Isolation and Characterization of Xylitol-Producing Yeasts from the Gut of Colleopteran Insects

A total of 35 yeasts were isolated from the gut of beetles collected from Hyderabad city, India. Twenty of these yeasts utilized xylose as a sole carbon source but only 12 of these converted xylose to xylitol. The ability to convert xylose to xylitol varied among the isolates and ranged from 0.12 to 0.58 g/g xylose. Based on the phenotypic characteristics and phylogenetic analysis of the D1/D2 domain sequence of 26S rRNA gene, these isolates were identified as members of Pichia, Candida, Issatchenkia, and Clavispora. Strain YS 54 (CBS 10446), which was phylogenetically similar to Pichia caribbica and which formed hat-shaped ascospore characteristics of the genus Pichia, was the best xylitol producer (0.58 g xylitol/g xylose). YS 54 was also capable of producing xylitol from sugarcane bagasse hydrolysate and the efficiency of conversion was 0.32 g xylitol/g xylose after 20 cycles of adaptation in medium containing sugarcane bagasse hydrolysate.     

Xylose chemostat isolates of Saccharomyces cerevisiae show altered metabolite and enzyme levels compared with xylose, glucose, and ethanol metabolism of the original strain

The efficient conversion of xylose-containing biomass hydrolysate by the ethanologenic yeast Saccharomyces cerevisiae to useful chemicals such as ethanol still remains elusive, despite significant efforts in both strain and process development. This study focused on the recovery and characterization of xylose chemostat isolates of a S. cerevisiae strain that overexpresses xylose reductase- and xylitol dehydrogenase-encoding genes from Pichia stipitis and the gene encoding the endogenous xylulokinase. The isolates were recovered from aerobic chemostat cultivations on xylose as the sole or main carbon source. Under aerobic conditions, on minimal medium with 30 g l^–1 xylose, the growth rate of the chemostat isolates was 3-fold higher than that of the original strain (0.15 h^–1 vs 0.05 h^–1). In a detailed characterization comparing the metabolism of the isolates with the metabolism of xylose, glucose, and ethanol in the original strain, the isolates showed improved properties in the assumed bottlenecks of xylose metabolism. The xylose uptake rate was increased almost 2-fold. Activities of the key enzymes in the pentose phosphate pathway (transketolase, transaldolase) increased 2-fold while the concentrations of their substrates (pentose 5-phosphates, sedoheptulose 7-phosphate) decreased correspondingly. Under anaerobic conditions, on minimal medium with 45 g l^–1 xylose, the ethanol productivity (in terms of cell dry weight; CDW) of one of the isolates increased from 0.012 g g^–1 CDW h^–1 to 0.017 g g^–1 CDW h^–1 and the yield from 0.09 g g^–1 xylose to 0.14 g g^–1 xylose, respectively.     

Revealing oxidative pentose metabolism in new Pseudomonas putida isolates

The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well-characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth-promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism (xylDXA) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism (araDXA). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.     

Xylose utilization and short-chain fatty acid production by selected components of the intestinal microflora of a rodent pollinator (Aethomys namaquensis)

Namaqua rock mice (Aethomys namaquensis) consume nectar xylose when visiting Protea flowers. Whole-animal metabolism studies suggest that the gastrointestinal microflora plays an important role in xylose metabolism in A. namaquensis. We collected caecal contents under anaerobic conditions, cultured caecal microflora both aerobically and anaerobically, and assessed caecal microbial xylose utilization using a ¹⁴C-xylose incubation assay. All four mice sampled hosted culturable caecal micro-organisms that tested positive for xylose utilization. These were classified by 16S rRNA based taxonomy as: Bacillus subtilis, Bacillus pumilus, Bacillus licheniformis, Shigella boydii, Arthrobacter sp. and members of the fungal genera Aspergillus and Penicillium. Cultures of these isolates were then analyzed by gas chromatography to determine the types and quantities of short-chain fatty acids produced by xylose fermentation. These results are discussed in the context of other studies of gut microflora in vertebrates.     

Isolation and characterization of xylose- and xylan-utilizing anaerobic bacteria

By enrichment with xylose, nine mesophilic strains of anaerobic bacteria were obtained from various sources. Two isolates appear to belong to the genus Eubacterium. Six other strains belong to the genus Clostridium. Three of the isolated strains utilized larch wood xylan. The percentage of utilization of xylose and xylan and the yield of fermentation end products — viz. acetic acid and butyric acid-are equivalent to that of Clostridium acetobutylicum (ATCC 824) and reported thermophilic strains.     

High-throughput screening and characterization of xylose-utilizing, ethanol-tolerant thermophilic bacteria for bioethanol production

Aims: To develop a high‐throughput assay for screening xylose‐utilizing and ethanol‐tolerant thermophilic bacteria owing to their abilities to be the promising ethanologens. Methods and Results: Based on alcohol oxidase and peroxidase‐coupled enzymatic reaction, an assay was developed by the formation of the coloured quinonimine to monitor the oxidation of ethanol in the reaction and calculate the concentration of ethanol. This assay was performed in 96‐well microtitre plate in a high‐throughput and had a well‐linear detection range of ethanol from 0 up to 2·5 g l^?1 with high accuracy. The assay was then verified by screening soil samples from hot spring for xylose‐utilizing and ethanol production at 60°C. Three isolates LM14‐1, LM14‐5 and LM18‐4 with 3–5% (v/v) ethanol tolerance and around 0·29–0·38 g g^?1 ethanol yield from xylose were obtained. Phylogenetic and phenotypic analysis showed that the isolates clustered with members of the genus Bacillus or Geobacillus subgroup. Conclusions: The developed double enzyme‐coupled, high‐throughput screening system is effective to screen and isolate xylose‐utilizing, ethanol‐producing thermophilic bacteria for bioethanol production at the elevated temperature. Significance and Impact of the Study: Our research presented a novel high‐throughput method to screen thermophilic bacteria for producing ethanol from xylose. This screening method is also very useful to screen all kinds of ethanologens either from natural habitats or from mutant libraries, to improve bioethanol production from lignocellulosic feedstocks.     

Fermentation behavior of osmophilic yeast Candida tropicalis isolated from the nectar of Hibiscus rosa sinensis flowers for xylitol production

Eighteen yeast species belonging to seven genera were isolated from ten samples of nectar from Hibiscus rosa sinensis and investigated for xylitol production using d-xylose as sole carbon source. Amongst these isolates, no. 10 was selected as the best xylitol producer and identified as Candida tropicalis on the basis of morphological, biochemical and 26S rDNA sequencing. C. tropicalis produced 12.11 gl⁻¹ of xylitol in presence of 50 gl⁻¹ of xylose in 72 h at pH 5, 30°C and 200 rpm. The strain of C. tropicalis obtained through xylose enrichment technique has resulted in a yield of 0.5 gg⁻¹ with a xylitol volumetric productivity of 1.07 gl⁻¹h⁻¹ in the presence of 300 gl⁻¹ of xylose through batch fermentation. This organism has been reported for the first time from Hibiscus rosa sinensis flowers. Realizing, the importance of this high valued compound, as a sugar substitute, xylose enrichment technique was developed in order to utilize even higher concentrations of xylose as substrate for maximum xylitol production.     

NADH-linked aldose reductase: the key to anaerobic alcoholic fermentation of xylose by yeasts

Summary The kinetics and enzymology of d-xylose utilization were studied in aerobic and anaerobic batch cultures of the facultatively fermentative yeasts Candida utilis, Pachysolen tannophilus, and Pichia stipitis. These yeasts did not produce ethanol under aerobic conditions. When shifted to anaerobiosis cultures of C. utilis did not show fermentation of xylose; in Pa. tannophilus a very low rate of ethanol formation was apparent, whereas with Pi. stipitis rapid fermentation of xylose occurred. The different behaviour of these yeasts ist most probably explained by differences in the nature of the initial steps of xylose metabolism: in C. utilis xylose is metabolized via an NADPH-dependent xylose reductase and an NAD⁺-linked xylitol dehydrogenase. As a consequence, conversion of xylose to ethanol by C. utilis leads to an overproduction of NADH which blocks metabolic activity in the absence of oxygen. In Pa. tannophilus and Pi. stipitis, however, apart from an NADPH-linked xylose reductase also an NADH-linked xylose reductase was present. Apparently xylose metabolism via the NADH-dependent reductase circumvents the imbalance of the NAD⁺/NADH redox system, thus allowing fermentation of xylose to ethanol under anaerobic conditions. The finding that the rate of xylose fermentation in Pa. tannophilus and Pi. stipitis corresponds with the activity of the NADH-linked xylose reductase activity is in line with this hypothesis. Furthermore, a comparative study with various xylose-assimilating yeasts showed that significant alcoholic fermentation of xylose only occurred in those organisms which possessed NADH-linked aldose reductase.     

Improvement of xylose utilization in Clostridium acetobutylicum via expression of the talA gene encoding transaldolase from Escherichia coli

Clostridium acetobutylicum ATCC 824 was metabolically engineered for improved xylose utilization. The gene talA, which encodes transaldolase from Escherichia coli K-12, was cloned and overexpressed in C. acetobutylicum ATCC 824. Compared with C. acetobutylicum ATCC 824 (824-WT), the transformant bearing the E. coli talA gene (824-TAL) showed improved ability on xylose utilization and solvents production using xylose as the sole carbon source. During the fermentation of xylose and glucose mixtures with three xylose/glucose ratios (approximately 1:2, 1:1 and 2:1), the rate of xylose consumption and final solvents titers of 824-TAL were all higher than those of 824-WT, despite glucose repression on xylose uptake still existing. These results suggest that the insufficiency of transaldolase in the pentose phosphate pathway (PPP) of C. acetobutylicum is one of the bottlenecks for xylose metabolism and therefore, overexpressing the gene encoding transaldolase is able to improve xylose utilization and solvent production.     

Identification of a xylulokinase catalyzing xylulose phosphorylation in the xylose metabolic pathway of <Emphasis Type="Italic">Kluyveromyces marxianus</Emphasis> NBRC1777

Xylulokinase is one of the key enzymes in xylose metabolism and fermentation, and fine-tuned expression of xylulokinase can improve xylose fermentation in yeast. To improve the efficiency of xylose fermentation in Kluyveromyces marxianus, the gene KmXYL3, which encodes a d-xylulokinase (E.C. 2.7.1.17), was isolated from K. marxianus NBRC1777. KmXYL3 was expressed in Escherichia coli BL21 (DE3) cells, and the specific activity of the resulting recombinant purified xylulokinase was 23.5 mU/mg. Disruption of KmXYL3 resulted in both loss of xylitol utilization and marked decrease in xylose utilization, proving that KmXYL3 encodes a xylulokinase that catalyzes the reaction from xylulose to xylulose 5-phosphate in the xylose metabolic pathway. The slow assimilation of xylose observed in the KmXYL3-disrupted strain indicates that KmXYL3 is critical for xylose and xylitol utilization; however, K. marxianus utilizes a bypass pathway for xylose assimilation, and this pathway does not involve xylitol or xylulose.     

Xylitol does not inhibit xylose fermentation by engineered <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> expressing <Emphasis Type="Italic">xylA</Emphasis> as severely as it inhibits xylose isomerase reaction in vitro

Efficient fermentation of xylose, which is abundant in hydrolysates of lignocellulosic biomass, is essential for producing cellulosic biofuels economically. While heterologous expression of xylose isomerase in Saccharomyces cerevisiae has been proposed as a strategy to engineer this yeast for xylose fermentation, only a few xylose isomerase genes from fungi and bacteria have been functionally expressed in S. cerevisiae. We cloned two bacterial xylose isomerase genes from anaerobic bacteria (Bacteroides stercoris HJ-15 and Bifidobacterium longum MG1) and introduced them into S. cerevisiae. While the transformant with xylA from B. longum could not assimilate xylose, the transformant with xylA from B. stercoris was able to grow on xylose. This result suggests that the xylose isomerase (BsXI) from B. stercoris is functionally expressed in S. cerevisiae. The engineered S. cerevisiae strain with BsXI consumed xylose and produced ethanol with a good yield (0.31 g/g) under anaerobic conditions. Interestingly, significant amounts of xylitol (0.23 g xylitol/g xylose) were still accumulated during xylose fermentation even though the introduced BsXI might not cause redox imbalance. We investigated the potential inhibitory effects of the accumulated xylitol on xylose fermentation. Although xylitol inhibited in vitro BsXI activity significantly (K _I = 5.1 ± 1.15 mM), only small decreases (less than 10%) in xylose consumption and ethanol production rates were observed when xylitol was added into the fermentation medium. These results suggest that xylitol accumulation does not inhibit xylose fermentation by engineered S. cerevisiae expressing xylA as severely as it inhibits the xylose isomerase reaction in vitro.     

Xylose isomerase from polycentric fungus Orpinomyces: gene sequencing, cloning, and expression in Saccharomyces cerevisiae for bioconversion of xylose to ethanol

The cDNA sequence of the gene for xylose isomerase from the rumen fungus Orpinomyces was elucidated by rapid amplification of cDNA ends. The 1,314-nucleotide gene was cloned and expressed constitutively in Saccharomyces cerevisiae. The deduced polypeptide sequence encoded a protein of 437 amino acids which showed the highest similarity to the family II xylose isomerases. Further, characterization revealed that the recombinant enzyme was a homodimer with a subunit of molecular mass 49 kDa. Cell extract of the recombinant strain exhibited high specific xylose isomerase activity. The pH optimum of the enzyme was 7.5, while the low temperature optimum at 37°C was the property that differed significantly from the majority of the reported thermophilic xylose isomerases. In addition to the xylose isomerase gene, the overexpression of the S. cerevisiae endogenous xylulokinase gene and the Pichia stipitis SUT1 gene for sugar transporter in the recombinant yeast facilitated the efficient production of ethanol from xylose.     

Isolation of Streptococcus thoraltensis from Rabbit Faeces

Bacteria were isolated from rabbit faeces using equine caecal fluid as a growth medium. Two new isolates of the genus Streptococcus are described in terms of their biochemical properties. One of these has a 16S rRNA gene with 97.7%, and the other 98.5%, identity to Streptococcus thoraltensis. While S. thoraltensis has been described in the intestinal tract of pigs, it is generally considered to inhabit the porcine genital tract. The biochemical properties of these bacteria indicate that both new isolates showed an ability to digest xylose, an adaptation beneficial for survival in a niche where much of the nutrient supply is of plant origin. Moreover, having bacteria able to digest xylose in the digestive tract should be beneficial to the rabbit, allowing more effective utilisation and digestion of food. This work provides one of the few examples of an analysis of the physiological properties of a bacterium found in the hindgut of the rabbit. By building up a number of such studies, the mechanisms of bacterial digestion in the rabbit will become better understood.     

Xylose metabolism in a thermophilic mouldMalbranchea pulchella var.sulfurea TMD-8

The thermophilic mouldMalbranchea pulchella var.sulfurea TMD-8 produced extracellular xylanases in wheat straw hemicellulose as well as wheat straw. This mould utilized xylose less efficiently than glucose. Mycelial extracts contained xylose isomerase, xylose reductase, and xylitol dehydrogenase. Xylose isomerase was less thermostable than that from other microorganisms. However, xylitol dehydrogenase and xylose reductase were relatively more thermostable in comparison with these enzymes from other microorganisms. The affinity of xylose isomerase for xylose was very high (Km 10mM), while that of xylose reductase was low (Km 23.5mM). The xylitol dehydrogenase exhibited relatively high affinity for xylitol (Km 0.02mM). The activity of this enzyme, however, declined steeply, in the alkaline range. This is the first report on the occurrence of three intracellular enzymes, xylose isomerase, xylose reductase, and xylitol dehydrogenase in a thermophilic mould, which play an important role in xylose metabolism.     

Novel two‐stage fermentation process for bioethanol production using Saccharomyces pastorianus

Bioethanol produced from lignocellulosic materials has the potential to be economically feasible, if both glucose and xylose released from cellulose and hemicellulose can be efficiently converted to ethanol. Saccharomyces spp. can efficiently convert glucose to ethanol; however, xylose conversion to ethanol is a major hurdle due to lack of xylose‐metabolizing pathways. In this study, a novel two‐stage fermentation process was investigated to improve bioethanol productivity. In this process, xylose is converted into biomass via non‐Saccharomyces microorganism and coupled to a glucose‐utilizing Saccharomyces fermentation. Escherichia coli was determined to efficiently convert xylose to biomass, which was then killed to produce E. coli extract. Since earlier studies with Saccharomyces pastorianus demonstrated that xylose isomerase increased ethanol productivities on pure sugars, the addition of both E. coli extract and xylose isomerase to S. pastorianus fermentations on pure sugars and corn stover hydrolysates were investigated. It was determined that the xylose isomerase addition increased ethanol productivities on pure sugars but was not as effective alone on the corn stover hydrolysates. It was observed that the E. coli extract addition increased ethanol productivities on both corn stover hydrolysates and pure sugars. The ethanol productivities observed on the corn stover hydrolysates with the E. coli extract addition was the same as observed on pure sugars with both E. coli extract and xylose isomerase additions. These results indicate that the two‐stage fermentation process has the capability to be a competitive alternative to recombinant Saccharomyces cerevisiae‐based fermentations. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:300–310, 2014     

Xylose transport studies with xylose-utilizing <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> strains expressing heterologous and homologous permeases

In the present study, we modified xylose uptake properties of a recombinant xylose-utilizing yeast Saccharomyces cerevisiae by expression of heterologous and homologous permease-encoding genes. In a mutant yeast strain with the main seven hexose transporter genes deleted, and engineered for xylose utilization, we screened an expression cDNA library of the filamentous fungus Trichoderma reesei (Hypocrea jecorina) for enhanced growth on xylose plates. One cDNA clone with significant homology to fungal sugar transporters was obtained, but when the clone was retransformed into the host, it did not support significant growth on xylose. However, during a long liquid culture of the strain carrying the cDNA clone, adaptive mutations apparently occurred in the host, which led to growth on xylose but not on glucose. The new transporter homologue, Trxlt1 thus appears to code for a protein specific for xylose uptake. In addition, xylose-transporting properties of some homologous hexose transporters were studied. All of them, i.e., Hxt1, Hxt2, Hxt4, and Hxt7 were capable of xylose uptake. Their affinities for xylose varied, K _m values between 130 and 900 mM were observed. The single-Hxt strains showed a biphasic growth mode on xylose, alike the Trxlt1 harboring strain. The initial, slow growth was followed by a long lag and finally by exponential growth.     

Identification of a xylose reductase gene in the xylose metabolic pathway of <Emphasis Type="Italic">Kluyveromyces marxianus</Emphasis> NBRC1777

Kluyveromyces marxianus is thermotolerant yeast that is able to utilize a wider range of substrates and has greater thermal tolerance than most other yeast species. K. marxianus can assimilate xylose, but its ability to produce ethanol from xylose in oxygen-limited environments is poor. In the present study, the K. marxianus xylose reductase (KmXR) gene (Kmxyl1) was cloned and the recombinant enzyme was characterized to clarify the factors that limit xylose fermentation in K. marxianus NBRC1777. KmXR is a key enzyme in the xylose metabolism of K. marxianus, which was verified by disruption of the Kmxyl1 gene. The Km of the recombinant KmXR for NADPH is 65.67 μM and KmXR activity is 1.295 U/mg, which is lower than those of most reported yeast XRs, and the enzyme has no activity with coenzyme NADH. This result demonstrates that the XR from K. marxianus is highly coenzyme specific; combined with the extremely low XDH activity of K. marxianus with NADP⁺, the limitation of xylose fermentation is due to a redox imbalance under anaerobic conditions and low KmXR activity.     

Transfer of genes fromPseudomonas saccharophila to construct xylose-utilizing strains ofAlcaligenes eutrophus

About 1500 hybrid broad-host-range plasmids from a genomic library ofPseudomonas saccharophila were individually transferred by conjugation fromEscherichia coli toAlcaligenes eutrophus. Direct selection for pentose-utilizing transconjugants yielded three clones capable of growth on xylose. Growth ofP. saccharophila as well as the transconjugants ofA. eutrophus on xylose was relatively slow, exhibiting doubling times of about 9.5 h. Plasmid pGN3 harbored by one transconjugant contained a 28-kb DNA insert, 16.4 kb of which comprised the minimal information required for xylose utilization byA. eutrophus. At least thexyl genes encoding xylose isomerase and xylulokinase were located within this region, as indicated by their induction during growth ofA. eutrophus (pGN3) on xylose. Southern hybridizations with a heterologous gene probe confirmed the presence of thesexyl genes. In bothP. saccharophila andA. eutrophus (pGN3), low activities of several enzymes operating in the pentose phosphate and Entner-Doudoroff pathways might limit the rate of xylose catabolism.     

Fermentation performance of Candida guilliermondii for xylitol production on single and mixed substrate media

Semidefined media fermentation simulating the sugar composition of hemicellulosic hydrolysates (around 85 g l^-1 xylose, 17 g l^-1 glucose, and 9 g l^-1 arabinose) was investigated to evaluate the glucose and arabinose influence on xylose-to-xylitol bioconversion by Candida guilliermondii. The results revealed that glucose reduced the xylose consumption rate by 30%. Arabinose did not affect the xylose consumption but its utilization by the yeast was fully repressed by both glucose and xylose sugars. Arabinose was only consumed when it was used as a single carbon source. Xylitol production was best when glucose was not present in the fermentation medium. On the other hand, the arabinose favored the xylitol yield (which attained 0.74 g g^-1 xylose consumed) and it did not interfere with xylitol volumetric productivity (Q _P=0.85 g g^-1), the value of which was similar to that obtained with xylose alone.