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Glycoside hydrolase

Tristan Barbeyron, François Thomas, Valérie Barbe, Hanno Teeling, Chantal Schenowitz, Carole Dossat, Alexander Goesmann, Catherine Leblanc, Frank Oliver Glöckner, Mirjam Czjzek, Rudolf Amann, Gurvan Michel
The marine flavobacterium Zobellia galactanivorans Dsij(T) was isolated from a red alga and by now constitutes a model for studying algal polysaccharide bioconversions. We present an in-depth analysis of its complete genome and link it to physiological traits. Z. galactanivorans exhibited the highest gene numbers for glycoside hydrolases, polysaccharide lyases and carbohydrate esterases and the second highest sulfatase gene number in a comparison to 125 other marine heterotrophic bacteria (MHB) genomes. Its genome contains 50 Polysaccharide Utilization Loci, 22 of which contain sulfatase genes...
October 21, 2016: Environmental Microbiology
Hee Jin Lee, In Jung Kim, Hak Jin Youn, Eun Ju Yun, In-Geol Choi, Kyoung Heon Kim
Processivity is a typical characteristic of cellobiohydrolases (CBHs); it enables the enzyme to successively hydrolyze the ends of cellulose chains and to produce cellobiose as the major product. Some microbes, which do not have CBHs, utilize endoglucanases (EGs) that exhibit processivity, commonly referred to as processive EGs. A processive EG identified from Hahella chejuensis, HcCel5, has a catalytic domain (CD) belonging to the glycoside hydrolase family 5 (GH5) and two carbohydrate-binding modules (CBM6s)...
October 19, 2016: Bioprocess and Biosystems Engineering
Tao Song, Hui Xu, Congchong Wei, Tengfei Jiang, Shishang Qin, Weijia Zhang, Yu Cao, Chao Hu, Fan Zhang, Dairong Qiao, Yi Cao
Seaweed is receiving an increasing amount of attention as a "sea vegetable". The microbiota of coastal populations may acquire seaweed associated enzymes through marine food. Several agarases have been found in non-marine environments; however, their origin is unknown. In this study, a hypothetical protein, Aga1, was identified as an agarase from an inland soil agar-degrading bacterium, Paenibacillus sp. SSG-1.Having low similarity to known glycoside hydrolases, Aga1 may be a distant member of the glycoside hydrolase family 86...
October 19, 2016: Scientific Reports
Kaleigh Giles, Benjamin Pluvinage, Alisdair B Boraston
The polysaccharide utilization locus in Bacteroides plebeius that confers the ability to catabolize porphyran contains a putative GH50 β-agarase (BACPLE_01683, BpGH50). BpGH50 did not show any clear activity on agarose or on the related algal galactans porphyran and carrageenan. However, the 1.4 Å resolution x-ray crystal structure of BpGH50 confirmed its possession of the core (α/β)8 barrel fold found in GH50 enzymes as well as the structural conservation of the catalytic residues and some substrate binding residues...
October 18, 2016: Proteins
Hafiz Mamoon Rehman, Zahid Hussain Shah, Muhammad Amjad Nawaz, Muhammad Qadir Ahmad, Seung Hwan Yang, Kang Hee Kho, Gyuhwa Chung
This review provides an insight into the beta-cyanoalanine synthase pathway in higher plants for cyanide (CN) detoxification and describes how it contributes to various physiological activities, such as plant growth and development. In higher plants, CN is produced as a natural toxin through the biosynthesis of ethylene and camalexin, the degradation of glucosinolates and cyanogenic glycosides, the oxidation of amino acids, and the metabolism of glyoxylate and hydroxylamine. To maintain cellular homeostasis by maintaining CN at non-toxic levels, plants have evolved four different biochemical pathways: the β-cyanoalanine synthase pathway (beta-CASP), the thiocyanate pathway, the formamide hydrolase pathway, and the natural release of CN through volatilization...
October 15, 2016: Planta
Diogo R B Ducatti, Madison A Carroll, David L Jakeman
A phosphorolytic activity has been reported for beta-N-acetylglucosaminidases from glycoside hydrolase family 3 (GH3) giving an interesting explanation for an unusual histidine as catalytic acid/base residue and suggesting that members from this family may be phosphorylases [J. Biol. Chem. 2015, 290, 4887]. Here, we describe the characterization of Hsero1941, a GH3 beta-N-acetylglucosaminidase from the endophytic nitrogen-fixing bacterium Herbaspirillum seropedicae SmR1. The enzyme has significantly higher activity against pNP-beta-D-GlcNAcp (Km = 0...
September 23, 2016: Carbohydrate Research
Subin Jung, Byeong-Chul Jeong, Soon-Kwang Hong, Chang-Ro Lee
A novel β-agarase AgaJ11 belonging to the glycoside hydrolase (GH) 16 family was identified from an agar-degrading bacterium Gayadomonas joobiniege G7. AgaJ11 was composed of 317 amino acids (35 kDa), including a 26-amino acid signal peptide, and had the highest similarity (44 % identity) to a putative β-agarase from an agarolytic marine bacterium Agarivorans albus MKT 106. The agarase activity of purified AgaJ11 was confirmed by zymogram analysis. The optimum pH and temperature for AgaJ11 activity were determined to be 4...
October 14, 2016: Applied Biochemistry and Biotechnology
Sirilak Baramee, Thitiporn Teeravivattanakit, Paripok Phitsuwan, Rattiya Waeonukul, Patthra Pason, Chakrit Tachaapaikoon, Akihiko Kosugi, Kazuo Sakka, Khanok Ratanakhanokchai
We recently discovered a novel glycoside hydrolase family 6 (GH6) cellobiohydrolase from Paenibacillus curdlanolyticus B-6 (PcCel6A), which is rarely found in bacteria. This enzyme is a true exo-type cellobiohydrolase which exhibits high substrate specificity on amorphous cellulose and low substrate specificity on crystalline cellulose, while this showed no activity on substitution substrates, carboxymethyl cellulose and xylan, distinct from all other known GH6 cellobiohydrolases. Product profiles, HPLC analysis of the hydrolysis products and a schematic drawing of the substrate-binding subsites catalysing cellooligosaccharides can explain the new mode of action of this enzyme which prefers to hydrolyse cellopentaose...
October 14, 2016: Applied Microbiology and Biotechnology
Kedar Sharma, Arun Dhillon, Arun Goyal
β-mannanases have been shown to play an important role in various biological processes such as the cell wall component degradation, defence signalling in plants, the mobilization of storage reserves and in various industrial processes. To date, glycoside hydrolases (GHs) have been divided into 135 families and 14 clans from A to N based upon their sequence, overall structural fold and function. β-mannanases belong glycoside hydrolases and exist under four different glycoside hydrolase families, GH5, GH26, GH113 and GH134...
October 13, 2016: Current Protein & Peptide Science
Xiujun Zhang, Yinbo Qu, Yuqi Qin
BACKGROUND: Heterochromatin protein 1 (HP1, homologue HepA in Penicillium oxalicum) binding is associated with a highly compact chromatin state accompanied by gene silencing or repression. HP1 loss leads to the derepression of gene expression. We investigated HepA roles in regulating cellulolytic enzyme gene expression, as an increasingly number of studies have suggested that cellulolytic enzyme gene expression is not only regulated by transcription factors, but is also affected by the chromatin status...
2016: Biotechnology for Biofuels
Rebecca C Gregory, Glyn R Hemsworth, Johan P Turkenburg, Samuel J Hart, Paul H Walton, Gideon J Davies
The enzymatic deconstruction of recalcitrant polysaccharide biomass is central to the conversion of these substrates for societal benefit, such as in biofuels. Traditional models for enzyme-catalysed polysaccharide degradation involved the synergistic action of endo-, exo- and processive glycoside hydrolases working in concert to hydrolyse the substrate. More recently this model has been succeeded by one featuring a newly discovered class of mononuclear copper enzymes: lytic polysaccharide monooxygenases (LPMOs; classified as Auxiliary Activity (AA) enzymes in the CAZy classification)...
September 29, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Isabel E Olivera, Katrina C Fins, Sara A Rodriguez, Sumayyah K Abiff, Jaime L Tartar, Aurélien Tartar
BACKGROUND: Although interest in animal pathogenic oomycetes is increasing, the molecular basis mediating oomycete-animal relationships remains virtually unknown. Crinkler (CRN) genes, which have been traditionally associated with the cytotoxic activity displayed by plant pathogenic oomycetes, were recently detected in transcriptome sequences from the entomopathogenic oomycete Lagenidium giganteum, suggesting that these genes may represent virulence factors conserved in both animal and plant pathogenic oomycetes...
October 6, 2016: BMC Microbiology
Son G Nguyen, Jungman Kim, Robin B Guevarra, Ji-Hoon Lee, Eungpil Kim, Su-Il Kim, Tatsuya Unno
We investigated the anti-obesity effects of the potential prebiotic, laminarin, on mice fed a high-fat diet. A metagenomics approach was applied to characterize the ecological and functional differences of gut microbiota among mice fed a normal diet (CTL), a high-fat diet (HFD), and a laminarin-supplemented high-fat diet (HFL). The HFL mice showed a slower weight gain than the HFD mice during the laminarin-feeding period, but the rate of weight gain increased after the termination of laminarin supplementation...
October 12, 2016: Food & Function
Emma L Summers, Christina D Moon, Renee Atua, Vickery L Arcus
Glycoside hydrolase (GH) family 29 consists solely of α-L-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29_0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes. The microbial species that provided the source of this enzyme is unknown. This enzyme contains a second carbohydrate-binding domain at its C-terminal end in addition to the typical N-terminal catalytic domain and carbohydrate-binding domain arrangement of GH29-family proteins...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
Cun-Duo Tang, Hong-Ling Shi, Qing-Hai Tang, Jun-Shi Zhou, Lun-Guang Yao, Zhu-Jin Jiao, Yun-Chao Kan
Two novel glycosyl hydrolase family 5 (GH5) β-mannanases (AoMan5A and AoMan5B) were identified from Aspergillus oryzae RIB40 by genome mining. The AoMan5A contains a predicted family 1 carbohydrate binding module (CBM-1), located at its N-terminal. The AoMan5A, AoMan5B and truncated mutant AoMan5AΔCL (truncating the N-terminal CBM and linker of AoMan5A) were expressed retaining the N-terminus of the native protein in Pichia pastoris GS115 by pPIC9K(M). The specific enzyme activity of the purified reAoMan5A, reAoMan5B and reAoMan5AΔCL towards locust bean gum at pH 3...
November 2016: Enzyme and Microbial Technology
Niël van Wyk, Michel Drancourt, Bernard Henrissat, Laurent Kremer
Glycoside hydrolases (GHs) are enzymes that catalyze the hydrolysis of glycosidic bonds in glycoconjugates, oligo- and polysaccharides. A classification of these enzymes based on conserved sequence and structure motifs supported by the Carbohydrate active enzyme (CAZy) database has proven useful in the systematic groupings of similar enzymes into families.The human pathogen Mycobacterium tuberculosis employs 30 GHs to perform a variety of different functions which can be divided into four broad categories: α-glucan metabolism, peptidoglycan remodelling, β-glycan hydrolysis and α-demannosylation...
October 3, 2016: Glycobiology
Maryam Pourhajibagher, Abbas Bahador
BACKGROUND: Periodontitis is a polymicrobial, chronic, and degenerative disease that can lead to destruction of the teeth-supporting tissues and eventually to loss of teeth. Aggregatibacter actinomycetemcomitans is predominantly associated with periodontal diseases. Outer membrane protein (Omp) 100 is a more important virulence factor of A. actinomycetemcomitans due to the effect of adhesion and invasion into human gingival epithelial cells. Attachment of A. actinomycetemcomitans inhibition is significant in the treatment process...
September 30, 2016: Photodiagnosis and Photodynamic Therapy
Xun Sun, Meng-Dan Qian, Shan-Shan Guan, Ya-Ming Shan, Ying Dong, Hao Zhang, Song Wang, Wei Han
Cel7A from Rasamsonia emersonii is one of the processive endocellulases classified under family 7 glycoside hydrolase. Molecular dynamics simulations were carried out to obtain the optimized sliding and hydrolyzing conformations, in which the reducing ends of sugar chains are located on different sites. Hydrogen bonds are investigated to clarify the interactions between protein and substrate in either conformation. Nine hydrogen bonding interactions are identified in the sliding conformation, and six similar interactions are also found correspondingly in the hydrolyzing conformation...
October 1, 2016: Biopolymers
Chao Zhao, Yanan Chu, Yanhong Li, Chengfeng Yang, Yuqing Chen, Xumin Wang, Bin Liu
OBJECTIVES: To analyze the microbial diversity and gene content of a thermophilic cellulose-degrading consortium from hot springs in Xiamen, China using 454 pyrosequencing for discovering cellulolytic enzyme resources. RESULTS: A thermophilic cellulose-degrading consortium, XM70 that was isolated from a hot spring, used sugarcane bagasse as sole carbon and energy source. DNA sequencing of the XM70 sample resulted in 349,978 reads with an average read length of 380 bases, accounting for 133,896,867 bases of sequence information...
September 30, 2016: Biotechnology Letters
Takatsugu Miyazaki, Atsushi Nishikawa, Takashi Tonozuka
Glycoside hydrolases are divided into two groups, known as inverting and retaining enzymes, based on their hydrolytic mechanisms. Glycoside hydrolase family 63 (GH63) is composed of inverting α-glycosidases, which act mainly on α-glucosides. We previously found that Escherichia coli GH63 enzyme, YgjK, can hydrolyze 2-O-α-d-glucosyl-d-galactose. Two constructed glycosynthase mutants, D324N and E727A, which catalyze the transfer of a β-glucosyl fluoride donor to galactose, lactose, and melibiose. Here, we determined the crystal structures of D324N and E727A soaked with a mixture of glucose and lactose at 1...
September 26, 2016: Journal of Structural Biology
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