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Glycoside hydrolase

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https://www.readbyqxmd.com/read/28338992/identification-of-the-eucalyptus-grandis-chitinase-gene-family-and-expression-characterization-under-different-biotic-stress-challenges
#1
Peri A Tobias, Nanette Christie, Sanushka Naidoo, David I Guest, Carsten Külheim
Eucalyptus grandis (W. Hill ex Maiden) is an Australian Myrtaceae tree grown for timber in many parts of the world and for which the annotated genome sequence is available. Known to be susceptible to a number of pests and diseases, E. grandis is a useful study organism for investigating defense responses in woody plants. Chitinases are widespread in plants and cleave glycosidic bonds of chitin, the major structural component of fungal cell walls and arthropod exoskeletons. They are encoded by an important class of genes known to be up-regulated in plants in response to pathogens...
March 13, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28330074/catalytic-properties-functional-attributes-and-industrial-applications-of-%C3%AE-glucosidases
#2
Gopal Singh, A K Verma, Vinod Kumar
β-Glucosidases are diverse group of enzymes with great functional importance to biological systems. These are grouped in multiple glycoside hydrolase families based on their catalytic and sequence characteristics. Most studies carried out on β-glucosidases are focused on their industrial applications rather than their endogenous function in the target organisms. β-Glucosidases performed many functions in bacteria as they are components of large complexes called cellulosomes and are responsible for the hydrolysis of short chain oligosaccharides and cellobiose...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328971/mapping-the-n-linked-glycosites-of-rice-oryza-sativa-l-germinating-embryos
#3
Jiezheng Ying, Juan Zhao, Yuxuan Hou, Yifeng Wang, Jiehua Qiu, Zhiyong Li, Xiaohong Tong, Zhaomei Shi, Jun Zhu, Jian Zhang
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered...
2017: PloS One
https://www.readbyqxmd.com/read/28319083/structures-of-human-o-glcnacase-and-its-complexes-reveal-a-new-substrate-recognition-mode
#4
Baobin Li, Hao Li, Lei Lu, Jiaoyang Jiang
Human O-GlcNAcase (hOGA) is the unique enzyme responsible for the hydrolysis of the O-linked β-N-acetyl glucosamine (O-GlcNAc) modification, an essential protein glycosylation event that modulates the function of numerous cellular proteins in response to nutrients and stress. Here we report crystal structures of a truncated hOGA, which comprises the catalytic and stalk domains, in apo form, in complex with an inhibitor, and in complex with a glycopeptide substrate. We found that hOGA forms an unusual arm-in-arm homodimer in which the catalytic domain of one monomer is covered by the stalk domain of the sister monomer to create a substrate-binding cleft...
March 20, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28314725/a-genome-survey-and-postharvest-transcriptome-analysis-in-lentinula-edodes
#5
Yuichi Sakamoto, Keiko Nakade, Shiho Sato, Kentaro Yoshida, Kazuhiro Miyazaki, Satoshi Natsume, Naotake Konno
Lentinula edodes is a popular cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction of Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and long reads by PacBio, resulting in a contig number of 1951 and an N50 of 1 Mb. Further, we predicted genes by Augustus using RNA-seq data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28303907/crystal-structure-of-a-raw-starch-degrading-bacterial-%C3%AE-amylase-belonging-to-subfamily-37-of-the-glycoside-hydrolase-family-gh13
#6
Yanhong Liu, Jigang Yu, Fudong Li, Hui Peng, Xuecheng Zhang, Yazhong Xiao, Chao He
Subfamily 37 of the glycoside hydrolase family GH13 was recently established on the basis of the discovery of a novel α-amylase, designated AmyP, from a marine metagenomic library. AmyP exhibits raw-starch-degrading activity and consists of an N-terminal catalytic domain and a C-terminal starch-binding domain. To understand this newest subfamily, we determined the crystal structure of the catalytic domain of AmyP, named AmyPΔSBD, complexed with maltose, and the crystal structure of the E221Q mutant AmyPΔSBD complexed with maltotriose...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28303550/enhancement-of-active-compound-genipin-from-gardeniae-fructus-using-immobilized-glycosyl-hydrolase-family-3-%C3%AE-glucosidase-from-lactobacillus-antri
#7
Young Soo Kim, Chung-Jo Lee, Jin Yeul Ma
Geniposide is an iridoid glycoside, which is abundant in Gardeniae Fructus. Despite the various pharmaceutical effects of geniposide on a human body, its hydrolysis into a smaller molecule, genipin, by β-glucosidase produced by bacteria in the intestines is particularly important to improve geniposide uptake into the body. Since geniposide is much more abundant in Gardeniae Fructus than its aglycone genipin, we herein transformed geniposide into genipin using purified recombinant β-glucosidase from Lactobacillus antri (rBGLa), which was expressed in Escherichia coli to enhance the genipin content...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28302998/distribution-and-diversity-of-enzymes-for-polysaccharide-degradation-in-fungi
#8
Renaud Berlemont
Fungi are important polysaccharide degraders in the environment and for biotechnology. Here, the increasing number of sequenced fungal genomes allowed for systematic identification of genes and proteins involved in polysaccharide degradation in 218 fungi. Globally, 9,003 sequences for glycoside hydrolases and lytic polysaccharide mono-oxygenases targeting cellulose, xylan, and chitin, were identified. Although abundant in most lineages, the distribution of these enzymes is variable even between organisms from the same genus...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28295743/characterization-of-surface-binding-sites-in-glycoside-hydrolases-a-computational-study
#9
Samaneh Samaei-Daryan, Bahram Goliaei, Azadeh Ebrahim-Habibi
Structural properties of carbohydrate surface binding sites (SBSs) were investigated with computational methods. Eighty-five SBSs of 44 enzymes in 119 Protein Data Bank (PDB) files were collected as a dataset. On the basis of SBSs shape, they were divided into 3 categories: flat surfaces, clefts, and cavities (types A, B, and C, respectively). Ligand varieties showed the correlation between shape of SBSs and ligands size. To reduce cut-off differences in each SBSs with different ligand size, molecular docking were performed...
March 15, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28291519/structural-studies-of-neurospora-crassa-lpmo9d-and-redox-partner-cdhiia-using-neutron-crystallography-and-small-angle-scattering
#10
Annette M Bodenheimer, William B O'Dell, Christopher B Stanley, Flora Meilleur
Sensitivity to hydrogen/deuterium and lack of observable radiation damage makes cold neutrons an ideal probe the structural studies of proteins with highly photosensitive groups such as the copper center of lytic polysaccharide monooxygenases (LPMOs) and flavin adenine dinucleotide (FAD) and heme redox cofactors of cellobiose dehydrogenases (CDHs). Here, neutron crystallography and small-angle neutron scattering are used to investigate Neurospora crassa LPMO9D (NcLPMO9D) and CDHIIA (NcCDHIIA), respectively...
March 4, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28287181/a-new-group-of-glycoside-hydrolase-family-13-%C3%AE-amylases-with-an-aberrant-catalytic-triad
#11
Fean D Sarian, Štefan Janeček, Tjaard Pijning, Ihsanawati, Zeily Nurachman, Ocky K Radjasa, Lubbert Dijkhuizen, Dessy Natalia, Marc J E C van der Maarel
α-Amylases are glycoside hydrolase enzymes that act on the α(1→4) glycosidic linkages in glycogen, starch, and related α-glucans, and are ubiquitously present in Nature. Most α-amylases have been classified in glycoside hydrolase family 13 with a typical (β/α)8-barrel containing two aspartic acid and one glutamic acid residue that play an essential role in catalysis. An atypical α-amylase (BmaN1) with only two of the three invariant catalytic residues present was isolated from Bacillus megaterium strain NL3, a bacterial isolate from a sea anemone of Kakaban landlocked marine lake, Derawan Island, Indonesia...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28284522/in-depth-analysis-of-rumen-microbial-and-carbohydrate-active-enzymes-profile-in-indian-crossbred-cattle
#12
V Lyju Jose, Ravi P More, Thulasi Appoothy, A Sha Arun
Rumen houses a plethora of symbiotic microorganisms empowering the host to hydrolyze plant lignocellulose. In this study, NGS based metagenomic approach coupled with bioinformatic analysis was employed to gain an insight into the deconstruction of lignocellulose by carbohydrate-active enzymes (CAZymes) in Indian crossbred Holstein-Friesian cattle. Cattle rumen metagenomic DNA was sequenced using Illumina-MiSeq and 1.9 gigabases of data generated with an average read length of 871 bp. Analysis of the assembled sequences by Pfam-based Carbohydrate-active enzyme Analysis Toolkit identified 17,164 putative protein-encoding CAZymes belonging to different families of glycoside hydrolases (7574), glycosyltransferases (5185), carbohydrate-binding modules (2418), carbohydrate esterases (1516), auxiliary activities (434) and polysaccharide lyases (37)...
February 28, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28283459/characterization-of-novel-thermophilic-alpha-glucosidase-from-bifidobacterium-longum
#13
Na-Ri Kim, Da-Woon Jeong, Dam-Seul Ko, Jae-Hoon Shim
In this study, the gene encoding α-glucosidase from Bifidobacterium longum subsp. longum JCM1217 (BLAG) was cloned and expressed in Escherichia coli. The amino acid sequence alignment demonstrated that BLAG belongs to glycoside hydrolase (GH) family 13. The optimal temperature for enzyme activity was 75°C; about 80% of the catalytic activity was lost at 50°C, which is very unusual for enzymes from the Bifidobacterium genus. In the presence of 5mM of Co(2+) and Ca(2+), enzyme activity was reduced to 47% and 48%, respectively...
March 7, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28273103/functional-metagenomics-reveals-novel-%C3%AE-galactosidases-not-predictable-from-gene-sequences
#14
Jiujun Cheng, Tatyana Romantsov, Katja Engel, Andrew C Doxey, David R Rose, Josh D Neufeld, Trevor C Charles
The techniques of metagenomics have allowed researchers to access the genomic potential of uncultivated microbes, but there remain significant barriers to determination of gene function based on DNA sequence alone. Functional metagenomics, in which DNA is cloned and expressed in surrogate hosts, can overcome these barriers, and make important contributions to the discovery of novel enzymes. In this study, a soil metagenomic library carried in an IncP cosmid was used for functional complementation for β-galactosidase activity in both Sinorhizobium meliloti (α-Proteobacteria) and Escherichia coli (γ-Proteobacteria) backgrounds...
2017: PloS One
https://www.readbyqxmd.com/read/28270506/biochemical-and-structural-analyses-of-a-bacterial-endo-%C3%AE-1-2-glucanase-reveal-a-new-glycoside-hydrolase-family
#15
Koichi Abe, Masahiro Nakajima, Tetsuro Yamashita, Hiroki Matsunaga, Shinji Kamisuki, Takanori Nihira, Yuta Takahashi, Naohisa Sugimoto, Akimasa Miyanaga, Hiroyuki Nakai, Takatoshi Arakawa, Shinya Fushinobu, Hayao Taguchi
β-1,2-Glucan is an extracellular cyclic or linear polysaccharide from Gram-negative bacteria, with important roles in infection and symbiosis. Despite β-1,2-glucan's importance in bacterial persistence and pathogenesis, only few reports exist on enzymes acting on both cyclic and linear β-1,2-glucan. To this end, we purified an endo-β-1,2-glucanase to homogeneity from cell extracts of the environmental species Chitinophaga arvensicola, and an endo-β-1,2-glucanase candidate gene (Cpin_6279) was cloned from the related species Chitinophaga pinensis...
March 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28265262/genomic-analysis-of-caldithrix-abyssi-the-thermophilic-anaerobic-bacterium-of-the-novel-bacterial-phylum-calditrichaeota
#16
Ilya V Kublanov, Olga M Sigalova, Sergey N Gavrilov, Alexander V Lebedinsky, Christian Rinke, Olga Kovaleva, Nikolai A Chernyh, Natalia Ivanova, Chris Daum, T B K Reddy, Hans-Peter Klenk, Stefan Spring, Markus Göker, Oleg N Reva, Margarita L Miroshnichenko, Nikos C Kyrpides, Tanja Woyke, Mikhail S Gelfand, Elizaveta A Bonch-Osmolovskaya
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28261179/characterization-of-potential-polysaccharide-utilization-systems-in-the-marine-bacteroidetes-gramella-flava-jlt2011-using-a-multi-omics-approach
#17
Kai Tang, Yingfan Lin, Yu Han, Nianzhi Jiao
Members of phylum Bacteroidetes are distributed across diverse marine niches and Flavobacteria is often the predominant bacterial class decomposing algae-derived polysaccharides. Here, we report the complete genome of Gramella flava JLT2011 (Flavobacteria) isolated from surface water of the southeastern Pacific. A remarkable genomic feature is that the number of glycoside hydrolase (GH) genes in the genome of G. flava JLT2011 is more than 2-fold higher than that of other Gramella species. The functional profiles of the GHs suggest extensive variation in Gramella species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28257170/downregulation-of-rwa-genes-in-hybrid-aspen-affects-xylan-acetylation-and-wood-saccharification
#18
Prashant Mohan-Anupama Pawar, Christine Ratke, Vimal K Balasubramanian, Sun-Li Chong, Madhavi Latha Gandla, Mathilda Adriasola, Tobias Sparrman, Mattias Hedenström, Klaudia Szwaj, Marta Derba-Maceluch, Cyril Gaertner, Gregory Mouille, Ines Ezcurra, Maija Tenkanen, Leif J Jönsson, Ewa J Mellerowicz
High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21...
March 3, 2017: New Phytologist
https://www.readbyqxmd.com/read/28254341/identification-of-an-acidic-endo-polygalacturonase-from-penicillium-oxalicum-cz1028-and-its-broad-use-in-major-tropical-and-subtropical-fruit-juices-production
#19
Zhong Cheng, Dong Chen, Qingyan Wang, Liang Xian, Bo Lu, Yutuo Wei, Hongchi Tang, Zhilong Lu, Qixia Zhu, Yunlai Chen, Ribo Huang
Endo-polygalacturonases play an important role on depectinization in fruit juices industry. A putative endo-polygalacturonase gene PoxaEnPG28A was cloned from Penicillium oxalicum CZ1028. PoxaEnPG28A consisted of a putative signal peptide and a catalytic domain belonging to glycoside hydrolase family 28, and it shared 72% identity with that of a functionally characterized endo-polygalacturonase from Trichoderma harzianum. Gene PoxaEnPG28A was successfully expressed in Pichia pastoris with a high yield of 1828...
February 18, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28251851/development-and-application-of-cyclodextrin-hydrolyzing-mutant-enzyme-which-hydrolyzes-%C3%AE-and-%C3%AE-cd-selectively
#20
Ye-Seul Koo, Dam-Seul Ko, Da-Woon Jeong, Jae-Hoon Shim
Cyclodextrins (CDs) are produced from starch by cyclodextrin glucanotransferase (CGTase), which has cyclization activity. Specifically, α-CD is an important biomolecule, as it is a molecular carrier and soluble dietary fiber used in the food industry. Upon inspection of the conserved regions of the glycoside hydrolase (GH) 13 family amylases, the amino acids K232 and H233 of CGTase were identified as playing an important role in enzyme reaction specificity. A novel CD hydrolyzing enzyme, cyclodextrin glycosyl transferase (CGTase)-alpha, was developed using site-directed mutagenesis at these positions...
March 7, 2017: Journal of Agricultural and Food Chemistry
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