title: A comparative genomic analysis of the oxidative enzymes potentially involved in lignin degradation by Agaricus bisporus.
abstract: The oxidative enzymatic machinery for degradation of organic substrates in Agaricus bisporus (Ab) is at the core of the carbon recycling mechanisms in this fungus. To date, 156 genes have been tentatively identified as part of this oxidative enzymatic machinery, which includes 26 peroxidase encoding genes, nine copper radical oxidase [including three putative glyoxal oxidase-encoding genes (GLXs)], 12 laccases sensu stricto and 109 cytochrome P450 monooxygenases. Comparative analyses of these enzymes in Ab with those of the white-rot fungus, Phanerochaete chrysosporium, the brown-rot fungus, Postia placenta, the coprophilic litter fungus, Coprinopsis cinerea and the ectomychorizal fungus, Laccaria bicolor, revealed enzyme diversity consistent with adaptation to substrates rich in humic substances and partially degraded plant material. For instance, relative to wood decay fungi, Ab cytochrome P450 genes were less numerous (109 gene models), distributed among distinctive families, and lacked extensive duplication and clustering. Viewed together with P450 transcript accumulation patterns in three tested growth conditions, these observations were consistent with the unique Ab lifestyle. Based on tandem gene arrangements, a certain degree of gene duplication seems to have occurred in this fungus in the copper radical oxidase (CRO) and the laccase gene families. In Ab, high transcript levels and regulation of the heme-thiolate peroxidases, two manganese peroxidases and the three GLX-like genes are likely in response to complex natural substrates, including lignocellulose and its derivatives, thereby suggesting an important role in lignin degradation. On the other hand, the expression patterns of the related CROs suggest a developmental role in this fungus. Based on these observations, a brief comparative genomic overview of the Ab oxidative enzyme machinery is presented.
authors.affiliation: Carver Center for Genomics, Department of Biology, University of Iowa, Iowa City, IA 52242, USA. doddapan@bcm.edu
authors.forename: Harshavardhan
authors.initials: H
authors.lastname: Doddapaneni
authors.forename: Venkataramanan
authors.initials: V
authors.lastname: Subramanian
authors.forename: Bolei
authors.initials: B
authors.lastname: Fu
authors.forename: Dan
authors.initials: D
authors.lastname: Cullen
mesh_terms: D000364:Agaricus / Q000201:enzymology* / Q000235:genetics*; D001711:Biotransformation; D019295:Computational Biology; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D014644:Genetic Variation; D016681:Genome, Fungal; D008031:Lignin / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D010088:Oxidoreductases / Q000235:genetics* / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D008031:Lignin; D010088:Oxidoreductases