Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood
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Masahiro Samejima | Bernard Henrissat | Benjamin Held | Takuya Ishida | Jorge Rencoret | Ana Gutiérrez | Robert A. Blanchette | Kerrie Barry | Gerald Lackner | Andriy Kovalchuk | Christian P. Kubicek | Igor V. Grigoriev | Robert Riley | Monika Schmoll | Fred O. Asiegbu | J. Glasner | B. Henrissat | Hui Sun | R. Berka | E. Lindquist | K. Barry | R. Riley | I. Grigoriev | S. Covert | E. Master | J. Rencoret | A. Gutiérrez | M. Schmoll | R. Blanchette | L. Larrondo | D. Cullen | Paulo Canessa | Irina S Druzhinina | C. Kubicek | U. Kües | P. Kersten | Ángel T. Martínez | J. Yadav | P. Ferreira | J. Gaskell | C. Hori | K. Igarashi | F. J. Ruiz-Dueñas | G. Sabat | M. Samejima | Franz J. St John | K. Syed | B. Held | F. Asiegbu | D. Hoffmeister | G. Lackner | Patricia Ferreira | Kiyohiko Igarashi | Khajamohiddin Syed | Ursula Kües | Hui Sun | Andriy Kovalchuk | Hitoshi Suzuki | T. Ishida | Erika Lindquist | Randy M. Berka | Luis F. Larrondo | Irina S. Druzhinina | A. Mgbeahuruike | Hitoshi Suzuki | S. Splinter BonDurant | Daniel Cullen | Chiaki Hori | Emma Master | Francisco J. Ruiz-Dueñas | Paulo Canessa | Jill A. Gaskell | Phil Kersten | Franz St. John | Jeremy Glasner | Grzegorz Sabat | Sandra Splinter BonDurant | Jagjit Yadav | Anthony C. Mgbeahuruike | Dirk Hoffmeister | Angel T. Martínez | Sarah F. Covert | Angel T. Martı́nez
[1] Hong-Wei Sun,et al. Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family , 1992, Journal of Molecular Evolution.
[2] P. Kersten. Glyoxal oxidase of Phanerochaete chrysosporium: its characterization and activation by lignin peroxidase. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[3] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[4] Ichael,et al. Analysis of Character Correlations Among Wood Decay Mechanisms , Mating Systems , and Substrate Ranges in Homobasidiomycetes , 2001 .
[5] Andrey Rzhetsky,et al. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference , 1992, Journal of Molecular Evolution.
[6] R. Blanchette,et al. Structure, Organization, and Transcriptional Regulation of a Family of Copper Radical Oxidase Genes in the Lignin-Degrading Basidiomycete Phanerochaete chrysosporium , 2006, Applied and Environmental Microbiology.
[7] A. Salamov,et al. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis , 2012, Proceedings of the National Academy of Sciences.
[8] Inna Dubchak,et al. The Genome Portal of the Department of Energy Joint Genome Institute , 2011, Nucleic Acids Res..
[9] Katherine H. Huang,et al. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78 , 2004, Nature Biotechnology.
[10] Julie Dawn Thompson,et al. Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases , 1994, Nucleic Acids Res..
[11] S. Bastian,et al. Engineering of pyranose 2-oxidase from Peniophora gigantea towards improved thermostability and catalytic efficiency , 2005, Applied Microbiology and Biotechnology.
[12] D. Hibbett,et al. Molecular Evolution and Diversity of Lignin Degrading Heme Peroxidases in the Agaricomycetes , 2008, Journal of Molecular Evolution.
[13] Motoyuki Shimizu,et al. Metabolic regulation at the tricarboxylic acid and glyoxylate cycles of the lignin‐degrading basidiomycete Phanerochaete chrysosporium against exogenous addition of vanillin , 2005, Proteomics.
[14] Motoyuki Shimizu,et al. Proteomic and metabolomic analyses of the white-rot fungus Phanerochaete chrysosporium exposed to exogenous benzoic acid. , 2008, Journal of proteome research.
[15] P. Baldrian,et al. Degradation of cellulose by basidiomycetous fungi. , 2008, FEMS microbiology reviews.
[16] Albee Y. Ling,et al. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes , 2012, Science.
[17] A. Salamov,et al. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi , 2014, Proceedings of the National Academy of Sciences.
[18] J. Yadav,et al. P450 monooxygenases (P450ome) of the model white rot fungus Phanerochaete chrysosporium , 2012, Critical reviews in microbiology.
[19] B. Henrissat,et al. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes , 2013, Biotechnology for Biofuels.
[20] T. V. van Beek,et al. Elimination and detoxification of softwood extractives by white-rot fungi. , 2000, Journal of biotechnology.
[21] Igor Grigoriev,et al. Comparative Transcriptome and Secretome Analysis of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium , 2010, Applied and Environmental Microbiology.
[22] M. Nei,et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.
[23] K. Eriksson,et al. Pyranose 2-oxidase from Phanerochaete chrysosporium , 1988 .
[24] T. V. van Beek,et al. Fungal biotransformation products of dehydroabietic acid. , 2007, Journal of natural products.
[25] F. Giffhorn. Fungal pyranose oxidases: occurrence, properties and biotechnical applications in carbohydrate chemistry , 2000, Applied Microbiology and Biotechnology.
[26] T. Annesi,et al. Biological control of Heterobasidion annosum on Pinus pinea by Phlebiopsis gigantea , 2005 .
[27] A. Gutiérrez,et al. Microbial and enzymatic control of pitch in the pulp and paper industry , 2009, Applied Microbiology and Biotechnology.
[28] E. Panisko,et al. Proteomic and Functional Analysis of the Cellulase System Expressed by Postia placenta during Brown Rot of Solid Wood , 2011, Applied and Environmental Microbiology.
[29] L. Pauling,et al. Evolutionary Divergence and Convergence in Proteins , 1965 .
[30] Gordon Robertson,et al. A specialized ABC efflux transporter GcABC-G1 confers monoterpene resistance to Grosmannia clavigera, a bark beetle-associated fungal pathogen of pine trees. , 2013, The New phytologist.
[31] Alex L. Shigo,et al. Successions of Organisms in Discoloration and Decay of Wood , 1967 .
[32] R. Bourbonnais,et al. Reactivities of various mediators and laccases with kraft pulp and lignin model compounds , 1997, Applied and environmental microbiology.
[33] R. Aebersold,et al. A statistical model for identifying proteins by tandem mass spectrometry. , 2003, Analytical chemistry.
[34] Feng Xu,et al. Oxidoreductive Cellulose Depolymerization by the Enzymes Cellobiose Dehydrogenase and Glycoside Hydrolase 61 , 2011, Applied and Environmental Microbiology.
[35] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[36] Francisco Melo,et al. A Novel Extracellular Multicopper Oxidase from Phanerochaete chrysosporium with Ferroxidase Activity , 2003, Applied and Environmental Microbiology.
[37] A. Salamov,et al. Erratum: Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis (Proceedings of the National Academy of Sciences (2012) 109 (5458-5463) DOI: 10.1073/pnas. 1119912109) , 2012 .
[38] B. Henrissat,et al. Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5) , 2012, BMC Evolutionary Biology.
[39] Pramod P Wangikar,et al. Combined sequence and structure analysis of the fungal laccase family , 2003, Biotechnology and bioengineering.
[40] A. Salamov,et al. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion , 2009, Proceedings of the National Academy of Sciences.
[41] R. Blanchette,et al. Biological Processing of Pine Logs for Pulp and Paper Production with Phlebiopsis gigantea , 1997, Applied and environmental microbiology.
[42] A. Salamov,et al. 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. , 2006, Fungal genetics and biology : FG & B.
[43] M. Garbelotto,et al. Population genetic analyses provide insights on the introduction pathway and spread patterns of the North American forest pathogen Heterobasidion irregulare in Italy , 2013, Molecular ecology.
[44] V. Eijsink,et al. An Oxidative Enzyme Boosting the Enzymatic Conversion of Recalcitrant Polysaccharides , 2010, Science.
[45] D. Cullen,et al. Recent Advances on the Genomics of Litter- and Soil-Inhabiting Agaricomycetes , 2013 .
[46] R. Blanchette. Delignification by wood-decay fungi , 1991 .
[47] L. Lo Leggio,et al. Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components , 2011, Proceedings of the National Academy of Sciences.
[48] Brandi L. Cantarel,et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..
[49] W. V. van Berkel,et al. Site‐directed mutagenesis of selected residues at the active site of aryl‐alcohol oxidase, an H2O2‐producing ligninolytic enzyme , 2006, The FEBS journal.
[50] Robert A. Blanchette,et al. Microbial and Enzymatic Degradation of Wood and Wood Components , 2012, Springer Series in Wood Science.
[51] Keith Bradnam,et al. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..
[52] D. Cullen,et al. Isolation and Purification of Pyranose 2-Oxidase from Phanerochaete chrysosporium and Characterization of Gene Structure and Regulation , 2004, Applied and Environmental Microbiology.
[53] C. Divne,et al. Mechanism of the Reductive Half-reaction in Cellobiose Dehydrogenase* , 2003, The Journal of Biological Chemistry.
[54] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[55] A. Gutiérrez,et al. Biodegradability of Extractives in Sapwood and Heartwood from Scots Pine by Sapstain and White-Rot Fungi , 1999 .
[56] D. Hibbett,et al. Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay , 2013, Mycologia.
[57] J. Weiner,et al. Fundamentals and applications , 2003 .
[58] M. Hofrichter,et al. New and classic families of secreted fungal heme peroxidases , 2010, Applied Microbiology and Biotechnology.
[59] G. Suen,et al. Mountain Pine Beetles Colonizing Historical and Naïve Host Trees Are Associated with a Bacterial Community Highly Enriched in Genes Contributing to Terpene Metabolism , 2013, Applied and Environmental Microbiology.
[60] R. Blanchette,et al. An Antarctic Hot Spot for Fungi at Shackleton's Historic Hut on Cape Royds , 2010, Microbial Ecology.
[61] J. Ståhlberg,et al. The Putative Endoglucanase PcGH61D from Phanerochaete chrysosporium Is a Metal-Dependent Oxidative Enzyme that Cleaves Cellulose , 2011, PloS one.
[62] M. Mann,et al. Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein*S , 2005, Molecular & Cellular Proteomics.
[63] R. Blanchette,et al. Biological Control of Blue Stain in Pulpwood: Mechanisms of Control used by Phlebiopsis gigantea , 2001 .
[64] D. Sheehan,et al. Glutathione S-transferases from the white-rot fungus, Phanerochaete chrysosporium. , 1997, The Biochemical journal.
[65] Silvia Vidal‐Melgosa,et al. Discovery of LPMO activity on hemicelluloses shows the importance of oxidative processes in plant cell wall degradation , 2014, Proceedings of the National Academy of Sciences.
[66] Timothy Y James,et al. Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences , 2006, The FEBS journal.
[67] U. Kües,et al. Lcc1 and Lcc5 are the main laccases secreted in liquid cultures of Coprinopsis cinerea strains , 2013, Antonie van Leeuwenhoek.
[68] A. Salamov,et al. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. , 2012, The New phytologist.
[69] C. Evans,et al. Anisaldehyde and Veratraldehyde Acting as Redox Cycling Agents for H2O2 Production by Pleurotus eryngii , 1994, Applied and environmental microbiology.
[70] U. Temp,et al. Laccase is essential for lignin degradation by the white‐rot fungus Pycnoporus cinnabarinus , 1997, FEBS letters.
[71] A. Salamov,et al. The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi , 2011, Science.
[72] A. Gutiérrez,et al. Analysis of lipophilic extractives from wood and pitch deposits by solid-phase extraction and gas chromatography , 1998 .
[73] B. Henrissat,et al. Cello-Oligosaccharide Oxidation Reveals Differences between Two Lytic Polysaccharide Monooxygenases (Family GH61) from Podospora anserina , 2012, Applied and Environmental Microbiology.
[74] L. Birolo,et al. Identification of a new member of Pleurotus ostreatus laccase family from mature fruiting body. , 2010, Fungal biology.
[75] A. Käärik. 5 – Decomposition of Wood , 1974 .
[76] Lynne Boddy,et al. Fungal decomposition of wood. Its biology and ecology. , 1988 .
[77] M. Nei,et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.
[78] J. Reiser,et al. Aryl-alcohol dehydrogenase from the white-rot fungus Phanerochaete chrysosporium. Gene cloning, sequence analysis, expression, and purification of the recombinant enzyme. , 1994, The Journal of biological chemistry.
[79] M. Soellner,et al. Tandem cytochrome P450 monooxygenase genes and splice variants in the white rot fungus Phanerochaete chrysosporium: cloning, sequence analysis, and regulation of differential expression. , 2003, Fungal genetics and biology : FG & B.
[80] M. Hofrichter,et al. Substrate oxidation by dye-decolorizing peroxidases (DyPs) from wood- and litter-degrading agaricomycetes compared to other fungal and plant heme-peroxidases , 2012, Applied Microbiology and Biotechnology.
[81] D. Cavener,et al. GMC oxidoreductases. A newly defined family of homologous proteins with diverse catalytic activities. , 1992, Journal of molecular biology.
[82] J. Rishbeth. Stump protection against Fomes annosus. III. Inoculation with Peniophora gigantea. , 1963 .
[83] N. Blom,et al. Feature-based prediction of non-classical and leaderless protein secretion. , 2004, Protein engineering, design & selection : PEDS.
[84] Asaf Salamov,et al. Fungal Genomic Annotation , 2006 .
[85] Jamie H. D. Cate,et al. Cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by Neurospora crassa. , 2011, ACS chemical biology.
[86] T. Tokimatsu,et al. A physiological role for oxalic acid biosynthesis in the wood-rotting basidiomycete Fomitopsis palustris , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[87] S. Kilaru,et al. The laccase multi-gene family in Coprinopsis cinerea has seventeen different members that divide into two distinct subfamilies , 2006, Current Genetics.
[88] P. Halada,et al. Characteristics of Gloeophyllum trabeum Alcohol Oxidase, an Extracellular Source of H2O2 in Brown Rot Decay of Wood , 2007, Applied and Environmental Microbiology.
[89] Aleksey A. Porollo,et al. CYP63A2, a Catalytically Versatile Fungal P450 Monooxygenase Capable of Oxidizing Higher-Molecular-Weight Polycyclic Aromatic Hydrocarbons, Alkylphenols, and Alkanes , 2013, Applied and Environmental Microbiology.
[90] B. Horwitz,et al. Genomics of Soil- and Plant-Associated Fungi , 2013, Soil Biology.
[91] Jill Gaskell,et al. Transcriptome and Secretome Analyses of Phanerochaete chrysosporium Reveal Complex Patterns of Gene Expression , 2009, Applied and Environmental Microbiology.
[92] Jacqueline MacDonald,et al. Transcriptomic Responses of the Softwood-Degrading White-Rot Fungus Phanerochaete carnosa during Growth on Coniferous and Deciduous Wood , 2011, Applied and Environmental Microbiology.
[93] K. Messner,et al. Reduction of Resin Content in Wood Chips during Experimental Biological Pulping Processes , 1994 .
[94] C. Martius. Decomposition of Wood , 1997 .
[95] E. Sjöström,et al. Wood Chemistry: Fundamentals and Applications , 1981 .
[96] V. Bryson,et al. Evolving Genes and Proteins. , 1965, Science.
[97] U. Kües,et al. Multiple Multi-Copper Oxidase Gene Families in Basidiomycetes – What for? , 2011, Current genomics.
[98] S. Kawai,et al. Degradation of a non-phenolic β-O-4 substructure and of polymeric lignin model compounds by laccase of Coriolus versicolor in the presence of 1-hydroxybenzotriazole , 1999 .
[99] F. Asiegbu,et al. Identification and analysis of differentially expressed cDNAs during nonself-competitive interaction between Phlebiopsis gigantea and Heterobasidion parviporum. , 2006, FEMS microbiology ecology.