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Glycoside hydrolase

Stefan Becker, André Scheffel, Martin F Polz, Jan-Hendrik Hehemann
Marine algae produce varieties of glycans, which fulfill diverse biological functions and fuel the carbon and energy demand of heterotrophic microbes. A common approach to analyze marine organic matter uses acid to hydrolyze its glycans into measurable monosaccharides. These, however, may derive from different glycans that are built with the same monosaccharides, hence this approach does not distinguish between glycans in natural samples. Here we use enzymes to selectively digest and thereby quantify laminarin in particulate organic matter...
February 17, 2017: Applied and Environmental Microbiology
Yue-Jing Gui, Jie-Yin Chen, Dan-Dan Zhang, Nan-Yang Li, Ting-Gang Li, Wen-Qi Zhang, Xin-Yan Wang, Dylan P G Short, Lei Li, Wei Guo, Zhi-Qiang Kong, Yu-Ming Bao, Krishna V Subbarao, Xiao-Feng Dai
Glycoside hydrolase 12 (GH12) proteins act as virulence factors and pathogen-associated molecular patterns (PAMPs) in oomycetes. However, the pathogenic mechanisms of fungal GH12 proteins have not been characterized. In this study, we demonstrated that two of the six GH12 proteins produced by the fungus Verticillium dahliae Vd991, VdEG1 and VdEG3 acted as PAMPs to trigger cell death and PAMP-triggered immunity (PTI) independent of their enzymatic activity in Nicotiana benthamiana. A 63-amino-acid peptide of VdEG3 was sufficient for cell death-inducing activity, but this was not the case for the corresponding peptide of VdEG1...
February 15, 2017: Environmental Microbiology
Bokun Lin, Yan Liu, Guoyong Lu, Min Zhao, Zhong Hu
No abstract text is available yet for this article.
February 15, 2017: FEMS Microbiology Letters
Masahiro Nakajima, Nobukiyo Tanaka, Nayuta Furukawa, Takanori Nihira, Yuki Kodutsumi, Yuta Takahashi, Naohisa Sugimoto, Akimasa Miyanaga, Shinya Fushinobu, Hayao Taguchi, Hiroyuki Nakai
Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crystal structure. LpSOGP is a monomeric enzyme that contains a unique β-sandwich domain (Ndom1) at its N-terminus. Unlike the dimeric GH94 enzymes possessing catalytic pockets at their dimer interface, LpSOGP has a catalytic pocket between Ndom1 and the catalytic domain...
February 15, 2017: Scientific Reports
Salvatore Montella, Valeria Ventorino, Vincent Lombard, Bernard Henrissat, Olimpia Pepe, Vincenza Faraco
In this study, a high-throughput sequencing approach was applied to discover novel biocatalysts for lignocellulose hydrolysis from three dedicated energy crops, Arundo donax, Eucalyptus camaldulensis and Populus nigra, after natural biodegradation. The microbiomes of the three lignocellulosic biomasses were dominated by bacterial species (approximately 90%) with the highest representation by the Streptomyces genus both in the total microbial community composition and in the microbial diversity related to GH families of predicted ORFs...
February 15, 2017: Scientific Reports
Mari Hayashi, Ryuichiro Suzuki, Christophe Colleoni, Steven G Ball, Naoko Fujita, Eiji Suzuki
Branching enzyme (BE) catalyzes the formation of α-1,6-glucosidic linkages in amylopectin and glycogen. The reaction products are variable depending on the organism sources, and the mechanistic basis for these different outcomes is unclear. Although most cyanobacteria have only one BE isoform belonging to glycoside hydrolase (GH) family 13, Cyanothece sp. ATCC 51142 has three isoforms (BE1, BE2, and BE3) with distinct enzymatic properties, suggesting that investigations of these enzymes might provide unique insights into this system...
February 13, 2017: Journal of Biological Chemistry
Jian Gao, Jian-Wen Huang, Qian Li, Weidong Liu, Tzu-Ping Ko, Yingying Zheng, Xiansha Xiao, Chih-Jung Kuo, Chun-Chi Chen, Rey-Ting Guo
1,4-β-Endoglucanase is one of the most important biocatalysts in modern industries. Here, a glycoside hydrolase (GH) family 45 endoglucanase from thermophilic fungus Theilavia terrestris (TtCel45A) was expressed in Pichia pastoris. The recombinant protein shows optimal activity at 60°C, pH 4-5. The enzyme exhibits extraordinary thermostability that more than 80% activity was detected after heating at 80°C for 2.5h. The high resolution crystal structures of apo-form enzyme and that in complex with cellobiose and cellotetraose were solved to 1...
April 2017: Enzyme and Microbial Technology
Xiaoyu Chang, Bo Xu, Yingguo Bai, Huiying Luo, Rui Ma, Pengjun Shi, Bin Yao
N-Glycosylation is a posttranslational modification commonly occurred in fungi and plays roles in a variety of enzyme functions. In this study, a xylanase (Af-XYNA) of glycoside hydrolase (GH) family 10 from Aspergillus fumigatus harboring three potential N-glycosylation sites (N87, N124 and N335) was heterologously produced in Pichia pastoris. The N-glycosylated Af-XYNA (WT) exhibited favorable temperature and pH optima (75°C and pH 5.0) and good thermostability (maintaining stable at 60°C). To reveal the role of N-glycosylation on Af-XYNA, the enzyme was deglycosylated by endo-β-N-acetylglucosaminidase H (DE) or modified by site-directed mutagenesis at N124 (N124T)...
2017: PloS One
Johnnie A Walker, Sivakumar Pattathil, Lai F Bergeman, Emily T Beebe, Kai Deng, Maryam Mirzai, Trent R Northen, Michael G Hahn, Brian G Fox
BACKGROUND: Glycoside hydrolases (GHs) are enzymes that hydrolyze polysaccharides into simple sugars. To better understand the specificity of enzyme hydrolysis within the complex matrix of polysaccharides found in the plant cell wall, we studied the reactions of individual enzymes using glycome profiling, where a comprehensive collection of cell wall glycan-directed monoclonal antibodies are used to detect polysaccharide epitopes remaining in the walls after enzyme treatment and quantitative nanostructure initiator mass spectrometry (oxime-NIMS) to determine soluble sugar products of their reactions...
2017: Biotechnology for Biofuels
Soohui Na, Minjeong Park, Inseong Jo, Jaeho Cha, Nam-Chul Ha
Glycogen branching enzyme (GBE) catalyzes the formation of α-1,6-branching points during glycogenesis by cleaving α-1,4 bonds and making new α-1,6 bonds. Most GBEs belong to the glycoside hydrolase 13 family (GH13), but new GBEs in the GH57 family have been isolated from Archaea. Here, we determined the crystal structure of a GH57 GBE from the hyperthermophilic archaeon Pyrococcus horikoshii (PhGBE) at a resolution of 2.3 Å. PhGBE exhibits both α-1,6-branching activity and endo-α-1,4 hydrolytic activity...
February 2, 2017: Biochemical and Biophysical Research Communications
Md Imran, Poonam Pant, Yogini P Shanbhag, Samir V Sawant, Sanjeev C Ghadi
Microbulbifer mangrovi strain DD-13(T) is a novel-type species isolated from the mangroves of Goa, India. The draft genome sequence of strain DD-13 comprised 4,528,106 bp with G+C content of 57.15%. Out of 3479 open reading frames, functions for 3488 protein coding sequences were predicted on the basis of similarity with the cluster of orthologous groups. In addition to protein coding sequences, 34 tRNA genes and 3 rRNA genes were detected. Analysis of nucleotide sequence of predicted gene using a Carbohydrate-Active Enzymes (CAZymes) Analysis Toolkit indicates that strain DD-13 encodes a large set of CAZymes including 255 glycoside hydrolases, 76 carbohydrate esterases, 17 polysaccharide lyases, and 113 carbohydrate-binding modules (CBMs)...
February 4, 2017: Marine Biotechnology
Julie M Grondin, Da Duan, Alyssa C Kirlin, Kento T Abe, Seth Chitayat, Holly L Spencer, Craig Spencer, Alisha Campigotto, Scott Houliston, Cheryl H Arrowsmith, John S Allingham, Alisdair B Boraston, Steven P Smith
Clostridium perfringens is a commensal member of the human gut microbiome and an opportunistic pathogen whose genome encodes a suite of putative large, multi-modular carbohydrate-active enzymes that appears to play a role in the interaction of the bacterium with mucin-based carbohydrates. Among the most complex of these is an enzyme that contains a presumed catalytic module belonging to glycoside hydrolase family 31 (GH31). This large enzyme, which based on its possession of a GH31 module is a predicted α-glucosidase, contains a variety of non-catalytic ancillary modules, including three CBM32 modules that to date have not been characterized...
2017: PloS One
Hong Keat Looi, Yue Fen Toh, Su Mei Yew, Shiang Ling Na, Yung-Chie Tan, Pei-Sin Chong, Jia-Shiun Khoo, Wai-Yan Yee, Kee Peng Ng, Chee Sian Kuan
Corynespora cassiicola is a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011; Nghia et al., 2008). The isolation of UM 591 from a patient's contact lens indicates the pathogenic potential of this dematiaceous fungus in human. However, the underlying factors that contribute to the opportunistic cross-infection have not been fully studied. We employed genome sequencing and gene homology annotations in attempt to identify these factors in UM 591 using data obtained from publicly available bioinformatics databases...
2017: PeerJ
Xukai Jiang, Wen Li, Guanjun Chen, Lushan Wang
The temperature dependence of enzyme catalysis is highly debated. Specifically, how high temperatures induce enzyme inactivation has broad implications for both fundamental and applied science. Here, we explored the mechanism of the reversible thermal inactivation in glycoside hydrolase family 12 (GH12) using comparative molecular dynamics simulations. First, we investigated the distribution of structural flexibility over the enzyme and found that the active site was the general thermal-sensitive region in GH12 cellulases...
February 1, 2017: Journal of Chemical Information and Modeling
Shouhei Mine, Masahiro Watanabe, Saori Kamachi, Yoshito Abe, Tadashi Ueda
The archaeal exo-β-D-glucosaminidase (GlmA) is a dimeric enzyme that hydrolyzes chitosan oligosaccharides into monomer glucosamines. GlmA is a member of the glycosidase hydrolase (GH)-A superfamily-subfamily 35 and is a novel enzyme in terms of its primary structure. Here, we present the crystal structure of GlmA in complex with glucosamine at 1.27-Å resolution. The structure reveals that a monomeric form of GlmA shares structural homology with GH42 β-galactosidases, whereas most of the spatial positions of the active site residues are identical to those of GH35 β-galactosidases...
January 27, 2017: Journal of Biological Chemistry
Gerald N Presley, Jonathan S Schilling
: Brown rot fungi are wood-degrading fungi that employ both oxidative and hydrolytic mechanisms to degrade wood. Hydroxyl radicals that facilitate the oxidative component are powerful non-selective oxidants and are incompatible with hydrolytic enzymes unless they are spatially segregated in wood. Differential gene expression has been implicated in Postia placenta to segregate these reactions, but it is unclear if this two-step mechanism varies in other brown rot fungi with different traits and life history strategies, and that occupy different niches in nature...
January 27, 2017: Applied and Environmental Microbiology
Ayyappa Kumar Sista Kameshwar, Wensheng Qin
In literature, extensive studies have been conducted on popular wood degrading white rot fungus, Phanerochaete chrysosporium about its lignin degrading mechanisms compared to the cellulose and hemicellulose degrading abilities. This study delineates cellulose and hemicellulose degrading mechanisms through large scale metadata analysis of P. chrysosporium gene expression data (retrieved from NCBI GEO) to understand the common expression patterns of differentially expressed genes when cultured on different growth substrates...
2017: International Journal of Biological Sciences
Mikhail I Kusaykin, Alexey A Belik, Svetlana N Kovalchuk, Pavel S Dmitrenok, Valerii A Rasskazov, Vladimir V Isakov, Tatyana N Zvyagintseva
A specific endo-1,3-β-D-glucanase (GFA) gene was found in genome of marine bacterium Formosa algae KMM 3553. For today this is the only characterized endo-1,3-β-D-glucanase (EC in Formosa genus and the only bacterial EC GH16 endo-1,3-β-D-glucanase with described transglycosylation activity. It was expressed in E. coli and isolated in homogeneous state. Investigating the products of polysaccharides digestion with GFA allowed to establish it's substrate specificity and classify this enzyme as glucan endo-1,3-β-D-glucosidase (EC 3...
February 2017: World Journal of Microbiology & Biotechnology
Shotaro Matsumoto, Hiroyuki Yamada, Yuika Kunishige, Shigeo Takenaka, Masami Nakazawa, Mitsuhiro Ueda, Tatsuji Sakamoto
Rhamnogalacturonan (RG) I is one of the main components of pectins in the plant cell wall. We recently reported two RG I-degrading enzymes, endo-RG and exo-RG lyases, secreted by Penicillium chrysogenum 31B. Here, our aims were to purify a RG rhamnohydrolase (PcRGRH78A) from the culture filtrate of this strain and to characterize this enzyme. On the basis of the internal amino acid sequences, the encoding gene, Pcrgrh78A, was cloned and overexpressed in Aspergillus oryzae. The deduced amino acid sequence of PcRGRH78A is highly similar to an uncharacterized protein belonging to glycoside hydrolase family 78...
March 2017: Enzyme and Microbial Technology
Kiyota Sakai, Mai Mochizuki, Miyuki Yamada, Yuta Shinzawa, Miho Minezawa, Saran Kimoto, Shunsuke Murata, Yuhei Kaneko, Saaya Ishihara, Sadanari Jindou, Tetsuo Kobayashi, Masashi Kato, Motoyuki Shimizu
A β-1,4-mannanase, termed AoMan134A, that belongs to the GH 134 family was identified in the filamentous fungus Aspergillus oryzae. Recombinant AoMan134A was expressed in Pichia pastoris, and the purified enzyme produced mannobiose, mannotriose, mannotetraose, and mannopentaose from galactose-free β-mannan, with mannotriose being the predominant reaction product. The catalytic efficiency (k cat/K m ) of AoMan134A was 6.8-fold higher toward galactomannan from locust bean gum, than toward galactomannan from guar gum, but similar toward galactomannan from locust bean gum and glucomannan from konjac flour...
January 19, 2017: Applied Microbiology and Biotechnology
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