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https://www.readbyqxmd.com/read/27918587/an-alignment-free-algorithm-in-comparing-the-similarity-of-protein-sequences-based-on-pseudo-markov-transition-probabilities-among-amino-acids
#1
Yushuang Li, Tian Song, Jiasheng Yang, Yi Zhang, Jialiang Yang
In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences...
2016: PloS One
https://www.readbyqxmd.com/read/27917912/xylanase-treatment-suppresses-light-and-heat-induced-yellowing-of-pulp
#2
Daolei Zhang, Xuezhi Li, Meimei Wang, Yanxin Ye, Jian Du, Xianqin Lu, Jian Zhao
Xylanase is commonly applied in pulp and paper industries to ease cost-related and environmental pressures. The effect of xylanase treatment on pulp bleaching is well-established, however, few studies were conducted on the effects of xylanase treatment in pulp yellowing, especially the mechanism of pulp yellowing inhibition by xylanase treatment. In this study, pure xylanase (EC 3.2.1.8) was applied to treat wheat straw chemical pulp (CP) and poplar chemi-thermo-mechanical pulp (CTMP) to determine their effects on pulp brightness and on light- and heat-induced yellowing...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27914020/characterization-of-xylanase-and-cellulase-produced-by-a-newly-isolated-aspergillus-fumigatus-n2-and-its-efficient-saccharification-of-barley-straw
#3
Chaoyang Lin, Zhicheng Shen, Wensheng Qin
Aspergillus fumigatus N2 was isolated from decaying wood. This strain produces extracellular xylanases and cellulases. The highest xylanase (91.9 U/mL) and CMCase (5.61 U/mL) activity was produced when 1% barley straw was used as the carbon source. The optimum pH and temperature for xylanase activity were 6.0 and 65 °C, respectively. CMCase revealed maximum activity at pH 4.0 and in the range of 65 °C. The FPase was optimally active at pH 5.0 and 60 °C. The zymograms produced by the SDS-PAGE resolution of the crude enzymes indicated that multiple enzymes were secreted into the fermentation supernatant...
December 2, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27907079/identification-of-pectin-degrading-enzymes-secreted-by-xanthomonas-oryzae-pv-oryzae-and-determination-of-their-role-in-virulence-on-rice
#4
Lavanya Tayi, Roshan V Maku, Hitendra Kumar Patel, Ramesh V Sonti
Xanthomonas oryzae pv.oryzae (Xoo) causes the serious bacterial blight disease of rice. Xoo secretes a repertoire of plant cell wall degrading enzymes (CWDEs) like cellulases, xylanases, esterases etc., which act on various components of the rice cell wall. The major cellulases and xylanases secreted by Xoo have been identified and their role in virulence has been determined. In this study, we have identified some of the pectin degrading enzymes of Xoo and assessed their role in virulence. Bioinformatics analysis indicated the presence of four pectin homogalacturonan (HG) degrading genes in the genome of Xoo...
2016: PloS One
https://www.readbyqxmd.com/read/27900528/the-thermophilic-biomass-degrading-fungus-thielavia-terrestris-co3bag1-produces-a-hyperthermophilic-and-thermostable-%C3%AE-1-4-xylanase-with-exo-and-endo-activity
#5
Yolanda García-Huante, Maribel Cayetano-Cruz, Alejandro Santiago-Hernández, Claudia Cano-Ramírez, Rodolfo Marsch-Moreno, Jorge E Campos, Guillermo Aguilar-Osorio, Claudia G Benitez-Cardoza, Sergio Trejo-Estrada, María Eugenia Hidalgo-Lara
A hyperthermophilic and thermostable xylanase of 82 kDa (TtXynA) was purified from the culture supernatant of T. terrestris Co3Bag1, grown on carboxymethyl cellulose (CMC), and characterized biochemically. TtXynA showed optimal xylanolytic activity at pH 5.5 and at 85 °C, and retained more than 90% of its activity at a broad pH range (4.5-10). The enzyme is highly thermostable with a half-life of 23.1 days at 65 °C, and active in the presence of several metal ions. Circular dichroism spectra strongly suggest the enzyme gains secondary structures when temperature increases...
November 29, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/27898914/postprandial-portal-fluxes-of-essential-amino-acids-volatile-fatty-acids-and-urea-nitrogen-in-growing-pigs-fed-a-high-fiber-diet-supplemented-with-a-multi-enzyme-cocktail
#6
A K Agyekum, E Kiarie, M C Walsh, C M Nyachoti
The present study investigated the effects of adding a multi-enzyme cocktail (MC) to a high-fiber diet on net portal-drained viscera (PDV) fluxes of essential AA (EAA), volatile fatty acids (VFA), and blood urea-N (BUN) in growing pigs. Five female pigs (22.8 ± 1.6 kg BW), with catheters in the portal vein, ileal vein, and carotid artery, were fed 3 isocaloric-nitrogenous diets at 4% of their BW once daily at 0900 h for 7 d in a replicated 3 × 3 Latin square design. The diets contained corn and soybean meal with 0% (control) or 30% distillers' dried grains with solubles (DDGS; HF) produced from a 1:1 mixture of wheat and corn...
September 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898890/postprandial-portal-glucose-and-lactate-fluxes-insulin-production-and-portal-vein-drained-viscera-oxygen-consumption-in-growing-pigs-fed-a-high-fiber-diet-supplemented-with-a-multi-enzyme-cocktail
#7
A K Agyekum, E Kiarie, M C Walsh, C M Nyachoti
Information on effects of supplementing fibrous diets with exogenous enzymes on nutrient absorption and energetic demands of visceral organs is scarce. Therefore, this study investigated the effects of supplementing a high-fiber (HF) diet with a multi-enzyme cocktail (MC) on net glucose and lactate portal fluxes, insulin production, and O consumption by the portal-drained viscera (PDV) and whole animal in growing pigs. The MC supplied (analyzed values) 5,397 U of xylanase, 162 U of β-glucanase, and 2,000 U of protease per kg of diet, and guaranteed minimum activities of 1,000 U of α-amylase and 25 U of pectinase per kg of diet...
September 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898877/effects-of-full-fat-or-defatted-rice-bran-on-growth-performance-and-blood-characteristics-of-weanling-pigs
#8
G A Casas, H H Stein
The objective of this experiment was to determine the effect of increased concentrations of full fat rice bran (FFRB) or defatted rice bran (DFRB) in diets without or with supplementation of an exogenous xylanase on growth performance and blood characteristics in weanling pigs. A total of 532 pigs (9.3 ± 0.5 kg initial BW) were allotted to 14 diets in 4 blocks and 8 replicate pens per diet in a randomized complete block design. There were 4 or 5 pigs per pen. A basal diet containing corn, soybean meal, and whey powder and 6 diets containing corn, soybean meal, whey powder, and 10, 20, or 30% FFRB or 10, 20, or 30% DFRB were used...
October 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27897254/high-level-expression-of-improved-thermo-stable-alkaline-xylanase-variant-in-pichia-pastoris-through-codon-optimization-multiple-gene-insertion-and-high-density-fermentation
#9
Yihong Lu, Cheng Fang, Qinhong Wang, Yuling Zhou, Guimin Zhang, Yanhe Ma
In paper industry, xylanases are used to increase the pulp properties in bleaching process as its eco-friendly nature. The xylanases activity is hindered by high temperature and alkaline conditions with high enzyme production cost in the paper industry. Here, XynHB, an alkaline stable xylanase from Bacillus pumilus HBP8 was mutated at N188A to XynHBN188A. Expressed mutant in E. coli showed 1.5-fold higher xylanase activity than XynHB at 60 °C. The mutant expressed in Pichia pastoris was glycosylated, remained stable for 30 min at 60 °C...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27894041/valorization-of-exhausted-sugar-beet-cossettes-by-successive-hydrolysis-and-two-fermentations-for-the-production-of-bio-products
#10
A B Díaz, C Marzo, I Caro, I de Ory, A Blandino
Exhausted sugar beet cossettes (ESBC) show an enormous potential as a source of sugars for the production of bio-products. Enzyme hydrolysis with the combined effect of mainly cellulases, xylanases and pectinases, turned out to be very efficient, obtaining almost double the concentration of sugars measured with the sole action of Celluclast® and β-glucosidase, and increasing 5 times the hydrolysis rate. As the sole pretreatment, ESBC soaked in the hydrolysis buffer were autoclaved, avoiding the application of severe conventional biomass pretreatments...
November 19, 2016: Bioresource Technology
https://www.readbyqxmd.com/read/27891117/disruption-of-the-gene-encoding-endo-%C3%AE-1-4-xylanase-affects-the-growth-and-virulence-of-sclerotinia-sclerotiorum
#11
Yang Yu, Jifen Xiao, Jiao Du, Yuheng Yang, Chaowei Bi, Ling Qing
Sclerotinia sclerotiorum (Lib.) de Bary is a devastating fungal pathogen with worldwide distribution. S. sclerotiorum is a necrotrophic fungus that secretes many cell wall-degrading enzymes (CWDEs) that destroy plant's cell-wall components. Functional analyses of the genes that encode CWDEs will help explain the mechanisms of growth and pathogenicity of S. sclerotiorum. Here, we isolated and characterized a gene SsXyl1 that encoded an endo-β-1, 4-xylanase in S. sclerotiorum. The SsXyl1 expression showed a slight increase during the development and germination stages of sclerotia and a dramatic increase during infection...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27888008/extracellular-expression-of-alkali-tolerant-xylanase-from-bacillus-subtilis-lucky9-in-e-coli-and-application-for-xylooligosaccharides-production-from-agro-industrial-waste
#12
Siyuan Chang, Yalan Guo, Bin Wu, Bingfang He
An alkali tolerant xylanase gene from Bacillus subtilis Lucky9 was cloned and extracellular expressed in E. coli BL21. Xylanase amino acid sequence showed 99% identity with xylanase sequence from Bacillus subtilis 168, and was belonged to glycoside hydrolase family 11. The recombinant E. coli (pET-pelB-xynLC9) containing pelB signal peptide produced extracellular xylanase of 436.5U/mL for 8h, which was used arabinose as extra carbon source and inducer for enhancing extracellular production. The extracellular xylanase was determined by SDS-PAGE with a relative molecular mass of 21kDa...
November 22, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27879638/structural-investigation-of-cell-wall-xylan-polysaccharides-from-the-leaves-of-algerian-argania-spinosa
#13
Kadda Hachem, Céline Faugeron, Meriem Kaid-Harche, Vincent Gloaguen
Xylan-type polysaccharides were isolated from the leaves of Argania spinosa (L.) Skeels collected in the Tindouf area (southwestern Algeria). Xylan fractions were obtained by sequential alkaline extractions and purified on Sepharose CL-4B. The xylan structure was investigated by enzymatic hydrolysis with an endo-β(1→4)-xylanase followed by chromatography of the resulting fragments on Biogel P2, characterization by sugar analysis and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS )...
November 21, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27878934/two-degradation-strategies-for-overcoming-the-recalcitrance-of-natural-lignocellulosic-xylan-by-polysaccharides-binding-gh10-and-gh11-xylanases-of-filamentous-fungi
#14
Youzhi Miao, Pan Li, Guangqi Li, Dongyang Liu, Irina S Druzhinina, Christian P Kubicek, Qirong Shen, Ruifu Zhang
The recalcitrance of lignocellulose forms a strong barrier for the bioconversion of lignocellulosic biomass in chemical or biofuel industries. Filamentous fungi are major plant biomass decomposer, and capable of forming all the required enzymes. Here, we characterized the GH10 and GH11 endo-xylanases and a CE1 acetyl-xylan esterase (Axe1) from a superior biomass-degrading strain, Aspergillus fumigatus Z5, and examined how they interact in xylan degradation. Cellulose-binding (CBM1) domain inhibited GH10 xylanase activities for pure xylan, but afforded them an ability to hydrolyze washed corncob particles (WCCP)...
November 23, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27875966/recombinant-approaches-for-microbial-xylanases-recent-advances-and-perspectives
#15
Moumita Basu, Vishal Kumar, Pratyoosh Shukla
Xylanases are crucial enzymes to hydrolyse the xylan of plant hemicellulose in order to complete the carbon cycle. Xylanases have been used widely in a variety of industries ranging from food and feed industry to pulp and paper industry. Most of the industrial processes which using xylanase requires a thermostable and alkali stable enzyme. Therefore it is desired to produce high thermostable and alkali stable xylanase with high activity. In this review a number of molecular techniques are used in this genomic era have been utilized to enhance physiological properties of xylanases for greater commercial application in the industries...
November 22, 2016: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/27873329/one-step-zymogram-method-for-the-simultaneous-detection-of-cellulase-xylanase-activity-and-molecular-weight-estimation-of-the-enzyme
#16
Claudia Cano-Ramírez, Alejandro Santiago-Hernández, Flor Nohemí Rivera-Orduña, Rosa María Pineda-Mendoza, Gerardo Zúñiga, María Eugenia Hidalgo-Lara
Here, we describe a zymographic method for the simultaneous detection of enzymatic activity and molecular weight (MW) estimation, following a single electrophoresis step. This involved separating cellulase and xylanase activities from bacteria and fungi, obtained from different sources, such as commercial extracts, crude extract and purified proteins, under denaturing conditions, by 10% polyacrylamide gel electrophoresis, using polyacrylamide gels copolymerized with 1% (w/v) carboxymethylcellulose or beechwood xylan as substrates...
November 22, 2016: Electrophoresis
https://www.readbyqxmd.com/read/27871388/the-family-22-carbohydrate-binding-module-of-bifunctional-xylanase-%C3%AE-glucanase-xyn10e-from-paenibacillus-curdlanolyticus-b-6-has-an-important-role-in-lignocellulose-degradation
#17
Junjarus Sermsathanaswadi, Sirilak Baramee, Chakrit Tachaapaikoon, Patthra Pason, Khanok Ratanakhanokchai, Akihiko Kosugi
A newly isolated endo-β-1,4-xylanase (Xyn10E) from Paenibacillus curdlanolyticus B-6 has a modular structure consisting of a family 22 carbohydrate-binding module (CBM), a glycoside hydrolase (GH) family 10 catalytic domain, two fibronectin type III (Fn3) domains, and a family 3 CBM at the C-terminus. Intact Xyn10E (rXyn10E), CBM22-deleted Xyn10E (X-CBM3), CBM3-deleted Xyn10E (X-CBM22), and GH10 catalytic domain only (X-GH10) were expressed in Escherichia coli. rXyn10E showed bifunctional degradation activity toward xylan and β-glucan and also degraded microcrystalline cellulose...
January 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/27871378/deciphering-the-factors-defining-the-ph-dependence-of-a-commercial-glycoside-hydrolase-family-8-enzyme
#18
Mário Barroca, Gustavo Santos, Björn Johansson, Florian Gillotin, Georges Feller, Tony Collins
A prerequisite to the use of any enzyme in any industrial process is an understanding of its activity and stability under process conditions. Glycoside hydrolase family 8 enzymes include many important biotechnological biocatalysts yet little is known of the performance of these with respect to pH. A better understanding of this parameter and its relationship to structure and function in these enzymes will allow for an improved use of these in industry as well as an enhanced ability in their engineering and optimisation for a particular application...
January 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/27866295/characterization-of-a-neutral-recombinant-xylanase-from-thermoactinospora-rubra-yim-77501-t
#19
Yi-Rui Yin, Qing-Wen Hu, Wen-Dong Xian, Feng Zhang, En-Min Zhou, Hong Ming, Min Xiao, Xiao-Yang Zhi, Wen-Jun Li
A xylanase gene (TrXyn10) from Thermoactinospora rubra YIM 77501(T) was cloned and expressed in Escherichia coli. The amino acid sequence displayed 78% homology with Microbispora mesophila xylanase (WP_062413927.1). The recombinant xylanase (TrXyn10), with MW 46.1 kDa, could hydrolyse beechwood, birchwood and oatspelt xylan. Based on the sequence, enzymatic properties and tertiary structure of the protein, TrXyn10 belongs to glycoside hydrolase family 10 (GH10). The optimal pH and temperature for the recombinant enzyme were determined to be 7...
November 19, 2016: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/27833656/metagenomic-and-metaproteomic-analyses-of-a-corn-stover-adapted-microbial-consortium-emsd5-reveal-its-taxonomic-and-enzymatic-basis-for-degrading-lignocellulose
#20
Ning Zhu, Jinshui Yang, Lei Ji, Jiawen Liu, Yi Yang, Hongli Yuan
BACKGROUND: Microbial consortia represent promising candidates for aiding in the development of plant biomass conversion strategies for biofuel production. However, the interaction between different community members and the dynamics of enzyme complements during the lignocellulose deconstruction process remain poorly understood. We present here a comprehensive study on the community structure and enzyme systems of a lignocellulolytic microbial consortium EMSD5 during growth on corn stover, using metagenome sequencing in combination with quantitative metaproteomics...
2016: Biotechnology for Biofuels
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