title: Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins.
abstract: The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 'computational secretome,' 43% showed no significant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed significant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identified in culture filtrates by mass spectrometry (LS-MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identified in carbon-starved cultures. Beyond proteases and M6Pase, 28 specific gene products were identified including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium's extracellular enzyme systems.
authors.affiliation: Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Amber
authors.initials: A
authors.lastname: Vanden Wymelenberg
authors.forename: Patrick
authors.initials: P
authors.lastname: Minges
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Sabat
authors.forename: Diego
authors.initials: D
authors.lastname: Martinez
authors.forename: Andrea
authors.initials: A
authors.lastname: Aerts
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.forename: Igor
authors.initials: I
authors.lastname: Grigoriev
authors.forename: Harris
authors.initials: H
authors.lastname: Shapiro
authors.forename: Nik
authors.initials: N
authors.lastname: Putnam
authors.forename: Paula
authors.initials: P
authors.lastname: Belinky
authors.forename: Carlos
authors.initials: C
authors.lastname: Dosoretz
authors.forename: Jill
authors.initials: J
authors.lastname: Gaskell
authors.forename: Phil
authors.initials: P
authors.lastname: Kersten
authors.forename: Dan
authors.initials: D
authors.lastname: Cullen
mesh_terms: D002265:Carboxylic Ester Hydrolases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D003470:Culture Media / Q000737:chemistry; D030561:Databases, Nucleic Acid; D005656:Fungal Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D016681:Genome, Fungal; D006026:Glycoside Hydrolases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008049:Lipase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013058:Mass Spectrometry; D010447:Peptide Hydrolases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010544:Peroxidases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020075:Phanerochaete / Q000235:genetics* / Q000378:metabolism*; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D021381:Protein Transport; D017386:Sequence Homology, Amino Acid
chemical_list: D003470:Culture Media; D005656:Fungal Proteins; D010544:Peroxidases; C042858:lignin peroxidase; D002265:Carboxylic Ester Hydrolases; D008049:Lipase; C023553:mannose-6-phosphatase; D010744:Phosphoric Monoester Hydrolases; D006026:Glycoside Hydrolases; D010447:Peptide Hydrolases