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1
van Bastelaere, P., W. Vangrysperre, and H. Kersters-Hilderson. "Kinetic studies of Mg2+-, Co2+- and Mn2+-activated d-xylose isomerases." Biochemical Journal 278, no. 1 (August 15, 1991): 285–92. http://dx.doi.org/10.1042/bj2780285.
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The kinetic parameters for the interconverting substrates D-xylose in equilibrium D-xylulose and D-glucose in equilibrium D-fructose were determined for several D-xylose isomerases, with Mg2+, Co2+ and Mn2+ as metal ion activators. The Km, kcat. and kcat./Km values are tabulated for the anomeric mixtures (observed parameters) as well as for the respective reactive species, i.e. the alpha-pyranose anomers of D-xylose and D-glucose and the alpha-furanose forms of D-xylulose and D-fructose (real parameters). The real Km values and catalytic efficiencies are more favourable for the ketose sugars (reverse reaction) than for the aldose sugars (forward reaction). Comparisons of the kinetic parameters further support the existence of two distinct groups of D-xylose isomerases. Inhibition constants for the cyclic substrate analogues 5-thio-alpha-D-xylopyranose and alpha-D-xylopyranosyl fluoride and for the acyclic substrate analogue xylitol and its dehydrated form 1,5-anhydroxylitol were determined and are discussed.
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Wang, Zi-Han, Jing-Yan Tan, Yu-Tong Zhang, Nan-Qi Ren, and Lei Zhao. "Evaluating Bio-Hydrogen Production Potential and Energy Conversion Efficiency from Glucose and Xylose under Diverse Concentrations." Fermentation 8, no. 12 (December 14, 2022): 739. http://dx.doi.org/10.3390/fermentation8120739.
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Lignocellulose bioconversion to hydrogen has been proposed as a promising solution to augment the fossil fuel dominated energy market. However, little is known about the effects of the substrate concentration supplied on hydrogen production. Herein, the hydrogen producing bacteria Thermoanaerobacter thermosaccharolyticum W16 feeding with respective glucose, xylose, and glucose and xylose mixture (glucose–xylose) at different concentrations was evaluated, to study whether substrate concentration could impact the lignocellulose bioconversion to hydrogen and the associated kinetics. An average bio-hydrogen yield of 1.40 ± 0.23 mol H2·mol−1 substrate was obtained at an average substrate concentration of 60.89 mM. The maximum bio-hydrogen production rate of 0.25 and 0.24 mol H2·mol−1 substrate h−1 was achieved at a substrate concentration of 27.75 mM glucose and 30.82 mM glucose–xylose, respectively, while the value reached the high point of 0.08 mol H2·mol−1 xylose·h−1 at 66.61 mM xylose. Upon further energy conversion efficiency (ESE) analysis, a substrate of 10 g·L−1 (amounting to 55.51 mM glucose, 66.61 mM xylose or 60.55 mM glucose–xylose) provided the maximum ESE of 15.3 ± 0.3%, which was 15.3% higher than that obtained at a substrate concentration of 5 g·L−1 (amounting to 27.75 mM glucose, 33.30 mM xylose or 30.28 mM glucose–xylose). The findings could be helpful to provide effective support for the future development of efficient and sustainable lignocellulosic bio-hydrogen production.
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Hermansyah, Hermansyah, Fachrijal Fachrijal, Miksusanti Miksusanti, Fatma Fatma, Getari Kasmiarti, and Almunadi T. Panagan. "Xylose and Arabinose Fermentation to Produce Ethanol by Isolated Yeasts from Durian (Durio zibethinus L.) Fruit." Molekul 14, no. 2 (November 30, 2019): 133. http://dx.doi.org/10.20884/1.jm.2019.14.2.562.
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Xylose and arabinose are pentosesugars that present in hemicellulose, part of lignocellulose biomass.These pentose sugars can be fermented by yeast into ethanol.The aim of this research was to utilize yeast isolated from durian fruit (DuriozibethinusL.) in fermentation of xylose and arabinose to produce bioethanol.Phenotypic test of isolates was conducted by growingthe isolates in various agar media, i.e.YPD (Yeast Peptone Dextrose), YPA (Yeast Peptone Arabinose), and YPX (Yeast Peptone Xylose) containing dextrose, arabinose, xylose, respectively, assole carbon source to see cell growth. The yeast isolates were further identified using API AOC 20C kit method. Yeast isolates were applied for fermentation of glucose, arabinose, and xylosein incubated cultures. Ethanol production in the fermentation was analyzed bygaschromatography. Yeast isolates were identified as Kodamaea ohmeri, Candida famata, Candida guilliermondii, and Crytococcuc laurentii. Based on gas chromatography data, it was found that ethanol produced in the fermentation for three days, the highest ethanol content on xylose substrate was fermented by Candida famata-Awhich is0.021% (v/v) ethanol resulted from initial concentration of 5% xylose (w/v). While on arabinose substrate, the highest ethanol content was fermented by Crytococcus laurentii-Bwhich is 0.0034% (v/v) ethanol resulted from initial concentration of 5% arabinose (w/v).
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Zepeda, S., O. Monasterio, and T. Ureta. "NADP+-dependent d-xylose dehydrogenase from pig liver. Purification and properties." Biochemical Journal 266, no. 3 (March 15, 1990): 637–44. http://dx.doi.org/10.1042/bj2660637.
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An NADP(+)-dependent D-xylose dehydrogenase from pig liver cytosol was purified about 2000-fold to apparent homogeneity with a yield of 15% and specific activity of 6 units/mg of protein. An Mr value of 62,000 was obtained by gel filtration. PAGE in the presence of SDS gave an Mr value of 32,000, suggesting that the native enzyme is a dimer of similar or identical subunits. D-Xylose, D-ribose, L-arabinose, 2-deoxy-D-glucose, D-glucose and D-mannose were substrates in the presence of NADP+ but the specificity constant (ratio kcat./Km(app.)) is, by far, much higher for D-xylose than for the other sugars. The enzyme is specific for NADP+; NAD+ is not reduced in the presence of D-xylose or other sugars. Initial-velocity studies for the forward direction with xylose or NADP+ concentrations varied at fixed concentrations of the nucleotide or the sugar respectively revealed a pattern of parallel lines in double-reciprocal plots. Km values for D-xylose and NADP+ were 8.8 mM and 0.99 mM respectively. Dead-end inhibition studies to confirm a ping-pong mechanism showed that NAD+ acted as an uncompetitive inhibitor versus NADP+ (Ki 5.8 mM) and as a competitive inhibitor versus xylose. D-Lyxose was a competitive inhibitor versus xylose and uncompetitive versus NADP+. These results fit better to a sequential compulsory ordered mechanism with NADP+ as the first substrate, but a ping-pong mechanism with xylose as the first substrate has not been ruled out. The presence of D-xylose dehydrogenase suggests that in mammalian liver D-xylose is utilized by a pathway other than the pentose phosphate pathway.
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Muñoz-Páez, Karla María, and Germán Buitrón. "Role of xylose from acidic hydrolysates of agave bagasse during biohydrogen production." Water Science and Technology 84, no. 3 (June 24, 2021): 656–66. http://dx.doi.org/10.2166/wst.2021.242.
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Abstract This study compares the H2 production from glucose, xylose, and acidic hydrolysates of Agave tequilana bagasse as substrates. The fermentation was performed in a granular sludge reactor operated in two phases: (1) model substrates (glucose and xylose) and (2) acidic hydrolysates at 35 °C, pH 4.5 and a hydraulic retention time of 5.5 h with glucose (10 g L−1) and xylose (12 g L−1). A sequencing batch reactor was used to acclimate the biomass between the glucose and xylose continuous fermentation (with a mixture of xylose-glucose) and acidic hydrolysates. During the discontinuous acclimating step, the xylose/glucose ratio increment negatively affected the H2 productivity. Although the continuous H2 production with xylose was negligible, the co-fermentation with glucose (88–12%) allowed H2 productivity of 2,889 ± 502 mL H2 L−1d−1. An acidic hydrolysate concentration of 3.3 gcarbohydrate L−1 showed a three-fold higher H2 productivity than with a concentration of 10 g L−1. The results indicated that xylose, as the only substrate, was challenging to metabolize by the inoculum, and its mixture with glucose improved the H2 productivity. Therefore, the low H2 productivity with hydrolysates could be related to the presence of xylose.
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Kratzer, Regina, Stefan Leitgeb, David K. Wilson, and Bernd Nidetzky. "Probing the substrate binding site of Candida tenuis xylose reductase (AKR2B5) with site-directed mutagenesis." Biochemical Journal 393, no. 1 (December 12, 2005): 51–58. http://dx.doi.org/10.1042/bj20050831.
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Little is known about how substrates bind to CtXR (Candida tenuis xylose reductase; AKR2B5) and other members of the AKR (aldo–keto reductase) protein superfamily. Modelling of xylose into the active site of CtXR suggested that Trp23, Asp50 and Asn309 are the main components of pentose-specific substrate-binding recognition. Kinetic consequences of site-directed substitutions of these residues are reported. The mutants W23F and W23Y catalysed NADH-dependent reduction of xylose with only 4 and 1% of the wild-type efficiency (kcat/Km) respectively, but improved the wild-type selectivity for utilization of ketones, relative to xylose, by factors of 156 and 471 respectively. Comparison of multiple sequence alignment with reported specificities of AKR members emphasizes a conserved role of Trp23 in determining aldehyde-versus-ketone substrate selectivity. D50A showed 31 and 18% of the wild-type catalytic-centre activities for xylose reduction and xylitol oxidation respectively, consistent with a decrease in the rates of the chemical steps caused by the mutation, but no change in the apparent substrate binding constants and the pattern of substrate specificities. The 30-fold preference of the wild-type for D-galactose compared with 2-deoxy-D-galactose was lost completely in N309A and N309D mutants. Comparison of the 2.4 Å (1 Å=0.1 nm) X-ray crystal structure of mutant N309D bound to NAD+ with the previous structure of the wild-type holoenzyme reveals no major structural perturbations. The results suggest that replacement of Asn309 with alanine or aspartic acid disrupts the function of the original side chain in donating a hydrogen atom for bonding with the substrate C-2(R) hydroxy group, thus causing a loss of transition-state stabilization energy of 8–9 kJ/mol.
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Brink, Daniel P., Celina Borgström, Viktor C. Persson, Karen Ofuji Osiro, and Marie F. Gorwa-Grauslund. "D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers." International Journal of Molecular Sciences 22, no. 22 (November 17, 2021): 12410. http://dx.doi.org/10.3390/ijms222212410.
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Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker’s yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.
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Furlan, Sandra A., and Heizir F. de Castro. "Xylitol production by Candida parapsilosis under fed-batch culture." Brazilian Archives of Biology and Technology 44, no. 2 (June 2001): 125–28. http://dx.doi.org/10.1590/s1516-89132001000200003.
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Xylitol production by Candida parapsilosis was investigated under fed-batch cultivation, using single (xylose) or mixed (xylose and glucose) sugars as substrates. The presence of glucose in the medium induced the production of ethanol as secondary metabolite and improved specific rates of growth, xylitol formation and substrate consumption. Fractionated supply of the feed medium at constant sugar concentration did not promote any increase on the productivity compared to the single batch cultivation.
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Kuenz, Anja, Malee Jäger, Harri Niemi, Mari Kallioinen, Mika Mänttäri, and Ulf Prüße. "Conversion of Xylose from Birch Hemicellulose Hydrolysate to 2,3-Butanediol with Bacillus vallismortis." Fermentation 6, no. 3 (September 2, 2020): 86. http://dx.doi.org/10.3390/fermentation6030086.
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Biotechnologically produced 2,3-butanediol (2,3-BDO) is a potential starting material for industrial bulk chemicals, such as butadiene or methyl ethyl ketone, which are currently produced from fossil feedstocks. So far, the highest 2,3-BDO concentrations have been obtained with risk class 2 microorganisms and pure glucose as substrate. However, as glucose stays in competition to food and feed industries, a lot of effort has been done in the last years finding efficient alternative substrates. Thereby xylose from hydrolysed wood hemicelluloses is a promising substrate for the production of 2,3-BDO. The risk class 1 microorganism Bacillus vallismortis strain was identified as a very promising 2,3-BDO producer. The strain is able to utilize xylose almost in the same manner as glucose. B. vallismortis is less prone to common inhibiting compounds in lignocellulosic extracts/hydrolysates. When using a concentrated hemicellulose fraction from birch wood hydrolysate, which was produced with ultrafiltration and after which the acetate concentration was reduced, a yield of 0.43 g g−1 was achieved and the xylose consumption and the 2,3-BDO production is basically the same as using pure xylose.
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Milessi-Esteves, Thais, Felipe Corradini, Willian Kopp, Teresa Zangirolami, Paulo Tardioli, Roberto Giordano, and Raquel Giordano. "An Innovative Biocatalyst for Continuous 2G Ethanol Production from Xylo-Oligomers by Saccharomyces cerevisiae through Simultaneous Hydrolysis, Isomerization, and Fermentation (SHIF)." Catalysts 9, no. 3 (March 1, 2019): 225. http://dx.doi.org/10.3390/catal9030225.
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Many approaches have been considered aimed at ethanol production from the hemicellulosic fraction of biomass. However, the industrial implementation of this process has been hindered by some bottlenecks, one of the most important being the ease of contamination of the bioreactor by bacteria that metabolize xylose. This work focuses on overcoming this problem through the fermentation of xylulose (the xylose isomer) by native Saccharomyces cerevisiae using xylo-oligomers as substrate. A new concept of biocatalyst is proposed, containing xylanases and xylose isomerase (XI) covalently immobilized on chitosan, and co-encapsulated with industrial baker’s yeast in Ca-alginate gel spherical particles. Xylo-oligomers are hydrolyzed, xylose is isomerized, and finally xylulose is fermented to ethanol, all taking place simultaneously, in a process called simultaneous hydrolysis, isomerization, and fermentation (SHIF). Among several tested xylanases, Multifect CX XL A03139 was selected to compose the biocatalyst bead. Influences of pH, Ca2+, and Mg2+ concentrations on the isomerization step were assessed. Experiments of SHIF using birchwood xylan resulted in an ethanol yield of 0.39 g/g, (76% of the theoretical), selectivity of 3.12 gethanol/gxylitol, and ethanol productivity of 0.26 g/L/h.
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Barthe, Manon, Josué Tchouanti, Pedro Henrique Gomes, Carine Bideaux, Delphine Lestrade, Carl Graham, Jean-Philippe Steyer, et al. "Availability of the Molecular Switch XylR Controls Phenotypic Heterogeneity and Lag Duration during Escherichia coli Adaptation from Glucose to Xylose." mBio 11, no. 6 (December 22, 2020): e02938-20. http://dx.doi.org/10.1128/mbio.02938-20.
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ABSTRACTThe glucose-xylose metabolic transition is of growing interest as a model to explore cellular adaption since these molecules are the main substrates resulting from the deconstruction of lignocellulosic biomass. Here, we investigated the role of the XylR transcription factor in the length of the lag phases when the bacterium Escherichia coli needs to adapt from glucose- to xylose-based growth. First, a variety of lag times were observed when different strains of E. coli were switched from glucose to xylose. These lag times were shown to be controlled by XylR availability in the cells with no further effect on the growth rate on xylose. XylR titration provoked long lag times demonstrated to result from phenotypic heterogeneity during the switch from glucose to xylose, with a subpopulation unable to resume exponential growth, whereas the other subpopulation grew exponentially on xylose. A stochastic model was then constructed based on the assumption that XylR availability influences the probability of individual cells to switch to xylose growth. The model was used to understand how XylR behaves as a molecular switch determining the bistability set-up. This work shows that the length of lag phases in E. coli is controllable and reinforces the role of stochastic mechanism in cellular adaptation, paving the way for new strategies for the better use of sustainable carbon sources in bioeconomy.IMPORTANCE For decades, it was thought that the lags observed when microorganisms switch from one substrate to another are inherent to the time required to adapt the molecular machinery to the new substrate. Here, the lag duration was found to be the time necessary for a subpopulation of adapted cells to emerge and become the main population. By identifying the molecular mechanism controlling the subpopulation emergence, we were able to extend or reduce the duration of the lags. This work is of special importance since it demonstrates the unexpected complexity of monoclonal populations during growth on mixed substrates and provides novel mechanistic insights with regard to bacterial cellular adaptation.
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Xu, Wei, Rong Shao, Yan Li, Ming Yan, and Ping Kai Ouyang. "Study on the Substrate Specificity of Xylose Isomerase N91D Mutant from Thermus thermophilus HB8 by Molecular Simulation." Advanced Materials Research 236-238 (May 2011): 968–73. http://dx.doi.org/10.4028/www.scientific.net/amr.236-238.968.
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Compared withThermus thermophilusHB8 xylose isomerase(TthXI), the increase of the substrate specificity on D-xylose of its N91D mutant (TthXI-N91D) was observed in the previous study. In order to clarify the structural mechanism of TthXI-N91D, the complex model of TthXI with D-xylose was constructed by molecular docking method. The TthXI-N91D homology model was built by WATH IF5.0 based on the above complex. The results indicate that the distance between the conserved residue H53 NE2 and D-xylose O5 has decreased in 0.083 nm in the TthXI-N91D active site. The short distance is propitious to transfer the hydrogen atom during the open ring process of substrate. At the same time, the distance between the conserved residue T89 OG1, involving in combining glucose, and D-xylose C5 has reduced 0.133 nm. The shrunken space has an unfavorable effect on accommodating the larger glucose than xylose, and lead to the enhanced specificity for D-xylose.The above phenomenon maybe the main reason for explaining that TthXI-N91D is easy to combine D-xylose showing enhanced specificity. The results paly an important role in understanding the catalytic mechanism of xylose isomerase and provides the base for its molecular design.
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Meijnen, Jean-Paul, Johannes H. de Winde, and Harald J. Ruijssenaars. "Engineering Pseudomonas putida S12 for Efficient Utilization of d-Xylose and l-Arabinose." Applied and Environmental Microbiology 74, no. 16 (June 27, 2008): 5031–37. http://dx.doi.org/10.1128/aem.00924-08.
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ABSTRACT The solvent-tolerant bacterium Pseudomonas putida S12 was engineered to utilize xylose as a substrate by expressing xylose isomerase (XylA) and xylulokinase (XylB) from Escherichia coli. The initial yield on xylose was low (9% [g CDW g substrate−1], where CDW is cell dry weight), and the growth rate was poor (0.01 h−1). The main cause of the low yield was the oxidation of xylose into the dead-end product xylonate by endogenous glucose dehydrogenase (Gcd). Subjecting the XylAB-expressing P. putida S12 to laboratory evolution yielded a strain that efficiently utilized xylose (yield, 52% [g CDW g xylose−1]) at a considerably improved growth rate (0.35 h−1). The high yield could be attributed in part to Gcd inactivity, whereas the improved growth rate may be connected to alterations in the primary metabolism. Surprisingly, without any further engineering, the evolved d-xylose-utilizing strain metabolized l-arabinose as efficiently as d-xylose. Furthermore, despite the loss of Gcd activity, the ability to utilize glucose was not affected. Thus, a P. putida S12-derived strain was obtained that efficiently utilizes the three main sugars present in lignocellulosic hydrolysate: glucose, xylose, and arabinose. This strain will form the basis for a platform host for the efficient production of biochemicals from renewable feedstock.
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Ramsay, Juliana A., Marie-Claire Aly Hassan, and Bruce A. Ramsay. "Hemicellulose as a potential substrate for production of poly(β-hydroxyalkanoates)." Canadian Journal of Microbiology 41, no. 13 (December 15, 1995): 262–66. http://dx.doi.org/10.1139/m95-195.
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Pseudomonas cepacia was evaluated for its ability to utilize xylose, a major hemicellulosic sugar of hardwoods, for the production of the biodegradable, thermoplastic poly(β-hydroxybutyrate) (PHB). This culture produced 2.6 g∙L−1 of biomass containing 60% (w/w) PHB when grown in shake flasks on an ammonium-limited, mineral salts medium containing 10 g∙L−1 of xylose. Batch fermentation data showed that growth and PHB production kinetics on xylose were similar to previously published results for the same microorganism on fructose. On xylose, the maximum specific growth rate, the maximum specific PHB production rate (based on total biomass minus PHB biomass), the overall yield of biomass produced from substrate consumed, the yield of PHB produced from substrate consumed (YPHB/S), and the percentage of PHB were 0.22 h−1, 0.072 g∙g−1∙h−1, 0.29 g∙g−1, 0.11 g∙g−1 and 45% (w/w), respectively. A high maintenance energy (0.119 g of xylose∙g of biomass−1∙h−1) is probably responsible for the low overall yield. However, the product yield, YPHB/S, was still the highest reported for any microorganism grown on pentosic sugars. Using the YPHB/S of 0.11 g∙g−1, it was estimated that the substrate cost (in terms of hydrolyzed hemicellulose) for PHB production would be similar to that of cane molasses and half that of bulk glucose.Key words: poly(β-hydroxybutyrate), PHB, hemicellulose, xylose, Pseudomonas cepacia.
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Xiong, Xiaochao, Xi Wang, and Shulin Chen. "Engineering of a Xylose Metabolic Pathway in Rhodococcus Strains." Applied and Environmental Microbiology 78, no. 16 (May 25, 2012): 5483–91. http://dx.doi.org/10.1128/aem.08022-11.
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ABSTRACTThe two metabolically versatile actinobacteriaRhodococcus opacusPD630 andR. jostiiRHA1 can efficiently convert diverse organic substrates into neutral lipids mainly consisting of triacylglycerol (TAG), the precursor of energy-rich hydrocarbon. Neither, however, is able to utilize xylose, the important component present in lignocellulosic biomass, as the carbon source for growth and lipid accumulation. In order to broaden their substrate utilization range, the metabolic pathway ofd-xylose utilization was introduced into these two strains. This was accomplished by heterogenous expression of two well-selected genes,xylA, encoding xylose isomerase, andxylB, encoding xylulokinase fromStreptomyces lividansTK23, under the control of thetacpromoter with anEscherichia coli-Rhodococcusshuttle vector. The recombinantR. jostiiRHA1 bearingxylAcould grow on xylose as the sole carbon source, and additional expression ofxylBfurther improved the biomass yield. The recombinant could consume both glucose and xylose in the sugar mixture, although xylose metabolism was still affected by the presence of glucose. The xylose metabolic pathway was also introduced into the high-lipid-producing strainR. opacusPD630 by expression ofxylAandxylB. Under nitrogen-limited conditions, the fatty acid composition was determined, and lipid produced from xylose by recombinants ofR. jostiiRHA1 andR. opacusPD630 carryingxylAandxylBrepresented up to 52.5% and 68.3% of the cell dry weight (CDW), respectively. This work demonstrates that it is feasible to produce lipid from the sugars, including xylose, derived from renewable feedstock by genetic modification of rhodococcus strains.
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Karimaki, J., T. Parkkinen, H. Santa, O. Pastinen, M. Leisola, J. Rouvinen, and O. Turunen. "Engineering the substrate specificity of xylose isomerase." Protein Engineering Design and Selection 17, no. 12 (February 16, 2005): 861–69. http://dx.doi.org/10.1093/protein/gzh099.
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Kanoh, Yoshitaka, Seiichiroh Uehara, Hideyuki Iwata, Kazunari Yoneda, Toshihisa Ohshima, and Haruhiko Sakuraba. "Structural insight into glucose dehydrogenase from the thermoacidophilic archaeonThermoplasma volcanium." Acta Crystallographica Section D Biological Crystallography 70, no. 5 (April 29, 2014): 1271–80. http://dx.doi.org/10.1107/s1399004714002363.
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Glucose dehydrogenase from the thermoacidophilic archaeonThermoplasma volcanium(tvGlcDH) is highly active towards D-glucose and D-galactose, but does not utilize aldopentoses such as D-xylose as substrates. In the present study, the crystal structures of substrate/cofactor-free tvGlcDH and of a tvGlcDH T277F mutant in a binary complex with NADP and in a ternary complex with D-glucose and nicotinic acid adenine dinucleotide phosphate, an NADP analogue, were determined at resolutions of 2.6, 2.25 and 2.33 Å, respectively. The overall structure of each monomer showed notable similarity to that of the enzyme fromSulfolobus solfataricus(ssGlcDH-1), which accepts a broad range of C5 and C6 sugars as substrates. However, the amino-acid residues of tvGlcDH involved in substrate binding markedly differed from those of ssGlcDH-1. Structural comparison revealed that a decreased number of interactions between the C3-hydroxyl group of the sugar and the enzyme are likely to be responsible for the lack of reactivity of tvGlcDH towards D-xylose.
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Taguchi, Fumiaki, Naoki Mizukami, Katsushige Hasegawa, and Tatsuo Saito-Taki. "Microbial conversion of arabinose and xylose to hydrogen by a newly isolated Clostridium sp. No. 2." Canadian Journal of Microbiology 40, no. 3 (March 1, 1994): 228–33. http://dx.doi.org/10.1139/m94-037.
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For 24 h at pH 6.0 and 36 °C, Clostridium sp. No. 2, isolated from termites, converted arabinose and xylose to hydrogen with yields of 14.55 and 13.73 mmol/g of substrate consumed, respectively. These yields were greater than the maximum value of 11.07 mmol/g of glucose consumed in 1 L of batch culture with 10 g of each substrate. The organism produced hydrogen from 45 g of glucose and xylose in 1 L of culture with a total accumulation of 380.6 mmol from glucose and 479.0 mmol from xylose, at a conversion rate of 270.9 mmol/g of dry cells from glucose and 405.9 mmol/g of dry cells from xylose. Hydrogen was produced at a maximum evolution rate of 27.2 mmol/h after 8 h of incubation with glucose and of 28.6 mmol/h after 6 h of incubation with xylose.Key words: hydrogen production, xylose, arabinose, Clostridium sp. No. 2.
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Beck, Ashley E. "Metabolic Efficiency of Sugar Co-Metabolism and Phenol Degradation in Alicyclobacillus acidocaldarius for Improved Lignocellulose Processing." Processes 8, no. 5 (April 27, 2020): 502. http://dx.doi.org/10.3390/pr8050502.
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Substrate availability plays a key role in dictating metabolic strategies. Most microorganisms consume carbon/energy sources in a sequential, preferential order. The presented study investigates metabolic strategies of Alicyclobacillus acidocaldarius, a thermoacidophilic bacterium that has been shown to co-utilize glucose and xylose, as well as degrade phenolic compounds. An existing metabolic model was expanded to include phenol degradation and was analyzed with both metabolic pathway and constraint-based analysis methods. Elementary flux mode analysis was used in conjunction with resource allocation theory to investigate ecologically optimal metabolic pathways for different carbon substrate combinations. Additionally, a dynamic version of flux balance analysis was used to generate time-resolved simulations of growth on phenol and xylose. Results showed that availability of xylose along with glucose did not predict enhanced growth efficiency beyond that of glucose alone, but did predict some differences in pathway utilization and byproduct profiles. In contrast, addition of phenol as a co-substrate with xylose predicted lower growth efficiency. Dynamic simulations predicted co-consumption of xylose and phenol in a similar pattern as previously reported experiments. Altogether, this work serves as a case study for combining both elementary flux mode and flux balance analyses to probe unique metabolic features, and also demonstrates the versatility of A. acidocaldarius for lignocellulosic biomass processing applications.
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Vangrysperre, W., M. Callens, H. Kersters-Hilderson, and C. K. De Bruyne. "Evidence for an essential histidine residue in d-xylose isomerases." Biochemical Journal 250, no. 1 (February 15, 1988): 153–60. http://dx.doi.org/10.1042/bj2500153.
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Diethyl pyrocarbonate inactivated D-xylose isomerases from Streptomyces violaceoruber, Streptomyces sp., Lactobacillus xylosus and Lactobacillus brevis with second-order rate constants of 422, 417, 99 and 92 M-1.min-1 respectively (at pH 6.0 and 25 degrees C). Activity was completely restored by the addition of neutral hydroxylamine, and total protection was afforded by the substrate analogue xylitol in the presence of either Mg2+ or Mn2+ according to the genus studied. The difference spectra of the modified enzymes revealed an absorption maximum at 237-242 nm, characteristic for N-ethoxycarbonylhistidine. In addition, the spectrum of ethoxycarbonylated D-xylose isomerase from L. xylosus showed absorption minima at both 280 and 230 nm, indicative for modification of tyrosine residues. Nitration with tetranitromethane followed by diethyl pyrocarbonate treatment eliminated the possibility that modification of tyrosine residues was responsible for inactivation, and resulted in modification of one non-essential tyrosine residue and six histidine residues. Inactivation of the other D-xylose isomerases with diethyl pyrocarbonate required the modification of one (L. brevis), two (Streptomyces sp.) and four (S. violaceoruber) histidine residues per monomer. Spectral analysis and maintenance of total enzyme activities further indicated that either xylitol Mg2+ (streptomycetes) or xylitol Mn2+ (lactobacilli) prevented the modification of one crucial histidine residue. The overall results thus provide evidence that a single active-site histidine residue is involved in the catalytic reaction mechanism of D-xylose isomerases.
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Bazarnova, Yuliya, Olga Bolotnikova, Natalia Michailova, and Jing Pu. "Optimization of parameters of alcohol fermentation of xylose-containing inedible substrates using the yeast Pachysolen Tannophilus." MATEC Web of Conferences 245 (2018): 18006. http://dx.doi.org/10.1051/matecconf/201824518006.
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This work presents economical and ecological advances of microbiological utilization of inedible sources of plant biomass, procedure which is associated with bioethanol obtaining. We study influence of forced aeration and initial concentration of biomass of xylose-assimilating yeast P. tannophilus Y-1532/B2 on ethanol output from various xylose-containing substrates during periodical fermentation. The highest ethanol output is observed for OTR values equal to 5.0-8.0 mMole/l×h and yeast seeding density equal to 0.25 g a.d.s./g of substrate sugars. We show the possibility for intensification of ethanol obtaining technology from xylose-containing substrates. This was made using traditional biotechnological approaches of fermentation productions by optimization parameters of forced aeration of the fermentation medium and density of P. tannophilus biomass seeding. The obtained results might be used as initial parameters for calculation of laboratory regulations of complex microbiological utilization of secondary inedible sources of plant biomass of various origin and content. Industrial implementation of this technology will allow one to increase the economical coefficient of ethanol production from secondary inedible sources of plant biomass for 59.7-96.8% due to fermentation of D-xylose.
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Simāo, R. C. G., C. G. M. Souza, and R. M. Peralta. "The use of methyl β-D-xyloside as a substrate for xylanase production by Aspergillus tamarii." Canadian Journal of Microbiology 43, no. 1 (January 1, 1997): 56–60. http://dx.doi.org/10.1139/m97-008.
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Aspergillus tamarii was able to produce biomass in media containing β-methyl D-xyloside, a synthetic analogue of xylobiose, as the only carbon source. β-Methyl D-xyloside was a more effective inducer than xylan at the same concentration for xylanase and β-xylosidase activities. The delayed consumption of β-methyl D-xyloside by A. tamarii cells suggests the requirement of a specific inducible transport system and a slow metabolic process. The synthesis of this transport system was probably repressed by the presence of easily metabolizable sugars. β-Methyl D-xyloside was hydrolyzed to xylose by an intracellular β-xylosidase.Key words: xyanolytic microorganisms, xylanase, β-xylosidase, Aspergillus tamarii.
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Meng, M., C. Lee, M. Bagdasarian, and J. G. Zeikus. "Switching substrate preference of thermophilic xylose isomerase from D-xylose to D-glucose by redesigning the substrate binding pocket." Proceedings of the National Academy of Sciences 88, no. 9 (May 1, 1991): 4015–19. http://dx.doi.org/10.1073/pnas.88.9.4015.
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Hasona, Adnan, Youngnyun Kim, F. G. Healy, L. O. Ingram, and K. T. Shanmugam. "Pyruvate Formate Lyase and Acetate Kinase Are Essential for Anaerobic Growth of Escherichia coli on Xylose." Journal of Bacteriology 186, no. 22 (November 15, 2004): 7593–600. http://dx.doi.org/10.1128/jb.186.22.7593-7600.2004.
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ABSTRACT During anaerobic growth of bacteria, organic intermediates of metabolism, such as pyruvate or its derivatives, serve as electron acceptors to maintain the overall redox balance. Under these conditions, the ATP needed for cell growth is derived from substrate-level phosphorylation. In Escherichia coli, conversion of glucose to pyruvate yields 2 net ATPs, while metabolism of a pentose, such as xylose, to pyruvate only yields 0.67 net ATP per xylose due to the need for one (each) ATP for xylose transport and xylulose phosphorylation. During fermentative growth, E. coli produces equimolar amounts of acetate and ethanol from two pyruvates, and these reactions generate one additional ATP from two pyruvates (one hexose equivalent) while still maintaining the overall redox balance. Conversion of xylose to acetate and ethanol increases the net ATP yield from 0.67 to 1.5 per xylose. An E. coli pfl mutant lacking pyruvate formate lyase cannot convert pyruvate to acetyl coenzyme A, the required precursor for acetate and ethanol production, and could not produce this additional ATP. E. coli pfl mutants failed to grow under anaerobic conditions in xylose minimal medium without any negative effect on their survival or aerobic growth. An ackA mutant, lacking the ability to generate ATP from acetyl phosphate, also failed to grow in xylose minimal medium under anaerobic conditions, confirming the need for the ATP produced by acetate kinase for anaerobic growth on xylose. Since arabinose transport by AraE, the low-affinity, high-capacity, arabinose/H+ symport, conserves the ATP expended in pentose transport by the ABC transporter, both pfl and ackA mutants grew anaerobically with arabinose. AraE-based xylose transport, achieved after constitutively expressing araE, also supported the growth of the pfl mutant in xylose minimal medium. These results suggest that a net ATP yield of 0.67 per pentose is only enough to provide for maintenance energy but not enough to support growth of E. coli in minimal medium. Thus, pyruvate formate lyase and acetate kinase are essential for anaerobic growth of E. coli on xylose due to energetic constraints.
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López-Contreras, Ana M., Krisztina Gabor, Aernout A. Martens, Bernadet A. M. Renckens, Pieternel A. M. Claassen, John van der Oost, and Willem M. de Vos. "Substrate-Induced Production and Secretion of Cellulases by Clostridium acetobutylicum." Applied and Environmental Microbiology 70, no. 9 (September 2004): 5238–43. http://dx.doi.org/10.1128/aem.70.9.5238-5243.2004.
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ABSTRACT Clostridium acetobutylicum ATCC 824 is a solventogenic bacterium that grows heterotrophically on a variety of carbohydrates, including glucose, cellobiose, xylose, and lichenan, a linear polymer of β-1,3- and β-1,4-linked β-d-glucose units. C. acetobutylicum does not degrade cellulose, although its genome sequence contains several cellulase-encoding genes and a complete cellulosome cluster of cellulosome genes. In the present study, we demonstrate that a low but significant level of induction of cellulase activity occurs during growth on xylose or lichenan. The celF gene, located in the cellulosome-like gene cluster and coding for a unique cellulase that belongs to glycoside hydrolase family 48, was cloned in Escherichia coli, and antibodies were raised against the overproduced CelF protein. A Western blot analysis suggested a possible catabolite repression by glucose or cellobiose and an up-regulation by lichenan or xylose of the extracellular production of CelF by C. acetobutylicum. Possible reasons for the apparent inability of C. acetobutylicum to degrade cellulose are discussed.
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Alencar, Bárbara Ribeiro Alves, Renan Anderson Alves de Freitas, Victor Emanuel Petrício Guimarães, Rayssa Karla Silva, Carolina Elsztein, Suzyanne Porfírio da Silva, Emmanuel Damilano Dutra, Marcos Antonio de Morais Junior, and Rafael Barros de Souza. "Meyerozyma caribbica Isolated from Vinasse-Irrigated Sugarcane Plantation Soil: A Promising Yeast for Ethanol and Xylitol Production in Biorefineries." Journal of Fungi 9, no. 8 (July 26, 2023): 789. http://dx.doi.org/10.3390/jof9080789.
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The production of fuels and other industrial products from renewable sources has intensified the search for new substrates or for the expansion of the use of substrates already in use, as well as the search for microorganisms with different metabolic capacities. In the present work, we isolated and tested a yeast from the soil of sugarcane irrigated with vinasse, that is, with high mineral content and acidic pH. The strain of Meyerozyma caribbica URM 8365 was able to ferment glucose, but the use of xylose occurred when some oxygenation was provided. However, some fermentation of xylose to ethanol in oxygen limitation also occurs if glucose was present. This strain was able to produce ethanol from molasses substrate with 76% efficiency, showing its tolerance to possible inhibitors. High ethanol production efficiencies were also observed in acidic hydrolysates of each bagasse, sorghum, and cactus pear biomass. Mixtures of these substrates were tested and the best composition was found for the use of excess plant biomass in supplementation of primary substrates. It was also possible to verify the production of xylitol from xylose when the acetic acid concentration is reduced. Finally, the proposed metabolic model allowed calculating how much of the xylose carbon can be directed to the production of ethanol and/or xylitol in the presence of glucose. With this, it is possible to design an industrial plant that combines the production of ethanol and/or xylitol using combinations of primary substrates with hydrolysates of their biomass.
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Chen, Xiu Ju, Xiao Qin Liu, Fang Lian Xu, and Xin Peng Bai. "Degradation Kinetics of Xylose and Arabinose in Subcritical Water in Unitary and Binary System." Advanced Materials Research 450-451 (January 2012): 710–14. http://dx.doi.org/10.4028/www.scientific.net/amr.450-451.710.
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The degradation process of xylose and arabinose in a binary compositions system at temperatures from 210 to 250°C was studied to clarify the reaction mechanism and to examine the effect of the degradation products of a substrate on the disappearance of another substrate. The activation energy and frequency factor for the degradation of each substrate were estimated from the temperature dependence of the rate constant. The molar yield of a pentose to furfural was ca. 0.3 at any temperature, Acidic compounds were also formed from the pentoses in proportion to the amount of consumed substrates. The formation of acidic compounds resulted in a rapid decrease in pH
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Hurlbert, Jason C., and James F. Preston. "Functional Characterization of a Novel Xylanase from a Corn Strain of Erwinia chrysanthemi." Journal of Bacteriology 183, no. 6 (March 15, 2001): 2093–100. http://dx.doi.org/10.1128/jb.183.6.2093-2100.2001.
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ABSTRACT A β-1,4-xylan hydrolase (xylanase A) produced by Erwinia chrysanthemi D1 isolated from corn was analyzed with respect to its secondary structure and enzymatic function. The pH and temperature optima for the enzyme were found to be pH 6.0 and 35°C, with a secondary structure under those conditions that consists of approximately 10 to 15% α-helices. The enzyme was still active at temperatures higher than 40°C and at pHs of up to 9.0. The loss of enzymatic activity at temperatures above 45°C was accompanied by significant loss of secondary structure. The enzyme was most active on xylan substrates with low ratios of xylose to 4-O-methyl-d-glucuronic acid and appears to require two 4-O-methyl-d-glucuronic acid residues for substrate recognition and/or cleavage of a β-1,4-xylosidic bond. The enzyme hydrolyzed sweetgum xylan, generating products with a 4-O-methyl-glucuronic acid-substituted xylose residue one position from the nonreducing terminus of the oligoxyloside product. No internal cleavages of the xylan backbone between substituted xylose residues were observed, giving the enzyme a unique mode of action in the hydrolysis compared to all other xylanases that have been described. Given the size of the oligoxyloside products generated by the enzyme during depolymerization of xylan substrates, the function of the enzyme may be to render substrate available for other depolymerizing enzymes instead of producing oligoxylosides for cellular metabolism and may serve to produce elicitors during the initiation of the infectious process.
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Schepers, Hans-Jürgen, Stephanie Bringer-Meyer, and Hermann Sahm. "Fermentation of D-Xylose to Ethanol by Bacillus macerans." Zeitschrift für Naturforschung C 42, no. 4 (April 1, 1987): 401–7. http://dx.doi.org/10.1515/znc-1987-0412.
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Abstract In the absence of oxygen Bacillus macerans is able to ferment xylose. The principal products are ethanol, formate,CO2, acetone and H2. The yield of ethanol was 61% based on the theoretical value of 0.51 g per g xylose consumed. The cells could grow in the presence of up to 4% (v/v) of added ethanol but the growth rate was already reduced to about 50% by 1% (v/v) of alcohol. Glucose and the pentoses arabinose and xylose were sequentially utilized when initially present as a mixed substrate. Enzymatic studies indicate that xylose was metabolized via the pentosephos-phate and Embden-Meyerhof pathways. At an oxygen concentration of 1-2% air saturation 42 g/l xylose were completely fermented within 160 h and 10 g/l ethanol were produced.
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Wagschal, Kurt, Diana Franqui-Espiet, Charles C. Lee, George H. Robertson, and Dominic W. S. Wong. "Enzyme-Coupled Assay for β-Xylosidase Hydrolysis of Natural Substrates." Applied and Environmental Microbiology 71, no. 9 (September 2005): 5318–23. http://dx.doi.org/10.1128/aem.71.9.5318-5323.2005.
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ABSTRACT We describe here a new enzyme-coupled assay for the quantitation of d-xylose using readily available enzymes that allows kinetic evaluation of hemicellulolytic enzymes using natural xylooligosaccharide substrates. Hydrogen peroxide is generated as an intermediary analyte, which allows flexibility in the choice of the chromophore or fluorophore used as the final reporter. Thus, we present d-xylose quantitation results for solution-phase assays performed with both the fluorescent reporter resorufin, generated from N-acetyl-3,7-dihydroxyphenoxazine (Amplex Red), and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS), whose corresponding radical cation has an absorbance maximum at ∼400 nm. We also describe a useful solid-phase variation of the assay performed with the peroxidase substrate 3,3′-diaminobenzidine tetrahydrochloride, which produces an insoluble brown precipitate. In addition, kinetic parameters for hydrolysis of the natural substrates xylobiose and xylotriose were obtained using this assay for a glycosyl hydrolase family 39 β-xylosidase from Thermoanaerobacterium sp. strain JW/SL YS485 (Swiss-Prot accession no. O30360 ). At higher xylobiose substrate concentrations the enzyme showed an increase in the rate indicative of transglycosylation, while for xylotriose marked substrate inhibition was observed. At lower xylobiose concentrations k cat was 2.7 ± 0.4 s−1, Km was 3.3 ± 0.7 mM, and k cat/Km was 0.82 ± 0.21 mM−1 · s−1. Nonlinear curve fitting to a substrate inhibition model showed that for xylotriose Ki was 1.7 ± 0.1 mM, k cat was 2.0 ± 0.1 s−1, Km was 0.144 ± 0.011 mM, and k cat/Km was 14 ± 1.3 mM−1 · s−1.
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Liu, Yunyun, Yunqi Cao, Qiang Yu, Jingliang Xu, and Zhenhong Yuan. "Enhanced sugars production with high conversion efficiency from alkali-pretreated sugarcane bagasse by enzymatic mixtures." BioResources 15, no. 2 (April 6, 2020): 3839–49. http://dx.doi.org/10.15376/biores.15.2.3839-3849.
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Complementary enzymes can considerably enhance the hydrolysis effectiveness of cellulase. The influence of hemicellulase supplementation on high solids saccharification of alkali-pretreated sugarcane bagasse was assessed. Hemicellulase addition of 1200 IU/g substrate with cellulase loading of 10 FPU/g substrate achieved high sugars yield with glucose and xylose conversion efficiency of 95.4% and 87.4%, respectively. To further improve the substrate conversion efficiency based on high sugars production, fed-batch hydrolysis was employed with high solids loading of 20% (w/v) to 25% (w/v). After 96 h hydrolysis with 25% solids loading at cellulase and hemicellulase loading of 20 FPU/g and 1200 IU/g substrate, respectively, the obtained highest total sugars was 242 g/L, with glucose and xylose conversion efficiencies of 98.6% and 94.9%, respectively. An increase in substrate digestibility upon supplementation of mixture enzymes with high sugars production can be realized in high solids fed-batch system with proper cellulase and hemicellulase synergism.
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Yulianto, Wisnu Adi, Kapti Rahayu Kuswanto, Tranggono Tranggono, and Retno Indrati. "Pengaruh Konsentrasi Xilosa dan Kosubstrat Terhadap Produksi Xilitol oleh Candida shehatae Way 08." agriTECH 25, no. 3 (February 23, 2017): 143. http://dx.doi.org/10.22146/agritech.13352.
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The objectives of the research were to determine the optimum cultivation condition of initial xylose concentration, type of cosubstrate and ratio of cosubstrate to substrate (xylose) for xylitol production by Candida shehatae WAY 08. The initial xylose concentrations were varied within the range of 2-14 %. The cosubstrates were arabinose, galactose, glucose, and mannose. Ratios of cosubstrate to xylose were the range of 1:6 - 3:6 %. The fermentation was performed at 30`C in a 500 ml Erlenmeyer flask placed in a shaker incubator at 200 rpm for 72 h. Biomass concentration was determined by drying method. Xylose, cosubstrate and xylitol concentrations were determined using HPLC. The result indicated that with the medium containing 6 % xylose produced the highest product yield ( 0,75 g/g) and xylitol volumetric productivity was 0,73 g/Lh. The addition of cosubstrate of arabinose increased xylitol production, while the addition of glucose, galactose, and mannose decreased its productions.
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Leandro, Maria José, Paula Gonçalves, and Isabel Spencer-Martins. "Two glucose/xylose transporter genes from the yeast Candida intermedia: first molecular characterization of a yeast xylose–H+ symporter." Biochemical Journal 395, no. 3 (April 11, 2006): 543–49. http://dx.doi.org/10.1042/bj20051465.
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Candida intermedia PYCC 4715 was previously shown to grow well on xylose and to transport this sugar by two different transport systems: high-capacity and low-affinity facilitated diffusion and a high-affinity xylose–proton symporter, both of which accept glucose as a substrate. Here we report the isolation of genes encoding both transporters, designated GXF1 (glucose/xylose facilitator 1) and GXS1 (glucose/xylose symporter 1) respectively. Although GXF1 was isolated by functional complementation of an HXT-null (where Hxt refers to hexose transporters) Saccharomyces cerevisiae strain, isolation of the GXS1 cDNA required partial purification and micro-sequencing of the transporter, identified by its relative abundance in cells grown on low xylose concentrations. Both genes were expressed in S. cerevisiae and the kinetic parameters of glucose and xylose transport were determined. Gxs1 is the first yeast xylose/glucose–H+ symporter to be characterized at the molecular level. Comparison of its amino acid sequence with available sequence data revealed the existence of a family of putative monosaccharide–H+ symporters encompassing proteins from several yeasts and filamentous fungi.
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Young, Eric, Ashley Poucher, Austin Comer, Alexandra Bailey, and Hal Alper. "Functional Survey for Heterologous Sugar Transport Proteins, Using Saccharomyces cerevisiae as a Host." Applied and Environmental Microbiology 77, no. 10 (March 18, 2011): 3311–19. http://dx.doi.org/10.1128/aem.02651-10.
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ABSTRACTMolecular transport is a key process in cellular metabolism. This step is often limiting when using a nonnative carbon source, as exemplified by xylose catabolism inSaccharomyces cerevisiae. As a step toward addressing this limitation, this study seeks to characterize monosaccharide transport preference and efficiency. A group of 26 known and putative monosaccharide transport proteins was expressed in a recombinantSaccharomyces cerevisiaehost unable to transport several monosaccharides. A growth-based assay was used to detect transport capacity across six different carbon sources (glucose, xylose, galactose, fructose, mannose, and ribose). A mixed glucose-and-xylose cofermentation was performed to determine substrate preference. These experiments identified 10 transporter proteins that function as transporters of one or more of these sugars. Most of these proteins exhibited broad substrate ranges, and glucose was preferred in all cases. The broadest transporters confer the highest growth rates and strongly prefer glucose. This study reports the first molecular characterization of the annotated XUT genes ofScheffersomyces stipitisand open reading frames from the yeastsYarrowia lipolyticaandDebaryomyces hansenii.Finally, a phylogenetic analysis demonstrates that transporter function clusters into three distinct groups. One particular group comprised ofD. hanseniiXylHPandS. stipitisXUT1andXUT3demonstrated moderate transport efficiency and higher xylose preferences.
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Siegbahn, Anna, Sophie Manner, Andrea Persson, Emil Tykesson, Karin Holmqvist, Agata Ochocinska, Jerk Rönnols, et al. "Rules for priming and inhibition of glycosaminoglycan biosynthesis; probing the β4GalT7 active site." Chem. Sci. 5, no. 9 (2014): 3501–8. http://dx.doi.org/10.1039/c4sc01244e.
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Klongklaew, Augchararat, Kridsada Unban, Apinun Kanpiengjai, Pairote Wongputtisin, Punnita Pamueangmun, Kalidas Shetty, and Chartchai Khanongnuch. "Improvement of Enantiomeric l-Lactic Acid Production from Mixed Hexose-Pentose Sugars by Coculture of Enterococcus mundtii WX1 and Lactobacillus rhamnosus SCJ9." Fermentation 7, no. 2 (June 10, 2021): 95. http://dx.doi.org/10.3390/fermentation7020095.
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Among 39 pentose-utilizing lactic acid bacteria (LAB) selected from acid-forming bacteria from the midgut of Eri silkworm, the isolate WX1 was selected with the highest capability to produce optically pure l-lactic acid (l-LA) from glucose, xylose and arabinose with furfural-tolerant properties. The isolate WX1 was identified as Enterococcus mundtii based on 16S rDNA sequence analysis. The conversion yields of l-LA from glucose and xylose by E. mundtii WX1 were 0.97 and 0.68 g/g substrate, respectively. Furthermore, l-LA production by E. mundtii WX1 in various glucose-xylose mixtures indicated glucose repression effect on xylose consumption. The coculture of E. mundtii WX1 and Lactobacillus rhamnosus SCJ9, a homofermentative LAB capable of producing l-LA from glucose clearly showed an improvement of l-LA production from 30 g/L total glucose-xylose (6:4). The results from Plackett–Burman design (PBD) indicated that Tween 80, MnSO4 and yeast extract (YE) were three medium components that significantly influenced (p < 0.05) l-LA production using the coculture strategy in the presence of 2 g/L furfural. Optimal concentrations of these variables revealed by central composite design (CCD) and response surface methodology (RSM) were 20.61 g/L YE, 1.44 g/L Tween 80 and 1.27 g/L MnSO4. Based on the optimized medium with 30 g/L total glucose-xylose (6:4), the maximum experimental l-LA value of 23.59 g/L reflecting 0.76 g/g substrate were achieved from 48 h fermentation at 37 °C. l-LA produced by coculture cultivated under standard MRS medium and new optimized conditions were 1.28 and 1.53 times higher than that obtained from single culture by E. mundtii WX1, respectively. This study provides the foundations for practical applications of coculture in bioconversion of lignocellulose particularly glucose-xylose-rich corn stover to l-LA.
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Vogl, Michael, and Lothar Brecker. "Substrate binding to Candida tenuis xylose reductase during catalysis." RSC Advances 3, no. 48 (2013): 25997. http://dx.doi.org/10.1039/c3ra41448e.
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Pateraki, Chrysanthi, Henrik Almqvist, Dimitris Ladakis, Gunnar Lidén, Apostolis A. Koutinas, and Anestis Vlysidis. "Modelling succinic acid fermentation using a xylose based substrate." Biochemical Engineering Journal 114 (October 2016): 26–41. http://dx.doi.org/10.1016/j.bej.2016.06.011.
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Mardawati, Efri, Andi Trirakhmadi, MTAP Kresnowati, and Tjandra Setiadi. "Kinetic study on Fermentation of xylose for The Xylitol Production." Journal of Industrial and Information Technology in Agriculture 1, no. 1 (August 13, 2017): 1. http://dx.doi.org/10.24198/jiita.v1i1.12214.
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Xylitol is a natural sugar that has the sweetness level similar to sucrose, but has lower calorie. It is an important sugar alternate for diabetics people. Reduction of xylose is a normally method to produce the xylitol. It Conducted via chemical hydrogenation of xylose at high pressures and temperatures by reacting pure xylose with hydrogen gas using a metal catalyst. This process requires pure xylose as the raw material. Alternatively, the reduction process can be carried out via fermentation. This process does not require high purity of xylose as the raw material, and thus the oil palm empty fruit bunch (EFB) hydrolysate, without any prior pretreatment, can be used. In order to scale up the xylitol production via fermentation, kinetic study of xylitol fermentation including growth and xylitol formation kinetic using the synthetic xylose as substrate will be required. Data used in the kinetic model development were obtained from series of batch fermentations of Debaryomycess hansenii ITB CCR85 varying the initial xylose and glucose concentrations. Yeast growth could be sufficiently modeled using the Monod kinetics, whereas xylitol production could be reasonably well modelled by Luedeking Piret kinetics.
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Kim, In Seop, Kevin D. Barrow, and Peter L. Rogers. "Kinetic and Nuclear Magnetic Resonance Studies of Xylose Metabolism by Recombinant Zymomonas mobilisZM4(pZB5)." Applied and Environmental Microbiology 66, no. 1 (January 1, 2000): 186–93. http://dx.doi.org/10.1128/aem.66.1.186-193.2000.
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ABSTRACT The specific rates of growth, substrate utilization, and ethanol production as well as yields of biomass and ethanol production on xylose for the recombinant Zymomonas mobilis ZM4(pZB5) were shown to be much less than those on glucose or glucose-xylose mixtures. Typical fermentations with ZM4(pZB5) growing on glucose-xylose mixtures followed two-phase growth kinetics with the initial uptakes of glucose and xylose being followed by slower growth and metabolic uncoupling on xylose after glucose depletion. The reductions in rates and yields from xylose metabolism were considered in the present investigation and may be due to a number of factors, including the following: (i) the increased metabolic burden from maintenance of plasmid-related functions, (ii) the production of by-products identified as xylitol, acetate, lactate, acetoin, and dihydroxyacetone by13C-nuclear magnetic resonance (NMR) spectroscopy and high-performance liquid chromatography, (iii) growth inhibition due to xylitol by the putative inhibitory compound xylitol phosphate, and (iv) the less energized state of ZM4(pZB5). In vivo 31P-NMR studies have established that the levels of NTP and UDP sugars on xylose were less than those on glucose, and this energy limitation is likely to restrict the growth of the recombinant strain on xylose media.
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Ahuja, Vishal, Aashima Sharma, Ranju Kumari Rathour, Vaishali Sharma, Nidhi Rana, and Arvind Kumar Bhatt. "In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans." Current Chemical Biology 13, no. 2 (July 12, 2019): 159–70. http://dx.doi.org/10.2174/2212796812666180622103906.
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Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.
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OHNISHI, Masatake, Yokox FUJIOKA, Shigeo TAKEWUTI, Takahito YOSHIDA, Chieko HASHIZUME, Keitaro HIROMI, and Benichiro TONOMURA. "Substrate binding site of Streptomyces xylose isomerase, studied by the fluorescence spectrophotometry using xylose and xylitol." Journal of the Japanese Society of Starch Science 38, no. 1 (1991): 41–44. http://dx.doi.org/10.5458/jag1972.38.41.
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Ambarsari, Laksmi, Suryani Suryani, Steffanus Gozales, and Puspa Julistia Puspita. "The Addition Effects of Glucose as a Co-substrate on Xylitol Production by Candida guilliermondii." Current Biochemistry 2, no. 1 (April 20, 2015): 13–21. http://dx.doi.org/10.29244/cb.2.1.13-21.
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High cost production is one of the constraints of the commercial xylitol production due to high energy needed and pure raw materials. Therefore, it is necessary to improve the xylitol production eficiently with lower production cost by using microorganisms. The research objectives were to determine the optimum xylitol production from xylose by metabolism of C. guilliermondii and effect of glucose as a co-substrate in fermentation medium. The ratio of glucose : xylose (g/L) was 1:25, 1:12, 1:5 and 1:2.5 respectively. The xylitol concentration was measured by spectrophotometer method (D-sorbytol/D-xylitol kit). The result showed that the exponential phase of Candida guilliermondii was 12 h to 36 of incubation and optimum of incubation time to produce the highest xylitol was 72 h. The best ratio- of glucose : xylose to produce xylitol was 9 g/L glucose : 45 g/L xylose (1 : 5). The xylitol concentration produced from medium with the addition of glucose was 2.85 g/L. This concentration increased five times compared to that in the medium without addition of glucose that only reached 2.85 g/L. According to this study, the addition of glucose as a co-substrate could increase the xylitol production.
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Palnitkar, Sanjay, and Anil Lachke. "Effect of nitrogen sources on oxidoreductive enzymes and ethanol production during D-xylose fermentation by Candida shehatae." Canadian Journal of Microbiology 38, no. 3 (March 1, 1992): 258–60. http://dx.doi.org/10.1139/m92-043.
Full textAbstract:
The effect on D-xylose utilization and the corresponding xylitol and ethanol production by Candida shehatae (ATCC 22984) were examined with different nitrogen sources. These included organic (urea, asparagine, and peptone) and inorganic (ammonium chloride, ammonium nitrate, ammonium sulphate, and potassium nitrate) sources. Candida shehatae did not grow on potassium nitrate. Improved ethanol production (Y(p/s), yield coefficient (grams product/grams substrate), 0.34) was observed when organic nitrogen sources were used. Correspondingly, the xylitol production was also higher with organic sources. Ammonium sulphate showed the highest ethanol:xylitol ratio (11.0) among all the nitrogen sources tested. The ratio of NADH- to NADPH-linked D-xylose reductase (EC 1.1.1.21) appeared to be rate limiting during ethanologenesis of D-xylose. The levels of xylitol dehydrogenase (EC 1.1.1.9) were also elevated in the presence of organic nitrogen sources. These results may be useful in the optimization of alcohol production by C. shehatae during continuous fermentation of D-xylose. Key words: xylose fermentation, Candida shehatae, nitrogen source, oxidoreductive enzymes.
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Levin, Ana M., Ronald P. de Vries, Ana Conesa, Charissa de Bekker, Manuel Talon, Hildegard H. Menke, Noel N. M. E. van Peij, and Han A. B. Wösten. "Spatial Differentiation in the Vegetative Mycelium of Aspergillus niger." Eukaryotic Cell 6, no. 12 (October 19, 2007): 2311–22. http://dx.doi.org/10.1128/ec.00244-07.
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ABSTRACT Fungal mycelia are exposed to heterogenic substrates. The substrate in the central part of the colony has been (partly) degraded, whereas it is still unexplored at the periphery of the mycelium. We here assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of Aspergillus niger. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 7-day-old maltose- and xylose-grown colonies. Expression profiles at the periphery and the center were clearly different. More than 25% of the active genes showed twofold differences in expression between the inner and outermost zones of the colony. Moreover, 9% of the genes were expressed in only one of the five concentric zones, showing that a considerable part of the genome is active in a restricted part of the colony only. Statistical analysis of expression profiles of colonies that had either been or not been transferred to fresh xylose-containing medium showed that differential expression in a colony is due to the heterogeneity of the medium (e.g., genes involved in secretion, genes encoding proteases, and genes involved in xylose metabolism) as well as to medium-independent mechanisms (e.g., genes involved in nitrate metabolism and genes involved in cell wall synthesis and modification). Thus, we conclude that the mycelia of 7-day-old colonies of A. niger are highly differentiated. This conclusion is also indicated by the fact that distinct zones of the colony grow and secrete proteins, even after transfer to fresh medium.
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Karekar, Supriya, Keerthi Srinivas, and Birgitte Ahring. "Kinetic Study on Heterotrophic Growth of Acetobacterium woodii on Lignocellulosic Substrates for Acetic Acid Production." Fermentation 5, no. 1 (February 2, 2019): 17. http://dx.doi.org/10.3390/fermentation5010017.
Full textAbstract:
Extensive research has been done on examining the autotrophic growth of Acetobacterium woodii with gaseous substrates (hydrogen and carbon dioxide) to produce acetic acid. However, only limited work has been performed on the heterotrophic growth of A. woodii using pure sugars or lignocellulosic feedstocks-derived sugars as substrates. In this study, we examine the growth kinetics and acetic acid production of A. woodii on glucose and xylose. While good growth was observed with glucose as substrate, no significant growth was obtained on xylose. Kinetic studies were performed in batch culture using different concentrations of glucose, ranging from 5 g/L to 40 g/L. The highest acetate production of 6.919 g/L with a product yield of 0.76 g acetic acid/g glucose was observed with 10 g/L glucose as initial substrate concentration. When testing A. woodii on corn stover hydrolysate (CSH) and wheat straw hydrolysate (WSH) formed after pretreatment and enzymatic hydrolysis, we found that A. woodii showed acetic acid production of 7.64 g/L and a product yield of 0.70 g acetic acid/g of glucose on WSH, while the acetic acid production was 7.83 g/L with a product yield of 0.65 g acetic acid/g of glucose on CSH. These results clearly demonstrate that A. woodii performed similarly on pure substrates and hydrolysates, and that the processes were not inhibited by the heterogenous components present in the lignocellulosic feedstock hydrolysates.
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Swart, Reuben Marc, Hendrik Brink, and Willie Nicol. "Rhizopus oryzae for Fumaric Acid Production: Optimising the Use of a Synthetic Lignocellulosic Hydrolysate." Fermentation 8, no. 6 (June 15, 2022): 278. http://dx.doi.org/10.3390/fermentation8060278.
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The hydrolysis of lignocellulosic biomass opens an array of bioconversion possibilities for producing fuels and chemicals. Microbial fermentation is particularly suited to the conversion of sugar-rich hydrolysates into biochemicals. Rhizopus oryzae ATCC 20344 was employed to produce fumaric acid from glucose, xylose, and a synthetic lignocellulosic hydrolysate (glucose–xylose mixture) in batch and continuous fermentations. A novel immobilised biomass reactor was used to investigate the co-fermentation of xylose and glucose. Ideal medium conditions and a substrate feed strategy were then employed to optimise the production of fumaric acid. The batch fermentation of the synthetic hydrolysate at optimal conditions (urea feed rate 0.625mgL−1h−1 and pH 4) produced a fumaric acid yield of 0.439gg−1. A specific substrate feed rate (0.164gL−1h−1) that negated ethanol production and selected for fumaric acid was determined. Using this feed rate in a continuous fermentation, a fumaric acid yield of 0.735gg−1 was achieved; this was a 67.4% improvement. A metabolic analysis helped to determine a continuous synthetic lignocellulosic hydrolysate feed rate that selected for fumaric acid production while achieving the co-fermentation of glucose and xylose, thus avoiding the undesirable carbon catabolite repression. This work demonstrates the viability of fumaric acid production from lignocellulosic hydrolysate; the process developments discovered will pave the way for an industrially viable process.
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PETSCHACHER, Barbara, Stefan LEITGEB, Kathryn L. KAVANAGH, David K. WILSON, and Bernd NIDETZKY. "The coenzyme specificity of Candida tenuis xylose reductase (AKR2B5) explored by site-directed mutagenesis and X-ray crystallography." Biochemical Journal 385, no. 1 (December 14, 2004): 75–83. http://dx.doi.org/10.1042/bj20040363.
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CtXR (xylose reductase from the yeast Candida tenuis; AKR2B5) can utilize NADPH or NADH as co-substrate for the reduction of D-xylose into xylitol, NADPH being preferred approx. 33-fold. X-ray structures of CtXR bound to NADP+ and NAD+ have revealed two different protein conformations capable of accommodating the presence or absence of the coenzyme 2′-phosphate group. Here we have used site-directed mutagenesis to replace interactions specific to the enzyme–NADP+ complex with the aim of engineering the co-substrate-dependent conformational switch towards improved NADH selectivity. Purified single-site mutants K274R (Lys274→Arg), K274M, K274G, S275A, N276D, R280H and the double mutant K274R–N276D were characterized by steady-state kinetic analysis of enzymic D-xylose reductions with NADH and NADPH at 25 °C (pH 7.0). The results reveal between 2- and 193-fold increases in NADH versus NADPH selectivity in the mutants, compared with the wild-type, with only modest alterations of the original NADH-linked xylose specificity and catalytic-centre activity. Catalytic reaction profile analysis demonstrated that all mutations produced parallel effects of similar magnitude on ground-state binding of coenzyme and transition state stabilization. The crystal structure of the double mutant showing the best improvement of coenzyme selectivity versus wild-type and exhibiting a 5-fold preference for NADH over NADPH was determined in a binary complex with NAD+ at 2.2 Å resolution.
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Sarkar, Nibedita, and Kaustav Aikat. "Kinetic Study of Acid Hydrolysis of Rice Straw." ISRN Biotechnology 2013 (December 22, 2013): 1–5. http://dx.doi.org/10.5402/2013/170615.
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Rice straw is a renewable, cheap, and abundant waste in tropical countries. The pentose content of rice straw can be used as a substrate for many types of value-added products such as xylitol and biofuel. Dilute acid hydrolysis mainly releases pentose from rice straw. The objective of the study was to determine the effect of H2SO4 concentration and reaction time on the xylose production. The variation of the main product xylose with the reaction time was described by a kinetic model and kinetic parameters were calculated to describe the variation of the xylose production with time. The optimum yield (19.35 g/L) was obtained at 0.24 mol/L H2SO4 and 30 minutes.
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Kopp, Dominik, Peter L. Bergquist, and Anwar Sunna. "Enzymology of Alternative Carbohydrate Catabolic Pathways." Catalysts 10, no. 11 (October 23, 2020): 1231. http://dx.doi.org/10.3390/catal10111231.
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The Embden–Meyerhof–Parnas (EMP) and Entner–Doudoroff (ED) pathways are considered the most abundant catabolic pathways found in microorganisms, and ED enzymes have been shown to also be widespread in cyanobacteria, algae and plants. In a large number of organisms, especially common strains used in molecular biology, these pathways account for the catabolism of glucose. The existence of pathways for other carbohydrates that are relevant to biomass utilization has been recognized as new strains have been characterized among thermophilic bacteria and Archaea that are able to transform simple polysaccharides from biomass to more complex and potentially valuable precursors for industrial microbiology. Many of the variants of the ED pathway have the key dehydratase enzyme involved in the oxidation of sugar derived from different families such as the enolase, IlvD/EDD and xylose-isomerase-like superfamilies. There are the variations in structure of proteins that have the same specificity and generally greater-than-expected substrate promiscuity. Typical biomass lignocellulose has an abundance of xylan, and four different pathways have been described, which include the Weimberg and Dahms pathways initially oxidizing xylose to xylono-gamma-lactone/xylonic acid, as well as the major xylose isomerase pathway. The recent realization that xylan constitutes a large proportion of biomass has generated interest in exploiting the compound for value-added precursors, but few chassis microorganisms can grow on xylose. Arabinose is part of lignocellulose biomass and can be metabolized with similar pathways to xylose, as well as an oxidative pathway. Like enzymes in many non-phosphorylative carbohydrate pathways, enzymes involved in L-arabinose pathways from bacteria and Archaea show metabolic and substrate promiscuity. A similar multiplicity of pathways was observed for other biomass-derived sugars such as L-rhamnose and L-fucose, but D-mannose appears to be distinct in that a non-phosphorylative version of the ED pathway has not been reported. Many bacteria and Archaea are able to grow on mannose but, as with other minor sugars, much of the information has been derived from whole cell studies with additional enzyme proteins being incorporated, and so far, only one synthetic pathway has been described. There appears to be a need for further discovery studies to clarify the general ability of many microorganisms to grow on the rarer sugars, as well as evaluation of the many gene copies displayed by marine bacteria.