Murphy, Caitlin and Powlowski, Justin and Wu, Min and Butler, Greg and Tsang, Adrian
Curation of characterized glycoside hydrolases of Fungal origin.
- Published Version
Official URL: http://dx.doi.org/10.1093/database/bar020
Fungi produce a wide range of extracellular enzymes to break down plant cell walls, which are composed mainly of cellulose, lignin and hemicellulose. Among them are the glycoside hydrolases (GH), the largest and most diverse family of enzymes active on these substrates. To facilitate research and development of enzymes for the conversion of cell-wall polysaccharides into fermentable sugars, we have manually curated a comprehensive set of characterized fungal glycoside hydrolases. Characterized glycoside hydrolases were retrieved from protein and enzyme databases, as well as literature repositories. A total of 453 characterized glycoside hydrolases have been cataloged. They come from 131 different fungal species, most of which belong to the phylum Ascomycota. These enzymes represent 46 different GH activities and cover 44 of the 115 CAZy GH families. In addition to enzyme source and enzyme family, available biochemical properties such as temperature and pH optima, specific activity, kinetic parameters and substrate specificities were recorded. To simplify comparative studies, enzyme and species abbreviations have been standardized, Gene Ontology terms assigned and reference to supporting evidence provided. The annotated genes have been organized in a searchable, online database called mycoCLAP (Characterized Lignocellulose-Active Proteins of fungal origin). It is anticipated that this manually curated collection of biochemically characterized fungal proteins will be used to enhance functional annotation of novel GH genes.
Database URL: http://mycoCLAP.fungalgenomics.ca/
References:Henrissat B, Davies G. Structural and sequence-based classification of glycoside hydrolases. Curr. Opin. Struct. Biol. 1997;7:637-644.
Davies G, Henrissat B. Structures and mechanisms of glycosyl hydrolases. Structure 1995;3:853-859.
Henrissat B, Bairoch A. Updating the sequence-based classification of glycosyl hydrolases. Biochem. J. 1996;316(Pt 2):695-696.
Henrissat B, Bairoch A. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 1993;293(Pt 3):781-788.
Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 1991;280(Pt 2):309-316.
Lundell TK, Makela MR, Hilden K. Lignin-modifying enzymes in filamentous basidiomycetes–ecological, functional and phylogenetic review. J. Basic Microbiol. 2010;50:5-20.
Sanchez C. Lignocellulosic residues: biodegradation and bioconversion by fungi. Biotechnol. Adv. 2009;27:185-194.
Coleman JJ, Rounsley SD, Rodriguez-Carres M, et al. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet. 2009;5:e1000618.
Ellwood SR, Liu Z, Syme RA, et al. A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres. Genome Biol. 2010;11:R109.
Magrini V, Warren WC, Wallis J, et al. Fosmid-based physical mapping of the Histoplasma capsulatum genome. Genome Res. 2004;14:1603-1609.
Martin F, Aerts A, Ahren D, et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 2008;452:88-92.
Martinez D, Berka RM, Henrissat B, et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat. Biotechnol. 2008;26:553-560.
Martinez D, Challacombe J, Morgenstern I, et al. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc. Natl Acad. Sci. USA 2009;106:1954-1959.
Martinez D, Larrondo LF, Putnam N, et al. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat. Biotechnol. 2004;22:695-700.
Nierman WC, Pain A, Anderson MJ, et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 2005;438:1151-1156.
Dean RA, Talbot NJ, Ebbole DJ, et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 2005;434:980-986.
Galagan JE, Calvo SE, Borkovich KA, et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature 2003;422:859-868.
Espagne E, Lespinet O, Malagnac F, et al. The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol. 2008;9:R77.
Kamper J, Kahmann R, Bolker M, et al. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 2006;444:97-101.
Chang A, Scheer M, Grote A, et al. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res. 2009;37:D588-D592.
Benson DA, Karsch-Mizrachi I, Lipman DJ, et al. GenBank. Nucleic Acids Res. 2008;36:D25-D30.
Consortium U. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res. 2009;37:D169-D174.
Consortium TGO. Gene Ontology: tool for the unification of biology. Nature Genet. 2000;25:25-29.
Hessing JG, van Rotterdam C, Verbakel JM, et al. Isolation and characterization of a 1,4-beta-endoxylanase gene of A. awamori. Curr. Genet. 1994;26:228-232.
Giesbert S, Lepping HB, Tenberge KB, et al. The xylanolytic system of claviceps purpurea: cytological evidence for secretion of xylanases in infected rye tissue and molecular characterization of two xylanase genes. Phytopathology 1998;88:1020-1030.
de Graaff LH, van den Broeck HC, van Ooijen AJ, et al. Regulation of the xylanase-encoding xlnA gene of Aspergillus tubigensis. Mol. Microbiol. 1994;12:479-490.
Steenbakkers PJ, Ubhayasekera W, Goossen HJ, et al. An intron-containing glycoside hydrolase family 9 cellulase gene encodes the dominant 90kDa component of the cellulosome of the anaerobic fungus Piromyces sp. strain E2. Biochem. J. 2002;365(Pt 1):193-204.
Desmet T, Cantaert T, Gualfetti P, et al. An investigation of the substrate specificity of the xyloglucanase Cel74A from Hypocrea jecorina. FEBS J. 2007;274:356-363.
Murray P, Aro N, Collins C, et al. Expression in Trichoderma reesei and characterisation of a thermostable family 3 beta-glucosidase from the moderately thermophilic fungus Talaromyces emersonii. Protein Expr. Purif. 2004;38:248-257.
Ohnishi Y, Nagase M, Ichiyanagi T, et al. Transcriptional regulation of two cellobiohydrolase encoding genes (cel1 and cel2) from the wood-degrading basidiomycete Polyporus arcularius. Appl. Microbiol. Biotechnol. 2007;76:1069-1078.
Alcocer MJ, Furniss CS, Kroon PA, et al. Comparison of modular and non-modular xylanases as carrier proteins for the efficient secretion of heterologous proteins from Penicillium funiculosum. Appl. Microbiol. Biotechnol. 2003;60:726-732.
Furniss CSM, Williamson G, Kroon PA. The substrate specificity and susceptibility to wheat inhibitor proteins of Penicillium funiculosum xylanase from a commercial enzyme preparation. J. Sci. Food Agriculture 2005;85:574-582.
Kongruang S, Han MJ, Breton CI, et al. Quantitative analysis of cellulose-reducing ends. Appl. Biochem. Biotechnol. 2004;113–116:213-231.
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