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Bernard Henrissat - One of the best experts on this subject based on the ideXlab platform.
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Discovery of genes coding for carbohydrate-Active Enzyme by metagenomic analysis of lignocellulosic biomasses
Scientific Reports, 2017Co-Authors: Salvatore Montella, Vincent Lombard, Bernard Henrissat, Valeria Ventorino, Olimpia Pepe, Vincenza FaracoAbstract: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. Moreover, the functional clustering of the predicted ORFs showed a prevalence of poorly characterized genes, suggesting these lignocellulosic biomasses are potential sources of as yet unknown genes. 1.2%, 0.6% and 3.4% of the total ORFs detected in A. donax, E. camaldulensis and P. nigra, respectively, were putative Carbohydrate-Active Enzymes (CAZymes). Interestingly, the glycoside hydrolases abundance in P. nigra (1.8%) was higher than that detected in the other biomasses investigated in this study. Moreover, a high percentage of (hemi)cellulases with different activities and accessory Enzymes (mannanases, polygalacturonases and feruloyl esterases) was detected, confirming that the three analyzed samples were a reservoir of diversified biocatalysts required for an effective lignocellulose saccharification.
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the cazy database the carbohydrate Active Enzyme cazy database principles and usage guidelines
2017Co-Authors: Elodie Drula, Pedro M. Coutinho, Vincent Lombard, Bernard Henrissat, Nicolas TerraponAbstract:Carbohydrate-Active Enzymes (CAZymes) assemble, breakdown, and modify glycans and glycoconjugates using their catalytic and binding modules (functional protein domains). The CAZy database offers since 1998 an online and continuously updated classification of CAZyme modules (Lombard et al. 2014). Each module family in the CAZy classification has been created based on experimentally characterized protein modules from the literature, and the families are populated by related module sequences from public protein sequence databases. Since no universal threshold allows the systematic classification of the various CAZyme families, CAZy annotations result from an expert combination of module modeling/calibration and human curation. CAZy annotations are made publicly available for all proteins released by GenBank (Benson et al. 2012), Swiss-Prot (Boutet et al. 2016) and the Protein Data Bank (PDB; http://www.rcsb.org; (Berman et al. 2000)). Further, functional and 3-D structural information, curated from the literature on a regular basis, constitute essential added values to the CAZy annotation. In this spirit, the display of ligand information from crystallographic complexes has been recently developed (Lombard et al. 2014). This chapter will guide the reader through the usage of CAZy to search Enzyme annotations. It will also answer frequent questions such as (i) how to obtain CAZy annotations for a specific protein, a genome, or a metagenome, (ii) how to have a newly characterized family included in the CAZy classification scheme, (iii) why CAZy does not cover all protein families related to glycans/glycoconjugates, and (iv) why CAZy does not transfer functional annotation to similar sequences. Finally, we present here a recent CAZy-associated tool, namely, the Polysaccharide Utilization Loci (PUL) predictor and database in Bacteroidetes species (Terrapon et al. 2015).
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Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2.
Genome Announcements, 2016Co-Authors: Otto Miettinen, Matthieu Hainaut, Robert Riley, Kerrie Barry, Daniel Cullen, Bernard Henrissat, Annele Hatakka, Kristiina HildénAbstract:We report here the first genome sequence of the white-rot fungus Obba rivulosa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate Active Enzyme (CAZy) content for wood-decomposing basidiomycetes.
Jan J. Enghild - One of the best experts on this subject based on the ideXlab platform.
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activated human plasma carboxypeptidase b is retained in the blood by binding to alpha2 macroglobulin and pregnancy zone protein
Journal of Biological Chemistry, 1996Co-Authors: Zuzana Valnickova, Salvatore V. Pizzo, I B Thogersen, Soren Christensen, Jan J. EnghildAbstract:Abstract A 66-kDa glycosylated carboxypeptidase, plasma pro-carboxypeptidase B (pro-plasma CPB), has recently been identified in human blood (Eaton, D. L., Malloy, B. E., Tsai, S. P., Henzel, W., and Drayna, D. (1991) J. Biol. Chem. 266, 21833-21838). The pro-Enzyme binds to plasminogen and the Active Enzyme is specific for COOH-terminal Lys or Arg residues. These properties implicate a role in the fibrinolytic or coagulation system. However, we show that the molecular mass of the Active plasma CPB is approximately 36 kDa, which is below the glomerular filtration limit. Since activated plasma CPB no longer binds plasminogen, the Active Enzyme may not be retained in the circulation. To investigate this, we performed plasma elimination studies in mice which showed that 125I-plasma CPB remains in the circulation despite its small size. Native polyacrylamide gel electrophoresis of blood samples removed from the mice revealed that plasma CPB migrated as a high molecular weight band. Similar bands were observed in vitro when 125I-plasma CPB was added to plasma from humans and other species. The plasma CPB-binding proteins were purified from human plasma and identified as α2-macroglobulin (α2M) and pregnancy zone protein. Only the Active Enzyme bound to the two α-macroglobulins, and the interaction was specific for α2M in its native conformation, but not its receptor recognized forms. The complex between human α2M and plasma CPB dissociated during SDS-polyacrylamide gel electrophoresis and transverse urea gel electrophoresis suggesting that the interaction was noncovalent and depended on the tertiary structure of the native α2M molecule. The catalytic activity of plasma CPB was not significantly affected by its binding to α2M. The specific binding of plasma CPB to α-macroglobulins suggest that these proteins may function as a “shuttle” in vivo to modulate the clearance of plasma CPB from the circulatory system.
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activated human plasma carboxypeptidase b is retained in the blood by binding to alpha2 macroglobulin and pregnancy zone protein
Journal of Biological Chemistry, 1996Co-Authors: Zuzana Valnickova, Salvatore V. Pizzo, I B Thogersen, Soren Christensen, Charleen T Chu, Jan J. EnghildAbstract:Abstract A 66-kDa glycosylated carboxypeptidase, plasma pro-carboxypeptidase B (pro-plasma CPB), has recently been identified in human blood (Eaton, D. L., Malloy, B. E., Tsai, S. P., Henzel, W., and Drayna, D. (1991) J. Biol. Chem. 266, 21833-21838). The pro-Enzyme binds to plasminogen and the Active Enzyme is specific for COOH-terminal Lys or Arg residues. These properties implicate a role in the fibrinolytic or coagulation system. However, we show that the molecular mass of the Active plasma CPB is approximately 36 kDa, which is below the glomerular filtration limit. Since activated plasma CPB no longer binds plasminogen, the Active Enzyme may not be retained in the circulation. To investigate this, we performed plasma elimination studies in mice which showed that 125I-plasma CPB remains in the circulation despite its small size. Native polyacrylamide gel electrophoresis of blood samples removed from the mice revealed that plasma CPB migrated as a high molecular weight band. Similar bands were observed in vitro when 125I-plasma CPB was added to plasma from humans and other species. The plasma CPB-binding proteins were purified from human plasma and identified as α2-macroglobulin (α2M) and pregnancy zone protein. Only the Active Enzyme bound to the two α-macroglobulins, and the interaction was specific for α2M in its native conformation, but not its receptor recognized forms. The complex between human α2M and plasma CPB dissociated during SDS-polyacrylamide gel electrophoresis and transverse urea gel electrophoresis suggesting that the interaction was noncovalent and depended on the tertiary structure of the native α2M molecule. The catalytic activity of plasma CPB was not significantly affected by its binding to α2M. The specific binding of plasma CPB to α-macroglobulins suggest that these proteins may function as a “shuttle” in vivo to modulate the clearance of plasma CPB from the circulatory system.
Ethan D Goddardborger - One of the best experts on this subject based on the ideXlab platform.
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structural and mechanistic insights into a bacteroides vulgatus retaining n acetyl β galactosaminidase that uses neighbouring group participation
Chemical Communications, 2016Co-Authors: Christian Roth, M Petricevic, Alan John, Ethan D Goddardborger, Gideon J Davies, Spencer J WilliamsAbstract:Bacteroides vulgatus is a member of the human microbiota whose abundance is increased in patients with Crohn's disease. We show that a B. vulgatus glycoside hydrolase from the carbohydrate Active Enzyme family GH123, BvGH123, is an N-acetyl-β-galactosaminidase that acts with retention of stereochemistry, and, through a 3-D structure in complex with Gal-thiazoline, provide evidence in support of a neighbouring group participation mechanism.
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fluoro glycosyl acridinones are ultra sensitive Active site titrating agents for retaining β glycosidases
Chemical Communications, 2014Co-Authors: Tianmeng Duo, Ethan D Goddardborger, Stephen G WithersAbstract:Novel fluorogenic 2-deoxy-2-fluoroglycosyl acridinone Active site titrating reagents were synthesised and kinetic parameters determined for their inactivation of two retaining β-glucosidases, a β-galactosidase, a β-xylosidase and several cellulases. Fluorescence-monitored Active site titration using this class of reagents reliably measured Active Enzyme concentrations down to 3 nM.
Zuzana Valnickova - One of the best experts on this subject based on the ideXlab platform.
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activated human plasma carboxypeptidase b is retained in the blood by binding to alpha2 macroglobulin and pregnancy zone protein
Journal of Biological Chemistry, 1996Co-Authors: Zuzana Valnickova, Salvatore V. Pizzo, I B Thogersen, Soren Christensen, Jan J. EnghildAbstract:Abstract A 66-kDa glycosylated carboxypeptidase, plasma pro-carboxypeptidase B (pro-plasma CPB), has recently been identified in human blood (Eaton, D. L., Malloy, B. E., Tsai, S. P., Henzel, W., and Drayna, D. (1991) J. Biol. Chem. 266, 21833-21838). The pro-Enzyme binds to plasminogen and the Active Enzyme is specific for COOH-terminal Lys or Arg residues. These properties implicate a role in the fibrinolytic or coagulation system. However, we show that the molecular mass of the Active plasma CPB is approximately 36 kDa, which is below the glomerular filtration limit. Since activated plasma CPB no longer binds plasminogen, the Active Enzyme may not be retained in the circulation. To investigate this, we performed plasma elimination studies in mice which showed that 125I-plasma CPB remains in the circulation despite its small size. Native polyacrylamide gel electrophoresis of blood samples removed from the mice revealed that plasma CPB migrated as a high molecular weight band. Similar bands were observed in vitro when 125I-plasma CPB was added to plasma from humans and other species. The plasma CPB-binding proteins were purified from human plasma and identified as α2-macroglobulin (α2M) and pregnancy zone protein. Only the Active Enzyme bound to the two α-macroglobulins, and the interaction was specific for α2M in its native conformation, but not its receptor recognized forms. The complex between human α2M and plasma CPB dissociated during SDS-polyacrylamide gel electrophoresis and transverse urea gel electrophoresis suggesting that the interaction was noncovalent and depended on the tertiary structure of the native α2M molecule. The catalytic activity of plasma CPB was not significantly affected by its binding to α2M. The specific binding of plasma CPB to α-macroglobulins suggest that these proteins may function as a “shuttle” in vivo to modulate the clearance of plasma CPB from the circulatory system.
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activated human plasma carboxypeptidase b is retained in the blood by binding to alpha2 macroglobulin and pregnancy zone protein
Journal of Biological Chemistry, 1996Co-Authors: Zuzana Valnickova, Salvatore V. Pizzo, I B Thogersen, Soren Christensen, Charleen T Chu, Jan J. EnghildAbstract:Abstract A 66-kDa glycosylated carboxypeptidase, plasma pro-carboxypeptidase B (pro-plasma CPB), has recently been identified in human blood (Eaton, D. L., Malloy, B. E., Tsai, S. P., Henzel, W., and Drayna, D. (1991) J. Biol. Chem. 266, 21833-21838). The pro-Enzyme binds to plasminogen and the Active Enzyme is specific for COOH-terminal Lys or Arg residues. These properties implicate a role in the fibrinolytic or coagulation system. However, we show that the molecular mass of the Active plasma CPB is approximately 36 kDa, which is below the glomerular filtration limit. Since activated plasma CPB no longer binds plasminogen, the Active Enzyme may not be retained in the circulation. To investigate this, we performed plasma elimination studies in mice which showed that 125I-plasma CPB remains in the circulation despite its small size. Native polyacrylamide gel electrophoresis of blood samples removed from the mice revealed that plasma CPB migrated as a high molecular weight band. Similar bands were observed in vitro when 125I-plasma CPB was added to plasma from humans and other species. The plasma CPB-binding proteins were purified from human plasma and identified as α2-macroglobulin (α2M) and pregnancy zone protein. Only the Active Enzyme bound to the two α-macroglobulins, and the interaction was specific for α2M in its native conformation, but not its receptor recognized forms. The complex between human α2M and plasma CPB dissociated during SDS-polyacrylamide gel electrophoresis and transverse urea gel electrophoresis suggesting that the interaction was noncovalent and depended on the tertiary structure of the native α2M molecule. The catalytic activity of plasma CPB was not significantly affected by its binding to α2M. The specific binding of plasma CPB to α-macroglobulins suggest that these proteins may function as a “shuttle” in vivo to modulate the clearance of plasma CPB from the circulatory system.
Zhenglu Yang - One of the best experts on this subject based on the ideXlab platform.
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dbcan2 a meta server for automated carbohydrate Active Enzyme annotation
Nucleic Acids Research, 2018Co-Authors: Han Zhang, Le Huang, Sarah Entwistle, Tanner Yohe, Zhenglu Yang, Peter Kamp Busk, Yanbin YinAbstract:Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate Active Enzymes (CAZymes) are the most important Enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes. Here, dbCAN2 (http://cys.bios.niu.edu/dbCAN2) is presented as an updated meta server, which integrates three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme sequence database and (iii) Hotpep search against the conserved CAZyme short peptide database. Combining the three outputs and removing CAZymes found by only one tool can significantly improve the CAZome annotation accuracy. In addition, dbCAN2 now also accepts nucleotide sequence submission, and offers the service to predict physically linked CAZyme gene clusters (CGCs), which will be a very useful online tool for identifying putative polysaccharide utilization loci (PULs) in microbial genomes or metagenomes.
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dbCAN-seq: a database of carbohydrate-Active Enzyme (CAZyme) sequence and annotation.
Nucleic Acids Research, 2017Co-Authors: Le Huang, Han Zhang, Peizhi Wu, Sarah Entwistle, Xueqiong Li, Tanner Yohe, Haidong Yi, Zhenglu YangAbstract:: Carbohydrate-Active Enzyme (CAZymes) are not only the most important Enzymes for bioenergy and agricultural industries, but also very important for human health, in that human gut microbiota encode hundreds of CAZyme genes in their genomes for degrading various dietary and host carbohydrates. We have built an online database dbCAN-seq (http://cys.bios.niu.edu/dbCAN_seq) to provide pre-computed CAZyme sequence and annotation data for 5,349 bacterial genomes. Compared to the other CAZyme resources, dbCAN-seq has the following new features: (i) a convenient download page to allow batch download of all the sequence and annotation data; (ii) an annotation page for every CAZyme to provide the most comprehensive annotation data; (iii) a metadata page to organize the bacterial genomes according to species metadata such as disease, habitat, oxygen requirement, temperature, metabolism; (iv) a very fast tool to identify physically linked CAZyme gene clusters (CGCs) and (v) a powerful search function to allow fast and efficient data query. With these unique utilities, dbCAN-seq will become a valuable web resource for CAZyme research, with a focus complementary to dbCAN (automated CAZyme annotation server) and CAZy (CAZyme family classification and reference database).
