Alcoholic Fermentation of d-Xylose by Yeasts

Natural trait variation across Saccharomycotina species

Among molecular biologists, the group of fungi called Saccharomycotina is famous for its yeasts. These yeasts in turn are famous for what they have in common-genetic, biochemical, and cell-biological characteristics that serve as models for plants and animals. But behind the apparent homogeneity of Saccharomycotina species lie a wealth of differences. In this review, we discuss traits that vary across the Saccharomycotina subphylum. We describe cases of bright pigmentation; a zoo of cell shapes; metabolic specialties; and species with unique rules of gene regulation. We discuss the genetics of this diversity and why it matters, including insights into basic evolutionary principles with relevance across Eukarya.

Molecular modeling and dynamics simulation of alcohol dehydrogenase enzyme from high efficacy cellulosic ethanol-producing yeast mutant strain Pichia kudriavzevii BGY1-γm

One of the major constraints limiting the use of abundantly available lignocellulosic biomass as potential feedstock for alcohol industry is the lack of C₆/C₅ co-sugar fermenting yeast. The present study explores a mutant yeast Pichia kudriavzevii BGY1-γm as a potential strain for bioconversion of glucose/xylose sugars of green biomass into ethanol under batch fermentation. The mutant strain having higher alcohol dehydrogenase activity (11.31%) showed significantly higher ethanol concentration during co-fermentation of glucose/xylose sugars (14.2%) as compared to the native strain. Based on 99% sequence similarity of ADH encoding gene from the mutant with the gene sequences from other yeast strains, the ADH enzyme was identified as ADH-1 type. The study reveals first three-dimensional model of ADH-1 utilizing glucose/xylose sugars from P. kudriavzevii BGY1-γm (PkADH mutant). The refined and validated model of PkADH mutant was used for molecular docking against the substrate (acetaldehyde) and product (ethanol). Molecular docking results showed that substrate and product exhibited a binding affinity of -4.55 and -4.5 kcal/mol with PkADH mutant. Acetaldehyde and ethanol interacted at the active site of PkADH mutant via hydrogen bonds (Ser42, His69 and Asp163) and hydrophobic interactions (Cys40, Ser42, His69, Cys95, Trp123 and Asp163) to form the stable protein-ligand complex. Molecular dynamics analysis revealed that PkADH-mutant acetaldehyde and PkADH-mutant ethanol complexes were more stable than PkADH mutant. MMPBSA binding energy confirmed that binding of substrate and product results in the formation of a lower energy stable protein-ligand complex.Communicated by Ramaswamy H. Sarma.

Metabolic engineering of non-conventional yeasts for construction of the advanced producers of biofuels and high-value chemicals

Non-conventional yeasts, i.e. yeasts different from Saccharomyces cerevisiae, represent heterogenous group of unicellular fungi consisting of near 1500 species. Some of these species have interesting and sometimes unique properties like ability to grow on methanol, n-alkanes, ferment pentose sugars xylose and l-arabinose, grow at high temperatures (50°С and more), overproduce riboflavin (vitamin B2) and others. These unique properties are important for development of basic science; moreover, some of them possess also significant applied interest for elaboration of new biotechnologies. Current paper represents review of the recent own results and of those of other authors in the field of non-conventional yeast study for construction of the advanced producers of biofuels (ethanol, isobutanol) from lignocellulosic sugars glucose and xylose or crude glycerol (Ogataea polymorpha, Magnusiomyces magnusii) and vitamin B2 (riboflavin) from glucose and cheese whey (Candida famata).

Xylo-Oligosaccharide Utilization by Engineered Saccharomyces cerevisiae to Produce Ethanol

The engineering of xylo-oligosaccharide-consuming Saccharomyces cerevisiae strains is a promising approach for more effective utilization of lignocellulosic biomass and the development of economic industrial fermentation processes. Extending the sugar consumption range without catabolite repression by including the metabolism of oligomers instead of only monomers would significantly improve second-generation ethanol production This review focuses on different aspects of the action mechanisms of xylan-degrading enzymes from bacteria and fungi, and their insertion in S. cerevisiae strains to obtain microbial cell factories able of consume these complex sugars and convert them to ethanol. Emphasis is given to different strategies for ethanol production from both extracellular and intracellular xylo-oligosaccharide utilization by S. cerevisiae strains. The suitability of S. cerevisiae for ethanol production combined with its genetic tractability indicates that it can play an important role in xylan bioconversion through the heterologous expression of xylanases from other microorganisms.

Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts

Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.

Combining Xylose Reductase from Spathaspora arborariae with Xylitol Dehydrogenase from Spathaspora passalidarum to Promote Xylose Consumption and Fermentation into Xylitol by Saccharomyces cerevisiae

In recent years, many novel xylose-fermenting yeasts belonging to the new genus Spathaspora have been isolated from the gut of wood-feeding insects and/or wood-decaying substrates. We have cloned and expressed, in Saccharomyces cerevisiae, a Spathaspora arborariae xylose reductase gene (SaXYL1) that accepts both NADH and NADPH as co-substrates, as well as a Spathaspora passalidarum NADPH-dependent xylose reductase (SpXYL1.1 gene) and the SpXYL2.2 gene encoding for a NAD+-dependent xylitol dehydrogenase. These enzymes were co-expressed in a S. cerevisiae strain over-expressing the native XKS1 gene encoding xylulokinase, as well as being deleted in the alkaline phosphatase encoded by the PHO13 gene. The S. cerevisiae strains expressing the Spathaspora enzymes consumed xylose, and xylitol was the major fermentation product. Higher specific growth rates, xylose consumption and xylitol volumetric productivities were obtained by the co-expression of the SaXYL1 and SpXYL2.2 genes, when compared with the co-expression of the NADPH-dependent SpXYL1.1 xylose reductase. During glucose-xylose co-fermentation by the strain with co-expression of the SaXYL1 and SpXYL2.2 genes, both ethanol and xylitol were produced efficiently. Our results open up the possibility of using the advantageous Saccharomyces yeasts for xylitol production, a commodity with wide commercial applications in pharmaceuticals, nutraceuticals, food and beverage industries.

Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540

Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.

AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution

Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. Insight into the evolution of orthologs, paralogs and xenologs in the yeast pan-genome can help bridge these genotypes; however, existing phylogenomic databases do not span diverse yeasts, and sometimes cannot distinguish between these homologs. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution. OrthoMCL and OrthoDB were used to cluster protein sequence into ortholog and homolog groups, respectively; MAFFT and PhyML reconstructed the phylogeny of all homolog groups. Ortholog assignments for enzymes and small metabolite transporters were compared to their phylogenetic reconstruction, and curated to resolve any discrepancies. Information on homolog and ortholog groups can be viewed in the AYbRAH web portal (https://lmse.github.io/aybrah/), including functional annotations, predictions for mitochondrial localization and transmembrane domains, literature references and phylogenetic reconstructions. Ortholog assignments in AYbRAH were compared to HOGENOM, KEGG Orthology, OMA, eggNOG and PANTHER. PANTHER and OMA had the most congruent ortholog groups with AYbRAH, while the other phylogenomic databases had greater amounts of under-clustering, over-clustering or no ortholog annotations for proteins. Future plans are discussed for AYbRAH, and recommendations are made for other research communities seeking to create curated ortholog databases.

Reassessment of requirements for anaerobic xylose fermentation by engineered, non-evolved Saccharomyces cerevisiae strains

Expression of a heterologous xylose isomerase, deletion of the GRE3 aldose-reductase gene and overexpression of genes encoding xylulokinase (XKS1) and non-oxidative pentose-phosphate-pathway enzymes (RKI1, RPE1, TAL1, TKL1) enables aerobic growth of Saccharomyces cerevisiae on d-xylose. However, literature reports differ on whether anaerobic growth on d-xylose requires additional mutations. Here, CRISPR-Cas9-assisted reconstruction and physiological analysis confirmed an early report that this basic set of genetic modifications suffices to enable anaerobic growth on d-xylose in the CEN.PK genetic background. Strains that additionally carried overexpression cassettes for the transaldolase and transketolase paralogs NQM1 and TKL2 only exhibited anaerobic growth on d-xylose after a 7–10 day lag phase. This extended lag phase was eliminated by increasing inoculum concentrations from 0.02 to 0.2 g biomass L⁻¹. Alternatively, a long lag phase could be prevented by sparging low-inoculum-density bioreactor cultures with a CO₂/N₂-mixture, thus mimicking initial CO₂ concentrations in high-inoculum-density, nitrogen-sparged cultures, or by using l-aspartate instead of ammonium as nitrogen source. This study resolves apparent contradictions in the literature on the genetic interventions required for anaerobic growth of CEN.PK-derived strains on d-xylose. Additionally, it indicates the potential relevance of CO₂ availability and anaplerotic carboxylation reactions for anaerobic growth of engineered S. cerevisiae strains on d-xylose.

Existence of a scaling relation in continuous cultures of Scheffersomyces stipitis: the steady states are completely determined by the ratio of carbon and oxygen uptake rates

BACKGROUND

Recently, we showed that steady-state continuous cultures of S. stipitis follow the principles of growth on mixture of two complementary substrates. More precisely, when such cultures are fed with progressively higher concentrations of glucose s _f at fixed dilution rate D = 0.1 h^-1, oxygen mass-transfer coefficient k _l a = 50 h^-1, and oxygen solubility c o ∗ , they transition from glucose- to oxygen-limited growth through an intermediate dual-limited regime in which both glucose and oxygen are limiting, and ethanol is produced without loss of glucose. It is, therefore, of considerable interest to characterize the dual-limited regime. We found that the dual-limited regime occurs precisely when the operating parameters D, s _f, k _l a, and c o ∗ satisfy the relation Y os < D s f / k l a · c o ∗ < Y os ' , where Y _os and Y os ' denote g of glucose consumed per g of oxygen consumed in the carbon- and oxygen-limited regimes. In this work, our goal was to determine if the above characterization of the dual-limited regime holds over a wider range of D, k _l a, and to understand why the dual-limited regime is determined by the dimensionless ratio D s f / k l a · c o ∗ .

RESULTS

To this end, we performed the foregoing experiments at three additional dilution rates (D = 0.07, 0.15, and 0.20 h^-1) and one additional mass-transfer coefficient (k _l a = 100 h^-1). We find that the above characterization of the dual-limited regime is valid for these conditions as well. Furthermore, the boundaries of the dual-limited regime are determined by the dimensionless ratio D s f / k l a · c o ∗ , because the steady-state concentrations are completely determined by this ratio. More precisely, if the steady-state concentrations of biomass, glucose, oxygen, and ethanol are suitably scaled, they collapse into a single curve with D s f / k l a · c o ∗ as the independent variable.

CONCLUSION

The dual-limited regime is characterized by the relation Y os < D s f / k l a · c o ∗ < Y os ' over the entire range of operating condition 0.07 h^-1 ≤ D ≤ 0.20 h^-1 and 50 h - 1 ≤ k l a ≤ 100 h - 1 . Since the effect of all operating parameters is embedded in the single parameter D s f / k l a · c o ∗ , the dimensionless plot provides a powerful tool to compare, with only a handful of data, various ethanol-producing strains over a wide range of operating conditions.

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.

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.

Review of Second Generation Bioethanol Production from Residual Biomass

In the context of climate change and the depletion of fossil fuels, there is a great need for alternatives to petroleum in the transport sector. This review provides an overview of the production of second generation bioethanol, which is distinguished from the first generation and subsequent generations of biofuels by its use of lignocellulosic biomass as raw material. The structural components of the lignocellulosic biomass such as cellulose, hemicellulose and lignin, are presented along with technological unit steps including pretreatment, enzymatic hydrolysis, fermentation, distillation and dehydration. The purpose of the pretreatment step is to increase the surface area of carbohydrate available for enzymatic saccharification, while minimizing the content of inhibitors. Performing the enzymatic hydrolysis releases fermentable sugars, which are converted by microbial catalysts into ethanol. The hydrolysates obtained after the pretreatment and enzymatic hydrolysis contain a wide spectrum of sugars, predominantly glucose and xylose. Genetically engineered microorganisms are therefore needed to carry out co-fermentation. The excess of harmful inhibitors in the hydrolysate, such as weak organic acids, furan derivatives and phenol components, can be removed by detoxification before fermentation. Effective saccharification further requires using exogenous hemicellulases and cellulolytic enzymes. Conventional species of distiller's yeast are unable to ferment pentoses into ethanol, and only a very few natural microorganisms, including yeast species like Candida shehatae, Pichia (Scheffersomyces) stipitis, and Pachysolen tannophilus, metabolize xylose to ethanol. Enzymatic hydrolysis and fermentation can be performed in a number of ways: by separate saccharification and fermentation, simultaneous saccharification and fermentation or consolidated bioprocessing. Pentose-fermenting microorganisms can be obtained through genetic engineering, by introducing xylose-encoding genes into metabolism of a selected microorganism to optimize its use of xylose accumulated in the hydrolysate.

Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species, Candida tenuis

Xylose fermentation is a rare trait that is immensely important to the cellulosic biofuel industry, and Candida tenuis is one of the few yeasts that has been reported with this trait. Here we report the isolation of two strains representing a candidate sister species to C. tenuis. Integrated analysis of genome sequence and physiology suggested the genetic basis of a number of traits, including variation between the novel species and C. tenuis in lactose metabolism due to the loss of genes encoding lactose permease and β-galactosidase in the former. Surprisingly, physiological characterization revealed that neither the type strain of C. tenuis nor this novel species fermented xylose in traditional assays. We reexamined three xylose-fermenting strains previously identified as C. tenuis and found that these strains belong to the genus Scheffersomyces and are not C. tenuis. We propose Yamadazyma laniorum f.a. sp. nov. to accommodate our new strains and designate its type strain as yHMH7 (=CBS 14780 = NRRL Y-63967T). Furthermore, we propose the transfer of Candida tenuis to the genus Yamadazyma as Yamadazyma tenuis comb. nov. This approach provides a roadmap for how integrated genome sequence and physiological analysis can yield insight into the mechanisms that generate yeast biodiversity.

The isolation of pentose-assimilating yeasts and their xylose fermentation potential

For the implementation of cellulosic ethanol technology, the maximum use of lignocellulosic materials is important to increase efficiency and to reduce costs. In this context, appropriate use of the pentose released by hemicellulose hydrolysis could improve de economic viability of this process. Since the Saccharomyces cerevisiae is unable to ferment the pentose, the search for pentose-fermenting microorganisms could be an alternative. In this work, the isolation of yeast strains from decaying vegetal materials, flowers, fruits and insects and their application for assimilation and alcoholic fermentation of xylose were carried out. From a total of 30 isolated strains, 12 were able to assimilate 30 g L⁻¹ of xylose in 120 h. The strain Candida tropicalis S4 produced 6 g L⁻¹ of ethanol from 56 g L⁻¹ of xylose, while the strain C. tropicalis E2 produced 22 g L⁻¹ of xylitol. The strains Candida oleophila G10.1 and Metschnikowia koreensis G18 consumed significant amount of xylose in aerobic cultivation releasing non-identified metabolites. The different materials in environment were source for pentose-assimilating yeast with variable metabolic profile.

Ethanol Production from Various Sugars and Cellulosic Biomass by White Rot Fungus Lenzites betulinus

Lenzites betulinus, known as gilled polypore belongs to Basidiomycota was isolated from fruiting body on broadleaf dead trees. It was found that the mycelia of white rot fungus Lenzites betulinus IUM 5468 produced ethanol from various sugars, including glucose, mannose, galactose, and cellobiose with a yield of 0.38, 0.26, 0.07, and 0.26 g of ethanol per gram of sugar consumed, respectively. This fungus relatively exhibited a good ethanol production from xylose at 0.26 g of ethanol per gram of sugar consumed. However, the ethanol conversion rate of arabinose was relatively low (at 0.07 g of ethanol per gram sugar). L. betulinus was capable of producing ethanol directly from rice straw and corn stalks at 0.22 g and 0.16 g of ethanol per gram of substrates, respectively, when this fungus was cultured in a basal medium containing 20 g/L rice straw or corn stalks. These results indicate that L. betulinus can produce ethanol efficiently from glucose, mannose, and cellobiose and produce ethanol very poorly from galactose and arabinose. Therefore, it is suggested that this fungus can ferment ethanol from various sugars and hydrolyze cellulosic materials to sugars and convert them to ethanol simultaneously.

Efficient conversion of xylose to ethanol by stress-tolerant Kluyveromyces marxianus BUNL-21

The fermentation ability of thermotolerant Kluyveromyces marxianus BUNL-21 isolated in Laos was investigated. Comparison with thermotolerant K. marxianus DMKU3-1042 as one of the most thermotolerant yeasts isolated previously revealed that the strain possesses stronger ability for conversion of xylose to ethanol, resistance to 2-deoxyglucose in the case of pentose, and tolerance to various stresses including high temperature and hydrogen peroxide. K. marxianus BUNL-21 was found to have ethanol fermentation activity from xylose that is slightly lower and much higher than that of Scheffersomyces stipitis (Pichia stipitis) at 30 °C and at higher temperatures, respectively. The lower ethanol production seems to be due to large accumulation of acetic acid. The possible mechanism of acetic acid accumulation is discussed. In addition, it was found that both K. marxianus strains produced ethanol in the presence of 10 mM hydroxymethylfurfural or furfural, at a level almost equivalent to that in their absence. Therefore, K. marxianus BUNL-21 is a highly competent yeast for high-temperature ethanol fermentation with lignocellulosic biomass.

Alcohol dehydrogenase gene ADH3 activates glucose alcoholic fermentation in genetically engineered Dekkera bruxellensis yeast

Dekkera bruxellensis is a non-conventional Crabtree-positive yeast with a good ethanol production capability. Compared to Saccharomyces cerevisiae, its tolerance to acidic pH and its utilization of alternative carbon sources make it a promising organism for producing biofuel. In this study, we developed an auxotrophic transformation system and an expression vector, which enabled the manipulation of D. bruxellensis, thereby improving its fermentative performance. Its gene ADH3, coding for alcohol dehydrogenase, was cloned and overexpressed under the control of the strong and constitutive promoter TEF1. Our recombinant D. bruxellensis strain displayed 1.4 and 1.7 times faster specific glucose consumption rate during aerobic and anaerobic glucose fermentations, respectively; it yielded 1.2 times and 1.5 times more ethanol than did the parental strain under aerobic and anaerobic conditions, respectively. The overexpression of ADH3 in D. bruxellensis also reduced the inhibition of fermentation by anaerobiosis, the “Custer effect”. Thus, the fermentative capacity of D. bruxellensis could be further improved by metabolic engineering.

Galactose utilization sheds new light on sugar metabolism in the sequenced strain Dekkera bruxellensis CBS 2499

Dekkera bruxellensis and Saccharomyces cerevisiae are considered two phylogenetically distant relatives, but they share several industrial relevant traits such as the ability to produce ethanol under aerobic conditions (Crabtree effect), high tolerance towards ethanol and acids, and ability to grow without oxygen. Beside a huge adaptability, D. bruxellensis exhibits a broader spectrum in utilization of carbon and nitrogen sources in comparison to S. cerevisiae. With the aim to better characterize its carbon source metabolism and regulation, the usage of galactose and the role that glucose plays on sugar metabolism were investigated in D. bruxellensis CBS 2499. The results indicate that in this yeast galactose is a non-fermentable carbon source, in contrast to S. cerevisiae that can ferment it. In particular, its metabolism is affected by the nitrogen source. Interestingly, D. bruxellensis CBS 2499 exhibits the 'short-term Crabtree effect', and the expression of genes involved in galactose utilization and in respiratory metabolism is repressed by glucose, similarly to what occurs in S. cerevisiae.

Identification of novel metabolic interactions controlling carbon flux from xylose to ethanol in natural and recombinant yeasts

BACKGROUND

Unlike xylose-converting natural yeasts, recombinant strains of Saccharomyces cerevisiae expressing the same xylose assimilation pathway produce under anaerobic conditions xylitol rather than ethanol from xylose at low specific xylose conversion rates. Despite intense research efforts over the last two decades, differences in these phenotypes cannot be explained by current metabolic and kinetic models. To improve our understanding how metabolic flux of xylose carbon to ethanol is controlled, we developed a novel kinetic model based on enzyme mechanisms and applied quantitative metabolite profiling together with enzyme activity analysis to study xylose-to-ethanol metabolisms of Candida tenuis CBS4435 (q xylose = 0.10 g/gdc/h, 25 °C; Y ethanol = 0.44 g/g; Y xylitol = 0.09 g/g) and the recombinant S. cerevisiae strain BP000 (q xylose = 0.07 g/gdc/h, 30 °C; Y ethanol = 0.24 g/g; Y xylitol = 0.43 g/g), both expressing the same xylose reductase (XR), comprehensively.

RESULTS

Results from strain-to-strain metabolic control analysis indicated that activity levels of XR and the maximal flux capacity of the upper glycolysis (UG; both ≥ tenfold higher in CBS4435) contributed predominantly to phenotype differentiation while reactions from the oxidative pentose phosphate pathway played minor roles. Intracellular metabolite profiles supported results obtained from kinetic modeling and indicated a positive correlation between pool sizes of UG metabolites and carbon flux through the UG. For CBS4435, fast carbon flux through the UG could be associated with an allosteric control of 6-phosphofructokinase (PFK) activity by fructose 6-phosphate. The ability of CBS4435 to keep UG metabolites at high levels could be explained by low glycerol 3-phosphate phosphatase (GPP, 17-fold lower in CBS4435) and high XR activities.

CONCLUSIONS

By applying a systems biology approach in which we combined results obtained from metabolic control analysis based on kinetic modeling with data obtained from quantitative metabolite profiling and enzyme activity analyses, we could provide new insights into metabolic and kinetic interactions contributing to the control of carbon flux from xylose to ethanol. Supported by evidences presented two new targets, PFK and GPP, could be identified that aside from XR play pivotal roles in phenotype differentiation. Design of efficient and fast microbial ethanol producers in the future can certainly benefit from results presented in this study.

In Delft: a personal account

The author looks back on his development in microbiology and yeast research, and on the establishment in Delft of the FEMS Central Office, FEMS Publications Office and the birth of FEMS Yeast Research.

Secreted xylanase XynA mediates utilization of xylan as sole carbon source in Candida utilis

The fodder yeast Candida utilis is able to use xylose mono- and oligomers as sources of carbon but not the abundant polymer xylan. C. utilis transformants producing the Penicillium simplicissimum xylanase XynA were constructed using expression vectors encoding fusions of the Saccharomyces cerevisiae Mfα1 pre-pro secretion leader to XynA. The Mfα1-XynA fusion was efficiently processed in transformants and XynA was secreted almost quantitatively into the culture medium. Secreted XynA was enzymatically active and allowed transformants to grow on xylan as the sole carbon source. Addition of a second expression unit for the heterologous green fluorescent protein (GFP) generated C. utilis transformants, which showed intracellular GFP fluorescence during growth on xylan. The results suggest that xylanase-producing C. utilis is suited as a cost-effective host organism for heterologous protein production and for other biotechnical applications.

Organic acids from lignocellulose: Candida lignohabitans as a new microbial cell factory

Biorefinery applications require microbial cell factories for the conversion of various sugars derived from lignocellulosic material into value-added chemicals. Here, the capabilities of the yeast Candida lignohabitans to utilize a range of such sugars is characterized. Substrates efficiently converted by this yeast include the pentoses xylose and arabinose. Genetic engineering of C. lignohabitans with the isolated endogenous GAP promoter and GAP terminator was successful. GFP expression was used as a proof of functionality for the isolated transcription elements. Expression of lactate dehydrogenase and cis-aconitate decarboxylase resulted in stable and reproducible production of lactic acid and itaconic acid, respectively. The desired organic acids were accumulated converting pure sugars as well as lignocellulosic hydrolysates. C. lignohabitans proved therefore to be a promising reliable microbial host for production of organic acids from lignocellulosic material.

Assessing the potential of wild yeasts for bioethanol production

Bioethanol fermentations expose yeasts to a new, complex and challenging fermentation medium with specific inhibitors and sugar mixtures depending on the type of carbon source. It is, therefore, suggested that the natural diversity of yeasts should be further exploited in order to find yeasts with good ethanol yield in stressed fermentation media. In this study, we screened more than 50 yeast isolates of which we selected five isolates with promising features. The species Candida bombi, Wickerhamomyces anomalus and Torulaspora delbrueckii showed better osmo- and hydroxymethylfurfural tolerance than Saccharomyces cerevisiae. However, S. cerevisiae isolates had the highest ethanol yield in fermentation experiments mimicking high gravity fermentations (25 % glucose) and artificial lignocellulose hydrolysates (with a myriad of inhibitors). Interestingly, among two tested S. cerevisiae strains, a wild strain isolated from an oak tree performed better than Ethanol Red, a S. cerevisiae strain which is currently commonly used in industrial bioethanol fermentations. Additionally, a W. anomalus strain isolated from sugar beet thick juice was found to have a comparable ethanol yield, but needed longer fermentation time. Other non-Saccharomyces yeasts yielded lower ethanol amounts.

Pathogenic eukaryotes in gut microbiota of western lowland gorillas as revealed by molecular survey

Although gorillas regarded as the largest extant species of primates and have a close phylogenetic relationship with humans, eukaryotic communities have not been previously studied in these populations. Herein, 35 eukaryotic primer sets targeting the 18S rRNA gene, internal transcribed spacer gene and other specific genes were used firstly to explore the eukaryotes in a fecal sample from a wild western lowland gorilla (Gorilla gorilla gorilla). Then specific real-time PCRs were achieved in additional 48 fecal samples from 21 individual gorillas to investigate the presence of human eukaryotic pathogens. In total, 1,572 clones were obtained and sequenced from the 15 cloning libraries, resulting in the retrieval of 87 eukaryotic species, including 52 fungi, 10 protozoa, 4 nematodes and 21 plant species, of which 52, 5, 2 and 21 species, respectively, have never before been described in gorillas. We also reported the occurrence of pathogenic fungi and parasites (i.e. Oesophagostomum bifurcum (86%), Necator americanus (43%), Candida tropicalis (81%) and other pathogenic fungi were identified). In conclusion, molecular techniques using multiple primer sets may offer an effective tool to study complex eukaryotic communities and to identify potential pathogens in the gastrointestinal tracts of primates.

Identification and characterisation of xylanolytic yeasts isolated from decaying wood and sugarcane bagasse in Brazil

In this study, yeasts associated with lignocellulosic materials in Brazil, including decaying wood and sugarcane bagasse, were isolated, and their ability to produce xylanolytic enzymes was investigated. A total of 358 yeast isolates were obtained, with 198 strains isolated from decaying wood and 160 strains isolated from decaying sugarcane bagasse samples. Seventy-five isolates possessed xylanase activity in solid medium and were identified as belonging to nine species: Candida intermedia, C. tropicalis, Meyerozyma guilliermondii, Scheffersomyces shehatae, Sugiyamaella smithiae, Cryptococcus diffluens, Cr. heveanensis, Cr. laurentii and Trichosporon mycotoxinivorans. Twenty-one isolates were further screened for total xylanase activity in liquid medium with xylan, and five xylanolytic yeasts were selected for further characterization, which included quantitative analysis of growth in xylan and xylose and xylanase and β-D-xylosidase activities. The yeasts showing the highest growth rate and cell density in xylan, Cr. laurentii UFMG-HB-48, Su. smithiae UFMG-HM-80.1 and Sc. shehatae UFMG-HM-9.1a, were, simultaneously, those exhibiting higher xylanase activity. Xylan induced the highest level of (extracellular) xylanase activity in Cr. laurentii UFMG-HB-48 and the highest level of (intracellular, extracellular and membrane-associated) β-D-xylosidase activity in Su. smithiae UFMG-HM-80.1. Also, significant β-D-xylosidase levels were detected in xylan-induced cultures of Cr. laurentii UFMG-HB-48 and Sc. shehatae UFMG-HM-9.1a, mainly in extracellular and intracellular spaces, respectively. Under xylose induction, Cr. laurentii UFMG-HB-48 showed the highest intracellular β-D-xylosidase activity among all the yeast tested. C. tropicalis UFMG-HB 93a showed its higher (intracellular) β-D-xylosidase activity under xylose induction and higher at 30 °C than at 50 °C. This study revealed different xylanolytic abilities and strategies in yeasts to metabolise xylan and/or its hydrolysis products (xylo-oligosaccharides and xylose). Xylanolytic yeasts are able to secrete xylanolytic enzymes mainly when induced by xylan and present different strategies (intra- and/or extracellular hydrolysis) for the metabolism of xylo-oligosaccharides. Some of the unique xylanolytic traits identified here should be further explored for their applicability in specific biotechnological processes.

Characterization of newly isolated oleaginous yeasts - Cryptococcus podzolicus, Trichosporon porosum and Pichia segobiensis

The yeast strains Cryptococcus podzolicus, Trichosporon porosum and Pichia segobiensis were isolated from soil samples and identified as oleaginous yeast strains beneficial for the establishment of microbial production processes for sustainable lipid production suitable for several industrial applications. When cultured in bioreactors with glucose as the sole carbon source C. podzolicus yielded 31.8% lipid per dry biomass at 20°C, while T. porosum yielded 34.1% at 25°C and P. segobiensis 24.6% at 25°C. These amounts correspond to lipid concentrations of 17.97 g/L, 17.02 g/L and 12.7 g/L and volumetric productivities of 0.09 g/Lh, 0.1 g/Lh and 0.07 g/Lh, respectively. During the culture of C. podzolicus 30 g/l gluconic acid was detected as by-product in the culture broth and 12 g/L gluconic acid in T. porosum culture. The production of gluconic acid was eliminated for both strains when glucose was substituted by xylose as the carbon source. Using xylose lipid yields were 11.1 g/L and 13.9 g/L, corresponding to 26.8% and 33.4% lipid per dry biomass and a volumetric productivity of 0.07 g/Lh and 0.09 g/Lh, for C. podzolicus and T. porosum respectively. The fatty acid profile analysis showed that oleic acid was the main component (39.6 to 59.4%) in all three strains and could be applicable for biodiesel production. Palmitic acid (18.4 to 21.1%) and linolenic acid (7.5 to 18.7%) are valuable for cosmetic applications. P. segobiensis had a considerable amount of palmitoleic acid (16% content) and may be suitable for medical applications.

Tolerance of pentose utilising yeast to hydrogen peroxide-induced oxidative stress

Background

Bioethanol fermentations follow traditional beverage fermentations where the yeast is exposed to adverse conditions such as oxidative stress. Lignocellulosic bioethanol fermentations involve the conversion of pentose and hexose sugars into ethanol. Environmental stress conditions such as osmotic stress and ethanol stress may affect the fermentation performance; however, oxidative stress as a consequence of metabolic output can also occur. However, the effect of oxidative stress on yeast with pentose utilising capabilities has yet to be investigated.

Results

Assaying for the effect of hydrogen peroxide-induced oxidative stress on Candida, Pichia and Scheffersomyces spp. has demonstrated that these yeast tolerate hydrogen peroxide-induced oxidative stress in a manner consistent with that demonstrated by Saccharomyces cerevisiae. Pichia guillermondii appears to be more tolerant to hydrogen peroxide-induced oxidative stress when compared to Candida shehatae, Candida succiphila or Scheffersomyces stipitis.

Conclusions

Sensitivity to hydrogen peroxide-induced oxidative stress increased in the presence of minimal media; however, addition of amino acids and nucleobases was observed to increase tolerance. In particular adenine increased tolerance and methionine reduced tolerance to hydrogen peroxide-induced oxidative stress.

Yeast biotechnology: teaching the old dog new tricks

Yeasts are regarded as the first microorganisms used by humans to process food and alcoholic beverages. The technology developed out of these ancient processes has been the basis for modern industrial biotechnology. Yeast biotechnology has gained great interest again in the last decades. Joining the potentials of genomics, metabolic engineering, systems and synthetic biology enables the production of numerous valuable products of primary and secondary metabolism, technical enzymes and biopharmaceutical proteins. An overview of emerging and established substrates and products of yeast biotechnology is provided and discussed in the light of the recent literature.

Bioconversion of xylose, hexoses and biomass to ethanol by a new isolate of the white rot basidiomycete Trametes versicolor

Second-generation bioethanol production requires the development of economically feasible and sustainable processes that use renewable lignocellulosic biomass as a starting material. However, the microbial fermentation of xylose, which is the principal pentose sugar in hemicellulose, is a limiting factor in developing such processes. Here, a strain of the white rot basidiomycete Trametes versicolor that was capable of efficiently fermenting xylose was newly isolated and characterized. This strain, designated KT9427, was capable of assimilating and converting xylose to ethanol under anaerobic conditions with a yield of 0.44 g ethanol per 1 g of sugar consumed. In culture medium containing low yeast extract concentrations, xylose consumption and ethanol productivity were enhanced. Adjusting the initial pH between 3.0 and 5.0 did not markedly influence xylose fermentation. T. versicolor KT9427 also produced ethanol from glucose, mannose, fructose, cellobiose and maltose at yields ranging from 0.45 to 0.49 g ethanol per 1 g of sugar consumed. In addition, strain KT9427 exhibited favourable conversion of non-pretreated starch, cellulose, xylan, wheat bran and rice straw into ethanol compared to common recombinant yeast strains. Taken together, the present findings suggest that T. versicolor KT9427 is a promising candidate for environmentally friendly ethanol production directly from lignocellulosic biomass.

Pichia anomala 29X: a resistant strain for lignocellulosic biomass hydrolysate fermentation

To efficiently use lignocellulosic biomass hydrolysates as fermentation media for bioethanol production, besides being capable of producing significant amount of ethanol, the fermenting host should also meet the following two requirements: (1) resistant to the inhibitory compounds formed during biomass pretreatment process, (2) capable of utilizing C5 sugars, such as xylose, as carbon source. In our laboratory, a screening was conducted on microorganisms collected from environmental sources for their tolerance to hydrolysate inhibitors. A unique resistant strain was selected and identified as Pichia anomala (Wickerhamomyces anomalus), deposited as CBS 132101. The strain is able to produce ethanol in various biomass hydrolysates, both with and without oxygen. Besides, the strain could assimilate xylose and use nitrate as N source. These physiological characteristics make P. anomala an interesting strain for bioethanol production from lignocellulosic biomass hydrolysates.

Strategies for the production of high concentrations of bioethanol from seaweeds: production of high concentrations of bioethanol from seaweeds

Bioethanol has attracted attention as an alternative to petroleum-derived fuel. Seaweeds have been proposed as some of the most promising raw materials for bioethanol production because they have several advantages over lignocellulosic biomass. However, because seaweeds contain low contents of glucans, i.e., polysaccharides composed of glucose, the conversion of only the glucans from seaweed is not sufficient to produce high concentrations of ethanol. Therefore, it is also necessary to produce ethanol from other specific carbohydrate components of seaweeds, including sulfated polysaccharides, mannitol, alginate, agar and carrageenan. This review summarizes the current state of research on the production of ethanol from seaweed carbohydrates for which the conversion of carbohydrates to sugars is a key step and makes comparisons with the production of ethanol from lignocellulosic biomass. This review provides valuable information necessary for the production of high concentrations of ethanol from seaweeds.

Diversity and physiological characterization of D-xylose-fermenting yeasts isolated from the Brazilian Amazonian Forest

Background

This study is the first to investigate the Brazilian Amazonian Forest to identify new D-xylose-fermenting yeasts that might potentially be used in the production of ethanol from sugarcane bagasse hemicellulosic hydrolysates.

Methodology/Principal Findings

A total of 224 yeast strains were isolated from rotting wood samples collected in two Amazonian forest reserve sites. These samples were cultured in yeast nitrogen base (YNB)-D-xylose or YNB-xylan media. Candida tropicalis, Asterotremella humicola, Candida boidinii and Debaryomyces hansenii were the most frequently isolated yeasts. Among D-xylose-fermenting yeasts, six strains of Spathaspora passalidarum, two of Scheffersomyces stipitis, and representatives of five new species were identified. The new species included Candida amazonensis of the Scheffersomyces clade and Spathaspora sp. 1, Spathaspora sp. 2, Spathaspora sp. 3, and Candida sp. 1 of the Spathaspora clade. In fermentation assays using D-xylose (50 g/L) culture medium, S. passalidarum strains showed the highest ethanol yields (0.31 g/g to 0.37 g/g) and productivities (0.62 g/L·h to 0.75 g/L·h). Candida amazonensis exhibited a virtually complete D-xylose consumption and the highest xylitol yields (0.55 g/g to 0.59 g/g), with concentrations up to 25.2 g/L. The new Spathaspora species produced ethanol and/or xylitol in different concentrations as the main fermentation products. In sugarcane bagasse hemicellulosic fermentation assays, S. stipitis UFMG-XMD-15.2 generated the highest ethanol yield (0.34 g/g) and productivity (0.2 g/L·h), while the new species Spathaspora sp. 1 UFMG-XMD-16.2 and Spathaspora sp. 2 UFMG-XMD-23.2 were very good xylitol producers.

Conclusions/Significance

This study demonstrates the promise of using new D-xylose-fermenting yeast strains from the Brazilian Amazonian Forest for ethanol or xylitol production from sugarcane bagasse hemicellulosic hydrolysates.