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Journal of Industrial Microbiology &... Oct 2017Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to...
Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in chemostats, followed by attempted induction of CCR with glucose or arabinose. Alicyclobacillus acidocaldarius grew while simultaneously metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating that CCR did not control carbon metabolism. Microarrays showed down-regulation of genes during growth on one sugar compared to two, and occurred primarily in genes encoding: (1) regulators; (2) enzymes for cell wall synthesis; and (3) sugar transporters.
Topics: Adenosine Triphosphate; Alicyclobacillus; Arabinose; Biological Transport; Biomass; Carbon; Catabolite Repression; Cell Wall; Down-Regulation; Fructose; Gene Expression Regulation, Bacterial; Glucose; Hexoses; Pentoses; Xylose
PubMed: 28776272
DOI: 10.1007/s10295-017-1968-2 -
Applied and Environmental Microbiology Apr 1994Ruminococcus albus is an important fibrolytic ruminal bacteria which degrades hemicellulose and ferments the resulting pentose sugars. However, little information is...
Ruminococcus albus is an important fibrolytic ruminal bacteria which degrades hemicellulose and ferments the resulting pentose sugars. However, little information is available on the utilization of pentoses by this organism or the effect of hexose sugars on pentose metabolism. Enzymatic studies indicated that R. albus metabolized pentoses via the pentose phosphate pathway and possessed constitutive transketolase activity. Cellobiose was preferred over xylose and arabinose, and it appeared that the disaccharide decreased pentose metabolism by repression of transport activity and catabolic enzymes (isomerases and kinases). Glucose and xylose were co-utilized, and transport studies suggested that there was a common transport system for both sugars. In contrast, glucose was preferred over arabinose and the hexose noncompetitively inhibited the transport of arabinose. Since R. albus lacks a glucose phosphotransferase system, the inhibition of arabinose uptake could not be explained by previously described models of inducer exclusion involving such a system. Because accumulation of radiolabeled xylose, arabinose, and glucose proceeded in the absence of a proton motive force and since transport was correlated with the intracellular ATP concentration, it appeared that monosaccharide uptake was driven by ATP hydrolysis.
Topics: Animals; Bacterial Proteins; Biological Transport, Active; Cellobiose; Cellulose; Glucose; Gram-Positive Cocci; Pentose Phosphate Pathway; Pentoses; Rumen; Substrate Specificity
PubMed: 8017905
DOI: 10.1128/aem.60.4.1087-1092.1994 -
Applied and Environmental Microbiology Feb 2018Pentoses, including xylose and arabinose, are the second most prevalent sugars in lignocellulosic biomass that can be harnessed for biological conversion. Although has...
Pentoses, including xylose and arabinose, are the second most prevalent sugars in lignocellulosic biomass that can be harnessed for biological conversion. Although has emerged as a promising industrial microorganism for production of high-value chemicals and biofuels, its native pentose metabolism is poorly understood. Our previous study demonstrated that (ATCC MYA-2613) has endogenous enzymes for d-xylose assimilation, but inefficient xylitol dehydrogenase causes to assimilate xylose poorly. In this study, we investigated the functional roles of native sugar-specific transporters for activating the dormant pentose metabolism in By screening a comprehensive set of 16 putative pentose-specific transporters, we identified two candidates, YALI0C04730p and YALI0B00396p, that enhanced xylose assimilation. The engineered mutants YlSR207 and YlSR223, overexpressing YALI0C04730p and YALI0B00396p, respectively, improved xylose assimilation approximately 23% and 50% in comparison to YlSR102, a parental engineered strain overexpressing solely the native xylitol dehydrogenase gene. Further, we activated and elucidated a widely unknown native l-arabinose assimilation pathway in through transcriptomic and metabolic analyses. We discovered that can coconsume xylose and arabinose, where arabinose utilization shares transporters and metabolic enzymes of some intermediate steps of the xylose assimilation pathway. Arabinose assimilation is synergistically enhanced in the presence of xylose, while xylose assimilation is competitively inhibited by arabinose. l-Arabitol dehydrogenase is the rate-limiting step responsible for poor arabinose utilization in Overall, this study sheds light on the cryptic pentose metabolism of and, further, helps guide strain engineering of for enhanced assimilation of pentose sugars. The oleaginous yeast is a promising industrial-platform microorganism for production of high-value chemicals and fuels. For decades since its isolation, has been known to be incapable of assimilating pentose sugars, xylose and arabinose, that are dominantly present in lignocellulosic biomass. Through bioinformatic, transcriptomic, and enzymatic studies, we have uncovered the dormant pentose metabolism of Remarkably, unlike most yeast strains, which share the same transporters for importing hexose and pentose sugars, we discovered that possesses the native pentose-specific transporters. By overexpressing these transporters together with the rate-limiting d-xylitol and l-arabitol dehydrogenases, we activated the dormant pentose metabolism of Overall, this study provides a fundamental understanding of the dormant pentose metabolism of and guides future metabolic engineering of for enhanced conversion of pentose sugars to high-value chemicals and fuels.
Topics: Arabinose; Biofuels; Biomass; Computational Biology; Ethanol; Fermentation; Glucose; Metabolic Engineering; Metabolic Networks and Pathways; Pentoses; Sugar Alcohols; Xylose; Yarrowia
PubMed: 29150499
DOI: 10.1128/AEM.02146-17 -
Environmental Technology Mar 2019In the search for alternative carbon sources for microalgae cultivation, pentoses can be considered interesting alternatives since the most abundant global source of...
In the search for alternative carbon sources for microalgae cultivation, pentoses can be considered interesting alternatives since the most abundant global source of renewable biomass is lignocellulosic waste, which contains significant quantities of pentoses. However, the use of pentoses (C5) in the cultivation of microalgae is still not widely studied and only recently the first metabolic pathway for pentose absorption in microalgae was proposed. So, the objective of this work was to evaluate if the use of pentoses affects the growth and carbohydrates content of Chlorella minutissima, Chlorella vulgaris, Chlorella homosphaera and Dunaliella salina. The kinetic parameters, carbohydrate and protein content and the theoretical potential for ethanol production were estimated for all strains. The highest cellular concentrations (1.25 g L) were obtained for D. salina with 5% of pentoses. The addition of pentoses leads to high levels of carbohydrates for C. minutissima (58.6%) cultured with 5% of pentoses, and from this biomass, it is possible to determine a theoretical production of ethanol of 38 mL per 100 g of biomass. The pentoses affect the growth and the biomass composition of the studied strains, generating biomass with potential use for bioethanol production.
Topics: Biomass; Carbohydrates; Carbon; Chlorella vulgaris; Microalgae; Pentoses
PubMed: 29251249
DOI: 10.1080/09593330.2017.1417491 -
Journal of Chemical Information and... Sep 2022To develop a realistic electrostatic model that allows for the anisotropy of the atomic electron density, high-rank atomic multipole moments computed by quantum chemical...
To develop a realistic electrostatic model that allows for the anisotropy of the atomic electron density, high-rank atomic multipole moments computed by quantum chemical calculations have been studied extensively. However, it is hard to process huge RNA systems only relying on quantum chemical calculations due to its highly computational cost. In this study, we employ five machine learning methods of Gaussian process regression with automatic relevance determination (ARDGPR), Kriging, radial basis function neural networks, Bagging, and generalized regression neural network to predict atomic multipole moments. Atom-atom electrostatic interaction energies are subsequently computed using the predicted atomic multipole moments in the pilot system pentose of RNA. Here, the performance of the five methods is compared in terms of both the multipole moment prediction errors and the electrostatic energy prediction errors. For the predicted high-rank multipole moments of the four elements (O, C, N, and H) in capped pentose, ARDGPR and Kriging consistently outperform the other three methods. Therefore, the multipole moments predicted by the two best methods of ARDGPR and Kriging are then used to predict electrostatic interaction energy of each pentose. Finally, the absolute average energy errors of ARDGPR and Kriging are 1.83 and 4.33 kJ mol, respectively. Compared to Kriging, the ARDGPR method achieves a 58% decrease in the absolute average energy error. These satisfactory results demonstrated that the ARDGPR method with the strong feature extraction ability can predict the electrostatic interaction energy of pentose in RNA correctly and reliably.
Topics: Machine Learning; Normal Distribution; Pentoses; RNA; Static Electricity
PubMed: 36036609
DOI: 10.1021/acs.jcim.2c00747 -
Journal of Microbiology and... Mar 2019L-Arabinose, a five carbon sugar, has not been considered as an important bioresource because most studies have focused on D-xylose, another type of five-carbon sugar... (Review)
Review
L-Arabinose, a five carbon sugar, has not been considered as an important bioresource because most studies have focused on D-xylose, another type of five-carbon sugar that is prevalent as a monomeric structure of hemicellulose. In fact, L-arabinose is also an important monomer of hemicellulose, but its content is much more significant in pectin (3-22%, g/g pectin), which is considered an alternative biomass due to its low lignin content and mass production as juiceprocessing waste. This review presents native and engineered microorganisms that can ferment L-arabinose. is highlighted as the most preferred engineering host for expressing a heterologous arabinose pathway for producing ethanol. Because metabolic engineering efforts have been limited so far, with this review as momentum, more attention to research is needed on the fermentation of L-arabinose as well as the utilization of pectin-rich biomass.
Topics: Arabinose; Bacteria; Biomass; Ethanol; Fermentation; Fungi; Lignin; Metabolic Engineering; Metabolic Networks and Pathways; Pectins; Pentoses; Polysaccharides; Saccharomyces cerevisiae; Xylose
PubMed: 30786700
DOI: 10.4014/jmb.1812.12015 -
Vaccine Sep 2017
Methyl pentose (6-deoxy hexose) content in the polysaccharides of Streptococcus pneumoniae serotypes 4, 5 and 12F: Incorrect sugar composition specification in WHO TRS977.
Topics: Humans; Pentoses; Polysaccharides, Bacterial; Rhamnose; Serotyping; Streptococcus pneumoniae; World Health Organization
PubMed: 28780979
DOI: 10.1016/j.vaccine.2017.07.052 -
Biotechnology Progress Jul 2017Itaconic acid (IA), an unsaturated 5-carbon dicarboxylic acid, is a building block platform chemical that is currently produced industrially from glucose by fermentation...
Itaconic acid (IA), an unsaturated 5-carbon dicarboxylic acid, is a building block platform chemical that is currently produced industrially from glucose by fermentation with Aspergillus terreus. However, lignocellulosic biomass has potential to serve as low-cost source of sugars for production of IA. Research needs to be performed to find a suitable A. terreus strain that can use lignocellulose-derived pentose sugars and produce IA. One hundred A. terreus strains were evaluated for the first time for production of IA from xylose and arabinose. Twenty strains showed good production of IA from the sugars. Among these, six strains (NRRL strains 1960, 1961, 1962, 1972, 66125, and DSM 23081) were selected for further study. One of these strains NRRL 1961 produced 49.8 ± 0.3, 38.9 ± 0.8, 34.8 ± 0.9, and 33.2 ± 2.4 g IA from 80 g glucose, xylose, arabinose and their mixture (1:1:1), respectively, per L at initial pH 3.1 and 33°C. This is the first report on the production of IA from arabinose and mixed sugar of glucose, xylose, and arabinose by A. terreus. The results presented in the article will be very useful in developing a process technology for production of IA from lignocellulosic feedstocks. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1059-1067, 2017.
Topics: Aspergillus; Pentoses; Succinates
PubMed: 28440059
DOI: 10.1002/btpr.2485 -
Extremophiles : Life Under Extreme... Mar 2008In spite of their common hypersaline environment, halophilic archaea are surprisingly different in their nutritional demands and metabolic pathways. The metabolic... (Comparative Study)
Comparative Study Review
In spite of their common hypersaline environment, halophilic archaea are surprisingly different in their nutritional demands and metabolic pathways. The metabolic diversity of halophilic archaea was investigated at the genomic level through systematic metabolic reconstruction and comparative analysis of four completely sequenced species: Halobacterium salinarum, Haloarcula marismortui, Haloquadratum walsbyi, and the haloalkaliphile Natronomonas pharaonis. The comparative study reveals different sets of enzyme genes amongst halophilic archaea, e.g. in glycerol degradation, pentose metabolism, and folate synthesis. The carefully assessed metabolic data represent a reliable resource for future system biology approaches as it also links to current experimental data on (halo)archaea from the literature.
Topics: Euryarchaeota; Folic Acid; Genome, Archaeal; Glycerol; Pentoses
PubMed: 18278431
DOI: 10.1007/s00792-008-0138-x -
Biochemical and Biophysical Research... May 1980
Topics: Ascomycota; Ethanol; Fermentation; Kinetics; Pentoses; Saccharomyces; Saccharomyces cerevisiae; Schizosaccharomyces; Xylulose
PubMed: 6446306
DOI: 10.1016/s0006-291x(80)80213-0