The carbohydrate-active ENZYMES database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37:D233-D238

Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, 163 Avenue de Luminy, 13288 Marseille, France.
Nucleic Acids Research (Impact Factor: 9.11). 11/2008; 37(Database issue):D233-8. DOI: 10.1093/nar/gkn663
Source: PubMed

ABSTRACT The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown
complex carbohydrates and glycoconjugates. As of September 2008, the database describes the present knowledge on 113 glycoside
hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families.
These families are created based on experimentally characterized proteins and are populated by sequences from public databases
with significant similarity. Protein biochemical information is continuously curated based on the available literature and
structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification
(i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the
evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties.
This resource has been available for over 10 years to the scientific community, contributing to information dissemination
and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality
of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL:

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    • "Different enzymes within a family share the same conserved active site residues in their GH modules, but contain specific NCR sequences . Several sequence characteristics and functions have been described in NCRs, such as carbohydrate binding modules (CBMs), thrombospondin type 3 repeats (TSP3), and bacterial immunoglobulin-like domains of group 2 (Big2 domains) (Bourne and Henrissat, 2001; Cantarel et al., 2009; Michel et al., 2009). The CBMs in * Corresponding author. "
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    ABSTRACT: A Glycoside hydrolase (GH) typically contains one catalytic module and varied non-catalytic regions (NCRs). However, effects of the NCRs to the catalytic modules remain mostly unclear except the carbohydrate-binding modules (CBMs). AgaG4 is a GH16 endo-β-agarase of the agarolytic marine bacterium Flammeovirga sp. MY04. The enzyme consists of an extra sugar-binding peptide within the catalytic module, with no predictable CBMs but function-unknown sequences in the NCR, which is a new characteristic of agarase sequences. In this study, we deleted the NCR sequence, a 140-amino acid peptide at the C-terminus and expressed the truncated gene, agaG4-T140, in Escherichia coli. After purification and refolding, the truncated agarase rAgaG4-T140 retained the same catalytic temperature and pH value as rAgaG4. Using combined fluorescent labeling, HPLC and MS/MS techniques, we identified the end-products of agarose degradation by rAgaG4-T140 as neoagarotetraose and neoagarohexaose, with a final molar ratio of 1.53:1 and a conversion ratio of approximately 70%, which were similar to those of rAgaG4. However, the truncated agarase rAgaG4-T140 markedly decreased in protein solubility by 15 times and increased in enzymatic activities by 35 times. The oligosaccharide production of rAgaG4-T140 was approximately 25 times the weight of that produced by equimolar rAgaG4. This study provides some insights into the influences of NCR on the biochemical characteristics of agarase AgaG4 and implies some new strategies to improve the properties of a GH enzyme.
    Journal of Ocean University of China 10/2015; 14(5). DOI:10.1007/s11802-015-2800-0 · 0.38 Impact Factor
    • "To profile the glycan digestion enzymes in the various individuals, cDNA contigs and singletons were assigned to CAZy families (Cantarel et al., 2009) using FASTY (e-value < 0.001) on sequence libraries built with the isolated catalytic modules of glycoside hydrolases, polysaccharide lyases, carbohydrate esterases and glycosyltransferases, supplemented with the isolated carbohydrate-binding modules borne by these enzymes. The cDNA libraries sequences were registered to EBI under project number ERA008162. "
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    ABSTRACT: Gut microbiota richness and stability are important parameters in host-microbe symbiosis. Diet modification, notably using dietary fibers, might be a way to restore a high richness and stability in the gut microbiota. In this work, during a six week nutritional trial, 19 healthy adults consumed a basal diet supplemented with 10 or 40 g dietary fiber per day for five days, followed by 15-day washout periods. Fecal samples were analyzed by a combination of 16S rRNA gene pyrosequencing, intestinal cell genotoxicity assay, metatranscriptomics sequencing approach and short chain fatty analysis. This short-term change in the dietary fiber level did not have the same impact for all individuals but remained significant within each individual gut microbiota at genus level. Higher microbiota richness was associated with higher microbiota stability upon increased dietary fiber intake. Increasing fiber modulated the expression of numerous microbiota metabolic pathways such as glycan metabolism, with genes encoding carbohydrate-active enzymes active on fiber or host glycans. High microbial richness was also associated with high proportions of Prevotella and Coprococcus species and high levels of caproate and valerate. This study provides new insights on the role of gut microbial richness in healthy adults upon dietary changes and host microbes' interaction. This article is protected by copyright. All rights reserved.
    Environmental Microbiology 07/2015; DOI:10.1111/1462-2920.13006 · 6.24 Impact Factor
    • "Metagenomic sequences were further searched against the Carbohydrate-Active enZYme (CAZy) database (Cantarel et al., 2009), which is particularly useful for the comparison of carbohydrate metabolic pathways. Comparison of the 6d-brine and 6d-NBW biofilms by SIMPER analysis revealed that the two biofilm groups were enriched with highly different CAZy categories (Fig. S3). "
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    ABSTRACT: The biology of biofilm in deep-sea environments is barely being explored. Here, biofilms were developed at the brine pool (characterized by limited carbon sources) and the normal bottom water adjacent to Thuwal cold seeps. Comparative metagenomics based on 50 Gb datasets identified polysaccharide degradation, nitrate reduction, and proteolysis as enriched functional categories for brine biofilms. The genomes of two dominant species: a novel deltaproteobacterium and a novel epsilonproteobacterium in the brine biofilms were reconstructed. Despite rather small genome sizes, the deltaproteobacterium possessed enhanced polysaccharide fermentation pathways, whereas the epsilonproteobacterium was a versatile nitrogen reactor possessing nar, nap and nif gene clusters. These metabolic functions, together with specific regulatory and hypersaline-tolerant genes, made the two bacteria unique compared with their close relatives including those from hydrothermal vents. Moreover, these functions were regulated by biofilm development, as both the abundance and the expression level of key functional genes were higher in later-stage biofilms, and co-occurrences between the two dominant bacteria were demonstrated. Collectively, unique mechanisms were revealed: i) polysaccharides fermentation, proteolysis interacted with nitrogen cycling to form a complex chain for energy generation; ii) remarkably, exploiting and organizing niche-specific functions would be an important strategy for biofilm-dependent adaptation to the extreme conditions. This article is protected by copyright. All rights reserved.
    Environmental Microbiology 07/2015; DOI:10.1111/1462-2920.12978 · 6.24 Impact Factor
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