Erratum: Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi (Proceedings of the National Academy of Sciences of the United States of America (2014) 111, 27 (9923-9928) DOI: 10.1073/pnas.1400592111);Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 27, 2014, Pages 9923-9928

  Riley, Robert ^a   Salamov, Asaf A ^a   Brown, Daren W ^b   Nagy, Laszlo G ^c   Floudas, Dimitrios ^c   Held, Benjamin W ^d   Levasseur, Anthony ^e   Lombard, Vincent ^e   Morin, Emmanuelle ^f   Otillar, Robert ^a   Lindquist, Erika A ^a   Sun, Hui ^a   LaButti, Kurt M ^a   Schmutz, Jeremy ^a,g   Jabbour, Dina ^h   Luo, Hong ^h   Baker, Scott E ⁱ   Pisabarro, Antonio G ^j   Walton, Jonathan D ^h   Blanchette, Robert A ^d   Henrissat, Bernard ^e   Martin, Francis ^f   Cullen, Dan ^k   Hibbett, David S ^c   Grigoriev, Igor V ^a   more..

^a U S DEPARTMENT OF ENERGY   (United States)

^b U S DEPARTMENT OF AGRICULTURE   (United States)

^c CLARK UNIVERSITY   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

^e CNRS   (France)

^f UNIVERSITÉ DE LORRAINE   (France)

^g HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^h MICHIGAN STATE UNIVERSITY   (United States)

ⁱ PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^j PUBLIC UNIVERSITY OF NAVARRE   (Spain)

^k FOREST PRODUCTS LABORATORY   (United States)

more..

Author keywords

Bioenergy; Lignocellulose; Phylogenomics

Indexed keywords

CELLULOSE; HEMICELLULOSE; LIGNIN; PEROXIDASE; POLYKETIDE SYNTHASE;

ARTICLE; BASIDIOMYCETES; BIOMASS; BOTRYOBA SIDIUM BOTRYOSUM; BROWN ROT FUNGUS; CELL WALL; FUNGAL GENOME; GENOME; GENOMICS; JAAPIA ARGILLACEA; MULTIGENE FAMILY; NONHUMAN; PHANEROCHAETE; PHYLOGENOMICS; PHYLOGENY; POLYMERIZATION; PRIORITY JOURNAL; SAMPLING; SYMBIONT; WOODY PLANT;

BIOENERGY; LIGNOCELLULOSE; PHYLOGENOMICS;

BASIDIOMYCOTA; GENOME, FUNGAL; LIGNIN; MOLECULAR SEQUENCE DATA; PHYLOGENY; WOOD;

EID: 84903975698     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1418116111     Document Type: Erratum

References (91)

1. Kirk PMCP, Minter DW, Stalpers JA (2008) Dictionary of the Fungi (CAB International, Wallingford, UK), 10th Ed, p 72.
2. Johansson M, Stenlid J (1985) Infection of roots of Norway spruce (Picea abies) by Heterobasidion Annosum: Initial reactions in sapwood by wounding and infection. Eur J Forest Pathol 15(1):32-45.
3. Otrosina WJ, Chase TE, Cobb FW, Korhonen K (1993) Population structure of Heterobasidion annosum from North America and Europe. Can J Bot 71(8):1064-1071.
4. Martin F, et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452(7183):88-92. (Pubitemid 351355085)
5. Jin Y, et al. (2007) Characterization of seedling infection types and adult plant infection responses of monogenic Sr gene lines to race TTKS of Puccinia graminis f. sp tritici. Plant Dis 91(9):1096-1099. (Pubitemid 47328781)
6. Jin Y, Wanyera R, Kinyua M, Jin Y, Singh R (2005) The spread of Puccinia graminis f. sp tritici with broad virulence in eastern Africa. Phytopathology 95(6):S49.
7. Duplessis S, et al. (2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci USA 108(22):9166-9171.
8. Rihs JD, Padhye AA, Good CB (1996) Brain abscess caused by Schizophyllum commune: An emerging basidiomycete pathogen. J Clin Microbiol 34(7):1628-1632. (Pubitemid 26190386)
9. Lacaz CdaS, Heins-Vaccari EM, De Melo NT, Hernandez-Arriagada GL (1996) Basidiomycosis: A review of the literature. Rev Inst Med Trop Sao Paulo 38(5):379-390.
10. Brown SM, Campbell LT, Lodge JK (2007) Cryptococcus neoformans, a fungus under stress. Curr Opin Microbiol 10(4):320-325. (Pubitemid 47404946)
11. Dawson TL, Jr. (2007) Malassezia globosa and restricta: Breakthrough understanding of the etiology and treatment of dandruff and seborrheic dermatitis through whole-genome analysis. J Investig Dermatol Symp Proc 12(2):15-19.
12. Morin E, et al. (2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci USA 109(43):17501-17506.
13. Ohm RA, et al. (2010) Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol 28(9):957-963.
14. Stajich JE, et al. (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci USA 107(26):11889-11894.
15. Griffith NT, Barnett HL (1967) Mycoparasitism by Basidiomycetes in culture. Mycologia 59(1):149-154.
16. Padamsee M, et al. (2012) The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet Biol 49(3):217-226.
17. Floudas D, et al. (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336(6089):1715-1719.
18. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009) GenBank. Nucleic Acids Res 37(Database issue):D26-D31.
19. Sayers EW, et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 37(Database issue):D5-D15.
20. Eastwood DC, et al. (2011) The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science 333(6043):762-765.
21. Fernandez-Fueyo E, et al. (2012) Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci USA 109(14):5458-5463, and correction (2012) 109(21):8352.
22. Martinez D, et al. (2009) Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci USA 106(6):1954-1959.
23. Martinez D, et al. (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 22(6):695-700. (Pubitemid 38702825)
24. Baldrian P, Valásková V (2008) Degradation of cellulose by basidiomycetous fungi. FEMS Microbiol Rev 32(3):501-521. (Pubitemid 351538746)
25. Lundell TK, Mäkelä MR, Hildén K (2010) Lignin-modifying enzymes in filamentous basidiomycetes - ecological, functional and phylogenetic review. J Basic Microbiol 50(1):5-20.
26. Morita T, Fukuoka T, Imura T, Kitamoto D (2009) Production of glycolipid biosurfactants by basidiomycetous yeasts. Biotechnol Appl Biochem 53(Pt 1):39-49.
27. Rasmussen ML, Shrestha P, Khanal SK, Pometto AL, 3rd, Hans van Leeuwen J (2010) Sequential saccharification of corn fiber and ethanol production by the brown rot fungus Gloeophyllum trabeum. Bioresour Technol 101(10):3526-3533.
28. Grigoriev IV, et al. (2011) Fueling the future with fungal genomics. Mycology 2(3): 192-209.
29. Daniel G (1994) Use of electron microscopy for aiding our understanding of wood biodegradation. FEMS Microbiol Rev 13:199-233.
30. Blanchette R (1991) Delignification by wood-decay fungi. Annu Rev Phytopathol 29:381-398.
31. Eriksson K-EL, Blanchette RA, Ander P (1990) Microbial and Enzymatic Degradation of Wood and Wood Components (Springer, Berlin).
32. Blanchette R (1995) Degradation of the lignocellulose complex in wood. Can J Bot 73(Suppl 1):999-1010.
33. Worrall JJ, Anagnost SE, Zabel RA (1997) Comparison of wood decay among diverse lignicolous fungi. Mycologia 89:199-219. (Pubitemid 27185267)
34. Yelle DJ, Ralph J, Lu F, Hammel KE (2008) Evidence for cleavage of lignin by a brown rot basidiomycete. Environ Microbiol 10(7):1844-1849. (Pubitemid 351793624)
35. 3]-labelled lignin model compounds by the brown-rot fungi Gloeophyllum trabeum and Poria (Postia) placenta. Biodegradation 19(4):555-565.
36. Kirk TK, Farrell RL (1987) Enzymatic "combustion": The microbial degradation of lignin. Annu Rev Microbiol 41:465-505.
37. Hammel KE, Cullen D (2008) Role of fungal peroxidases in biological ligninolysis. Curr Opin Plant Biol 11(3):349-355.
38. Martinez AT (2002) Molecular biology and structure-function of lignin-degrading heme peroxidases. Enzyme Microb Technol 30:425-444.
39. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42(Database issue):D490-D495.
40. Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-2690.
41. Matheny PB, et al. (2007) Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol Phylogenet Evol 43(2):430-451.
42. Binder M, Larsson KH, Matheny PB, Hibbett DS (2010) Amylocorticiales ord. nov. and Jaapiales ord. nov.: Early diverging clades of agaricomycetidae dominated by corticioid forms. Mycologia 102(4):865-880.
43. Hibbett DS (2006) A phylogenetic overview of the Agaricomycotina. Mycologia 98(6): 917-925.
44. Hibbett DS, et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111(Pt 5):509-547. (Pubitemid 46915419)
45. Matheny PB, Gossmann JA, Zalar P, Kumar TKA, Hibbett DS (2006) Resolving the phylogenetic position of the Wallemiomycetes: An enigmatic major lineage of Basidiomycota. Can J Bot 84(12):1794-1805. (Pubitemid 46996038)
46. Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30(7):1575-1584. (Pubitemid 34679732)
47. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410.
48. Koonin EV, et al. (2004) A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 5(2):R7.
49. Levasseur A, Drula E, Lombard V, Coutinho PM, Henrissat B (2013) Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels 6(1):41.
50. Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125(1):1-15.
51. Harris PV, et al. (2010) Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: Structure and function of a large, enigmatic family. Biochemistry 49(15):3305-3316.
52. Langston JA, et al. (2011) Oxidoreductive cellulose depolymerization by the enzymes cellobiose dehydrogenase and glycoside hydrolase 61. Appl Environ Microbiol 77(19): 7007-7015.
53. Quinlan RJ, et al. (2011) Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components. Proc Natl Acad Sci USA 108(37):15079-15084.
54. Vaaje-Kolstad G, et al. (2010) An oxidative enzyme boosting the enzymatic conversion of recalcitrant polysaccharides. Science 330(6001):219-222.
55. Schmidt O, Liese W (1980) Variability of wood degrading enzymes of Schizophyllum commune. Holzforschung 34(2):67-72.
56. Blodig W, et al. (1998) Autocatalytic formation of a hydroxy group at C beta of trp171 in lignin peroxidase. Biochemistry 37(25):8832-8838. (Pubitemid 28299650)
57. Poulos TL, Edwards SL, Wariishi H, Gold MH (1993) Crystallographic refinement of lignin peroxidase at 2 Å. J Biol Chem 268(6):4429-4440.
58. 2-requiring oxygenase. Proc Natl Acad Sci USA 81(8):2280-2284.
59. Wariishi H, Valli K, Gold MH (1992) Manganese(II) oxidation by manganese peroxidase from the basidiomycete Phanerochaete chrysosporium. Kinetic mechanism and role of chelators. J Biol Chem 267(33):23688-23695. (Pubitemid 23088173)
60. Kerem Z, hammel, Hammel KE (1999) Biodegradative mechanism of the brown rot basidiomycete Gloeophyllum trabeum: Evidence for an extracellular hydroquinonedriven fenton reaction. FEBS Lett 446(1):49-54.
61. Jensen KA, Jr., Houtman CJ, Ryan ZC, Hammel KE (2001) Pathways for extracellular Fenton chemistry in the brown rot basidiomycete Gloeophyllum trabeum. Appl Environ Microbiol 67(6):2705-2711. (Pubitemid 33639747)
62. Eggert C, Temp U, Eriksson KEL (1996) The ligninolytic system of the white rot fungus Pycnoporus cinnabarinus: Purification and characterization of the laccase. Appl Environ Microbiol 62(4):1151-1158. (Pubitemid 26113186)
63. Niku-Paavola ML, Karhunen E, Salola P, Raunio V (1988) Ligninolytic enzymes of the white-rot fungus Phlebia radiata. Biochem J 254(3):877-883.
64. Keller NP, Turner G, Bennett JW (2005) Fungal secondary metabolism - from biochemistry to genomics. Nat Rev Microbiol 3(12):937-947. (Pubitemid 43078157)
65. Arantes V, Milagres AM, Filley TR, Goodell B (2011) Lignocellulosic polysaccharides and lignin degradation by wood decay fungi: The relevance of nonenzymatic Fenton-based reactions. J Ind Microbiol Biotechnol 38(4):541-555.
66. Cohen R, Jensen KA, Houtman CJ, Hammel KE (2002) Significant levels of extracellular reactive oxygen species produced by brown rot basidiomycetes on cellulose. FEBS Lett 531(3):483-488. (Pubitemid 35336073)
67. Korripally P, Timokhin VI, Houtman CJ, Mozuch MD, Hammel KE (2013) Evidence from Serpula lacrymans that 2,5-dimethoxyhydroquinone is a lignocellulolytic agent of divergent brown rot basidiomycetes. Appl Environ Microbiol 79(7):2377-2383.
68. Shimokawa T, Nakamura M, Hayashi N, Ishihara M (2004) Production of 2,5-dimethoxyhydroquinone by the brown-rot fungus Serpuyla lacrymans to drive extracellular Fenton reaction. Holzforschung 58:305-310.
69. Lackner G, Misiek M, Braesel J, Hoffmeister D (2012) Genome mining reveals the evolutionary origin and biosynthetic potential of basidiomycete polyketide synthases. Fungal Genet Biol 49(12):996-1003.
70. Wawrzyn GT, Quin MB, Choudhary S, López-Gallego F, Schmidt-Dannert C (2012) Draft genome of Omphalotus olearius provides a predictive framework for sesquiterpenoid natural product biosynthesis in Basidiomycota. Chem Biol 19(6):772-783.
71. Revell LJ (2009) Size-correction and principal components for interspecific comparative studies. Evolution 63(12):3258-3268.
72. Gold MH, Alic M (1993) Molecular biology of the lignin-degrading basidiomycete Phanerochaete chrysosporium. Microbiol Rev 57(3):605-622. (Pubitemid 23262511)
73. Ander P, Eriksson KE (1976) Importance of phenol oxidase activity in lignin degradation by white-rot fungus Sporotrichum pulverulentum. Arch Microbiol 109(1-2): 1-8.
74. Hiroi T, Eriksson KE (1976) Microbiological degradation of lignin: Influence of cellulose on degradation of lignins by white-rot fungus Pleurotus ostreatus. Sven Papperstidn 79(5):157-161.
75. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821-829. (Pubitemid 351645072)
76. Jaffe DB, et al. (2003) Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 13(1):91-96.
77. Grigoriev IV, Martinez DA, Salamov AA (2006) Fungal genomic annotation. Appl Mycol Biotechnol 6:123-142.
78. Grigoriev IV, et al. (2014) MycoCosm portal: Gearing up for 1000 fungal genomes. Nucleic Acids Res 42(Database issue):D699-704.
79. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059-3066. (Pubitemid 34851225)
80. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17(4):540-552.
81. Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4 (Sinauer Associates, Sunderland, MA).
82. Larkin MA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21): 2947-2948. (Pubitemid 350162903)
83. Brown DW, Adams TH, Keller NP (1996) Aspergillus has distinct fatty acid synthases for primary and secondary metabolism. Proc Natl Acad Sci USA 93(25):14873-14877. (Pubitemid 26419062)
84. Li Y, Chooi YH, Sheng Y, Valentine JS, Tang Y (2011) Comparative characterization of fungal anthracenone and naphthacenedione biosynthetic pathways reveals an α-hydroxylation-dependent Claisen-like cyclization catalyzed by a dimanganese thioesterase. J Am Chem Soc 133(39):15773-15785.
85. Hopwood DA, Sherman DH (1990) Molecular genetics of polyketides and its comparison to fatty acid biosynthesis. Annu Rev Genet 24:37-66. (Pubitemid 120011540)
86. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) Distributed by the author. (Department of Genome Sciences, University of Washington, Seattle), Version 3.6.
87. Blanchette RA, et al. (2010) An Antarctic hot spot for fungi at Shackleton's historic hut on Cape Royds. Microb Ecol 60(1):29-38.
88. Brown A, Sims PFG, Raeder U, Broda P (1988) Multiple ligninase-related genes from Phanerochaete chrysosporium. Gene 73(1):77-85.
89. Kirk TK, Schultz E, Conners WJ, Lorentz LF, Zeikus JG (1978) Influence of culture parameters on lignin metabolism by Phanerochaete chrysosporium. Arch Microbiol 117: 277-285. (Pubitemid 8362081)
90. Hori C, et al. (2013) Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay. Mycologia 105(6):1412-1427.
91. 2 production by Phanerochaete chrysosporium. J Bacteriol 169(5):2195-2201.