title: FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds.
abstract: The breakdown of lignin by fungi is a key step during carbon recycling in terrestrial ecosystems. This process is of great interest for green and white biotechnological applications. Given the importance of these enzymatic processes, we have classified the enzymes potentially involved in lignin catabolism into sequence-based families and integrated them in a newly developed database, designated Fungal Oxidative Lignin enzymes (FOLy). Families were defined after sequence similarity searches starting from protein sequences and validated by the convergence of results with biochemical experiments reported in the literature. The resulting database was applied as a tool for the functional annotation of genomes from different fungi, namely (i) the Basidiomycota Coprinopsis cinerea, Phanerochaete chrysosporium and Ustilago maydis and (ii) the Ascomycota Aspergillus nidulans and Trichoderma reesei. Genomic comparison of the oxidoreductases of these fungi revealed significant differences in the putative enzyme arsenals. Two Ascomycota fungal genomes were annotated and new candidate genes were identified that could be useful for lignin degradation and (or) melanin synthesis, and their function investigated experimentally. This database efforts aims at providing the means to get new insights for the understanding and biotechnological exploitation of the lignin degradation. A WWW server giving access to the routinely updated FOLy classifications of enzymes potentially involved in lignin degradation can be found at http://foly.esil.univ-mrs.fr.
authors.affiliation: UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 Avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France.
authors.forename: Anthony
authors.initials: A
authors.lastname: Levasseur
authors.forename: François
authors.initials: F
authors.lastname: Piumi
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.forename: Corinne
authors.initials: C
authors.lastname: Rancurel
authors.forename: Michèle
authors.initials: M
authors.lastname: Asther
authors.forename: Michel
authors.initials: M
authors.lastname: Delattre
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Pierre
authors.initials: P
authors.lastname: Pontarotti
authors.forename: Marcel
authors.initials: M
authors.lastname: Asther
authors.forename: Eric
authors.initials: E
authors.lastname: Record
mesh_terms: D030562:Databases, Protein; D005656:Fungal Proteins / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D005658:Fungi / Q000201:enzymology*; D008031:Lignin / Q000378:metabolism*; D010088:Oxidoreductases / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid
chemical_list: D005656:Fungal Proteins; D008031:Lignin; D010088:Oxidoreductases