the molecular level. We herein purified NAD(P)H-dependent d-arabinose reductase from cells grown on d-arabinose, and found that the enzyme was identical to the known d-xylose reductase (XR). The enzyme activity of XR with d-arabinose was previously reported to be only 1% that with d-xylose. The kcat/Km value with d-arabinose (1.27 min−1 mM−1), which was determined using the recombinant enzyme, was 13.6- and 10.5-fold lower than those with l-arabinose and d-xylose, respectively. Among the 34 putative sugar transporters from P. stipitis, only seven genes exhibited uptake ability not only for d-arabinose, but also for d-glucose and other pentose sugars including d-xylose and l-arabinose in Saccharomyces cerevisiae.

Simultaneous fermentation of glucose and xylose at elevated temperatures co-produces ethanol and xylitol through overexpression of a xylose-specific transporter in engineered Kluyveromyces marxianus

Engineered Kluyveromyces marxianus strains were constructed through over-expression of various transporters for simultaneous co-fermentation of glucose and xylose. The glucose was converted into ethanol, whereas xylose was converted into xylitol which has higher value than ethanol. Over-expressing xylose-specific transporter ScGAL2-N376F mutant enabled yeast to co-ferment glucose and xylose and the co-fermentation ability was obviously improved through increasing ScGAL2-N376F expression. The production of glycerol was blocked and acetate production was reduced by disrupting gene KmGPD1. The obtained K. marxianus YZJ119 utilized 120g/L glucose and 60g/L xylose simultaneously and produced 50.10g/L ethanol and 55.88g/L xylitol at 42°C. The yield of xylitol from consumed xylose was over 98% (0.99g/g). Through simultaneous saccharification and co-fermentation at 42°C, YZJ119 produced a maximal concentration of 44.58g/L ethanol and 32.03g/L xylitol or 29.82g/L ethanol and 31.72g/L xylitol, respectively, from detoxified or non-detoxified diluted acid pretreated corncob.

Data for rapid ethanol production at elevated temperatures by engineered thermotolerant Kluyveromyces marxianus via the NADP(H)-preferring xylose reductase-xylitol dehydrogenase pathway

A thermo-tolerant NADP(H)-preferring xylose pathway was constructed in Kluyveromyces marxianus for ethanol production with xylose at elevated temperatures (Zhang et al., 2015 [25]). Ethanol production yield and efficiency was enhanced by pathway engineering in the engineered strains. The constructed strain, YZJ088, has the ability to co-ferment glucose and xylose for ethanol and xylitol production, which is a critical step toward enabling economic biofuel production from lignocellulosic biomass. This study contains the fermentation results of strains using the metabolic pathway engineering procedure. The ethanol-producing abilities of various yeast strains under various conditions were compared, and strain YZJ088 showed the highest production and fastest productivity at elevated temperatures. The YZJ088 xylose fermentation results indicate that it fermented well with xylose at either low or high inoculum size. When fermented with an initial cell concentration of OD₆₀₀=15 at 37 °C, YZJ088 consumed 200 g/L xylose and produced 60.07 g/L ethanol; when the initial cell concentration was OD₆₀₀=1 at 37 °C, YZJ088 consumed 98.96 g/L xylose and produced 33.55 g/L ethanol with a productivity of 0.47 g/L/h. When fermented with 100 g/L xylose at 42 °C, YZJ088 produced 30.99 g/L ethanol with a productivity of 0.65 g/L/h, which was higher than that produced at 37 °C.

Gene expression analysis using strains constructed by NHEJ-mediated one-step promoter cloning in the yeast Kluyveromyces marxianus

Gene expression analysis provides valuable information to evaluate cellular state. Unlike quantitative mRNA analysis techniques like reverse-transcription PCR and microarray, expression analysis using a reporter gene has not been commonly used for multiple-gene analysis, probably due to the difficulty in preparing multiple reporter-gene constructs. To circumvent this problem, we developed a novel one-step reporter-gene construction system mediated by non-homologous end joining (NHEJ) in the yeast Kluyveromyces marxianus. As a selectable reporter gene, the ScURA3 selection marker was fused in frame with a red fluorescent gene yEmRFP (ScURA3:yEmRFP). The N-terminally truncated ScURA3:yEmRFP fragment was prepared by PCR. Promoter sequences were also prepared by PCR using primers containing the sequence of the deleted ScURA3 N-terminus to attach at their 3(') ends. The two DNA fragments were used for the transformation of a ura3(-) strain of K. marxianus, in which two DNA fragments are randomly joined and integrated into the chromosome through NHEJ. Only the correctly aligned fragments produced transformants on uracil-deficient medium and expressed red fluorescence under the control of the introduced promoters. A total of 36 gene promoters involved in glycolysis and other pathways were analyzed. Fluorescence measurements of these strains allowed real-time gene expression analysis in different culture conditions.

Rapid ethanol production at elevated temperatures by engineered thermotolerant Kluyveromyces marxianus via the NADP(H)-preferring xylose reductase-xylitol dehydrogenase pathway

Conversion of xylose to ethanol by yeasts is a challenge because of the redox imbalances under oxygen-limited conditions. The thermotolerant yeast Kluyveromyces marxianus grows well with xylose as a carbon source at elevated temperatures, but its xylose fermentation ability is weak. In this study, a combination of the NADPH-preferring xylose reductase (XR) from Neurospora crassa and the NADP(+)-preferring xylitol dehydrogenase (XDH) mutant from Scheffersomyces stipitis (Pichia stipitis) was constructed. The xylose fermentation ability and redox balance of the recombinant strains were improved significantly by over-expression of several downstream genes. The intracellular concentrations of coenzymes and the reduced coenzyme/oxidized coenzyme ratio increased significantly in these metabolic strains. The byproducts, such as glycerol and acetic acid, were significantly reduced by the disruption of glycerol-3-phosphate dehydrogenase (GPD1). The resulting engineered K. marxianus YZJ088 strain produced 44.95 g/L ethanol from 118.39 g/L xylose with a productivity of 2.49 g/L/h at 42 °C. Additionally, YZJ088 realized glucose and xylose co-fermentation and produced 51.43 g/L ethanol from a mixture of 103.97 g/L xylose and 40.96 g/L glucose with a productivity of 2.14 g/L/h at 42 °C. These promising results validate the YZJ088 strain as an excellent producer of ethanol from xylose through the synthetic xylose assimilation pathway.

Improving xylitol production at elevated temperature with engineered Kluyveromyces marxianus through over-expressing transporters

Three transporter genes including Kluyveromyces marxianus aquaglyceroporin gene (KmFPS1), Candida intermedia glucose/xylose facilitator gene (CiGXF1) or glucose/xylose symporter gene (CiGXS1) were over-expressed in K. marxianus YZJ017 to improve xylitol production at elevated temperatures. The xylitol production of YZJ074 that harbored CiGXF1 was improved to 147.62g/L in Erlenmeyer flask at 42°C. In fermenter, 99.29 and 149.60g/L xylitol were produced from 99.55 and 151.91g/L xylose with productivity of 4.14 and 3.40g/L/h respectively at 42°C. Even at 45°C, YZJ074 could produce 101.30g/L xylitol from 101.41g/L xylose with productivity of 2.81g/L/h. Using fed-batch fermentation through repeatedly adding non-sterilized substrate directly, YZJ074 could produce 312.05g/L xylitol which is the highest yield reported to date. The engineered strains YZJ074 which can produce xylitol at elevated temperatures is an excellent foundation for xylitol bioconversion.

Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses

BACKGROUND

High-temperature fermentation technology with thermotolerant microbes has been expected to reduce the cost of bioconversion of cellulosic biomass to fuels or chemicals. Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. These capabilities have been found to exceed those of the traditional ethanol producer Saccharomyces cerevisiae or lignocellulose-bioconvertible ethanologenic Scheffersomyces stipitis.

RESULTS

The complete genome sequence of K. marxianus DMKU 3-1042 as one of the most thermotolerant strains in the same species has been determined. A comparison of its genomic information with those of other yeasts and transcriptome analysis revealed that the yeast bears beneficial properties of temperature resistance, wide-range bioconversion ability, and production of recombinant proteins. The transcriptome analysis clarified distinctive metabolic pathways under three different growth conditions, static culture, high temperature, and xylose medium, in comparison to the control condition of glucose medium under a shaking condition at 30°C. Interestingly, the yeast appears to overcome the issue of reactive oxygen species, which tend to accumulate under all three conditions.

CONCLUSIONS

This study reveals many gene resources for the ability to assimilate various sugars in addition to species-specific genes in K. marxianus, and the molecular basis of its attractive traits for industrial applications including high-temperature fermentation. Especially, the thermotolerance trait may be achieved by an integrated mechanism consisting of various strategies. Gene resources and transcriptome data of the yeast are particularly useful for fundamental and applied researches for innovative applications.

Effect of oxygenation and temperature on glucose-xylose fermentation in Kluyveromyces marxianus CBS712 strain

BACKGROUND

The yeast Kluyveromyces marxianus features specific traits that render it attractive for industrial applications. These include production of ethanol which, together with thermotolerance and the ability to grow with a high specific growth rate on a wide range of substrates, could make it an alternative to Saccharomyces cerevisiae as an ethanol producer. However, its ability to co-ferment C5 and C6 sugars under oxygen-limited conditions is far from being fully characterized.

RESULTS

In the present study, K. marxianus CBS712 strain was cultivated in defined medium with glucose and xylose as carbon source. Ethanol fermentation and sugar consumption of CBS712 were investigated under different oxygen supplies (1.75%, 11.00% and 20.95% of O2) and different temperatures (30°C and 41°C). By decreasing oxygen supply, independently from the temperature, both biomass production as well as sugar utilization rate were progressively reduced. In all the tested conditions xylose consumption followed glucose exhaustion. Therefore, xylose metabolism was mainly affected by oxygen depletion. Loss in cell viability cannot explain the decrease in sugar consumption rates, as demonstrated by single cell analyses, while cofactor imbalance is commonly considered as the main cause of impairment of the xylose reductase (KmXR) - xylitol dehydrogenase (KmXDH) pathway. Remarkably, when these enzyme activities were assayed in vitro, a significant decrease was observed together with oxygen depletion, not ascribed to reduced transcription of the corresponding genes.

CONCLUSIONS

In the present study both oxygen supply and temperature were shown to be key parameters affecting the fermentation capability of sugars in the K. marxianus CBS712 strain. In particular, a direct correlation was observed between the decreased efficiency to consume xylose with the reduced specific activity of the two main enzymes (KmXR and KmXDH) involved in its catabolism. These data suggest that, in addition to the impairment of the oxidoreductive pathway being determined by the cofactor imbalance, post-transcriptional and/or post-translational regulation of the pathway enzymes contributes to the efficiency of xylose catabolism in micro-aerobic conditions. Overall, the presented work provides novel information on the fermentation capability of the CBS712 strain that is currently considered as the reference strain of the genus K. marxianus.

Xylitol production at high temperature by engineered Kluyveromyces marxianus

Several recombinant Kluyveromyces marxianus strains were constructed through overexpressing the Neurospora crassa xylose reductase genes. YZJ015, which maintained the original xylitol dehydrogenase gene, produced xylitol with the highest productivity (1.49 g L(-1) h(-1)) from 100 g L(-1) xylose at 42 °C. Even at 45 °C, YZJ015 was still able to produce 60.03 g L(-1) xylitol from 100 g L(-1) xylose with a productivity of 1.25 g L(-1)h(-1). In addition, for 20 rounds of cell recycling at 42 °C, YZJ015 produced 71.35 g L(-1) xylitol from 100 g L(-1) xylose with a productivity of 4.43 g L(-1) h(-1) per cycle. YZJ017, in which the xylitol dehydrogenase gene was disrupted, produced 100.02 g L(-1) xylitol at a yield of 1.01 g g(-1) from 100 g L(-1) xylose with 40 g L(-1) glycerol as co-substrate at 42 °C. These engineered strains provide an excellent foundation for xylitol production at elevated temperatures.

Identification of a xylitol dehydrogenase gene from Kluyveromyces marxianus NBRC1777

Xylitol dehydrogenase (XDH) (EC 1.1.1.9) is one of the key enzymes in the xylose fermentation pathway in yeast and fungi. A xylitol dehydrogenase gene (XYL2) encoding a XDH was cloned from Kluyveromyces marxianus NBRC 1777, and the in vivo function was validated by disruption and complementation analysis. The highest activity of KmXDH could be observed at pH 9.5 during 55°C. The values of k(cat)/K(m) indicate that KmXDH prefers NAD(+) to NADP(+) (k(cat)/K(m NAD)(+) 3681/min mM and k(cat)/K(m NADP)(+) 1361/min mM). The different coenzyme preference between KmXR and KmXDH caused an accumulation of NADH in the xylose utilization pathway. The redox imbalance may be one of the reasons to cause the poor xylose fermentation under oxygen-limited conditions in K. marxianus NBRC1777.

Improved xylose fermentation of Kluyveromyces marxianus at elevated temperature through construction of a xylose isomerase pathway

To improve the xylose fermentation ability of Kluyveromyces marxianus, a xylose assimilation pathway through xylose isomerase was constructed. The genes encoding xylose reductase (KmXyl1) and xylitol dehydrogenase (KmXyl2) were disrupted in K. marxianus YHJ010 and the resultant strain was named YRL002. A codon-optimized xylose isomerase gene from Orpinomyces was transformed into K. marxianus YRL002 and expressed under GAPDH promoter. The transformant was adapted in the SD medium containing 1 % casamino acid with 2 % xylose as sole carbon source. After 32 times of trans-inoculation, a strain named YRL005, which can grow at a specific growth rate of 0.137/h with xylose as carbon source, was obtained. K. marxianus YRL005 could ferment 30.15 g/l of xylose and produce 11.52 g/l ethanol with a yield of 0.38 g/g, production rate of 0.069 g/l/h at 42 °C, and also could ferment 16.60 g/l xylose to produce 5.21 g/l ethanol with a yield of 0.31 g/g, and production rate of 0.054 g/l h at 45 °C. Co-fermentation with 2 % glucose could not improve the amount and yield of ethanol fermented from xylose obviously, but it could improve the production rate. Furthermore, K. marxianus YRL005 can ferment with the corn cob hydrolysate, which contained 20.04 g/l xylose to produce 8.25 g/l ethanol. It is a good platform to construct thermo-tolerant xylose fermentation yeast.

Bioethanol production from Lignocellulosic biomass by a novel Kluyveromyces marxianus strain

The yeast Kluyveromyces marxianus is considered as a potential alternative to Saccharomyces cerevisiae in producing ethanol as a biofuel. In this study, we investigated the ethanol fermentation properties of novel K. marxianus strain DMB1, isolated from bagasse hydrolysates. This strain utilized sorbitol as well as various pentoses and hexoses as single carbon sources under aerobic conditions and produced ethanol from glucose in hydrolysates of the Japanese cedar at 42 °C. Reference strains K. marxianus NBRC1777 and S. cerevisiae BY4743 did not assimilate sorbitol or ferment lignocellulosic hydrolysates to ethanol at this temperature. Thus strain DMB1 appears to be optimal for producing bioethanol at high temperatures, and might provide a valuable means of increasing the efficiency of ethanol fermentation.

Genome sequence of the thermotolerant yeast Kluyveromyces marxianus var. marxianus KCTC 17555

Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. marxianus KCTC 17555 (= CBS 6556 = ATCC 26548).

Improving ethanol and xylitol fermentation at elevated temperature through substitution of xylose reductase in Kluyveromyces marxianus

Thermo-tolerant yeast Kluyveromyces marxianus is able to utilize a wide range of substrates, including xylose; however, the xylose fermentation ability is weak because of the redox imbalance under oxygen-limited conditions. Alleviating the intracellular redox imbalance through engineering the coenzyme specificity of NADPH-preferring xylose reductase (XR) and improving the expression of XR should promote xylose consumption and fermentation. In this study, the native xylose reductase gene (Kmxyl1) of the K. marxianus strain was substituted with XR or its mutant genes from Pichia stipitis (Scheffersomyces stipitis). The ability of the resultant recombinant strains to assimilate xylose to produce xylitol and ethanol at elevated temperature was greatly improved. The strain YZB014 expressing mutant PsXR N272D, which has a higher activity with both NADPH and NADH as the coenzyme, achieved the best results, and produced 3.55 g l(-1) ethanol and 11.32 g l(-1) xylitol-an increase of 12.24- and 2.70-fold in product at 42 °C, respectively. A 3.94-fold increase of xylose consumption was observed compared with the K. marxianus YHJ010 harboring KmXyl1. However, the strain YZB015 expressing a mutant PsXR K21A/N272D, with which co-enzyme preference was completely reversed from NADPH to NADH, failed to ferment due to the low expression. So in order to improve xylose consumption and fermentation in K. marxianus, both higher activity and co-enzyme specificity change are necessary.