Genomic and proteomic dissection of the ubiquitous plant pathogen, armillaria mellea: Toward a new infection model system

Journal of Proteome Research

Volumn 12, Issue 6, 2013, Pages 2552-2570

  Collins, Cassandra ^a   Keane, Thomas M ^b   Turner, Daniel J ^b   O'Keeffe, Grainne ^a   Fitzpatrick, David A ^a   Doyle, Sean ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Armillaria mellea; basidiomycete genomics; basidiomycete proteomics; Candida; fungal proteomics; glycosidases; Next Generation Sequencing

Indexed keywords

CARBOHYDRATE; LACCASE; LIGNIN PEROXIDASE;

ARMILLARIA; ARMILLARIA MELLEA; ARTICLE; BASIDIOMYCETES; CANDIDA ALBICANS; COCULTURE; CONTROLLED STUDY; FUNGAL VIRULENCE; GENOMICS; MYCELIAL GROWTH; NONHUMAN; PLANT DISEASE; PLANT GENOME; PRIORITY JOURNAL; PROTEOMICS; TANDEM MASS SPECTROMETRY;

ARMILLARIA MELLEA; CANDIDA; CANDIDA ALBICANS;

EID: 84879399852     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr301131t     Document Type: Article

References (85)

1. Erjavec, J.; Kos, J.; Ravnikar, M.; Dreo, T.; Sabotic, J. Proteins of higher fungi - from forest to application Trends Biotechnol. 2012, 30 (5) 259-73
2. Kämper, J.; Kahmann, R.; Bölker, M.; Ma, L. J.; Brefort, T.; Saville, B. J.; Banuett, F.; Kronstad, J. W.; Gold, S. E.; M̧ller, O. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis Nature 2006, 444 (7115) 97-101
3. Martin, F.; Aerts, A.; Ahren, D.; Brun, A.; Danchin, E. G. J.; Duchaussoy, F.; Gibon, J.; Kohler, A.; Lindquist, E.; Pereda, V. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis Nature 2008, 452 (7183) 88-92
4. Rioux, R.; Manmathan, H.; Singh, P.; de los Reyes, B.; Jia, Y.; Tavantzis, S. Comparative analysis of putative pathogenesis-related gene expression in two Rhizoctonia solani pathosystems Curr. Genet. 2011, 57 (6) 391-408
5. Baumgartner, K.; Coetzee, M. P.; Hoffmeister, D. Secrets of the subterranean pathosystem of Armillaria Mol. Plant Pathol. 2011, 12 (6) 515-34
6. Desjardin, D. E.; Oliveira, A. G.; Stevani, C. V. Fungi bioluminescence revisited Photochem. Photobiol. Sci. 2008, 7 (2) 170-82
7. Baumgartner, K.; Fujiyoshi, P.; Foster, G. D.; Bailey, A. M. Agrobacterium tumefaciens-mediated transformation for investigation of somatic recombination in the fungal pathogen Armillaria mellea Appl. Environ. Microbiol. 2010, 76 (24) 7990-6
8. Muszynska, B.; Sulkowska-Ziaja, K.; Wolkowska, M.; Ekiert, H. Chemical, pharmacological, and biological characterization of the culinary-medicinal honey mushroom, Armillaria mellea (Vahl) P. Kumm. (Agaricomycetideae): a review Int. J. Med. Mushrooms 2011, 13 (2) 167-75
9. Donnelly, D. M.; Abe, F.; Coveney, D.; Fukuda, N.; O'Reilly, J.; Polonsky, J.; Prange, T. Antibacterial sesquiterpene aryl esters from Armillaria mellea J. Nat. Prod. 1985, 48 (1) 10-6
10. Martinez, D.; Larrondo, L. F.; Putnam, N.; Gelpke, M. D.; Huang, K.; Chapman, J.; Helfenbein, K. G.; Ramaiya, P.; Detter, J. C.; Larimer, F.; Coutinho, P. M.; Henrissat, B.; Berka, R.; Cullen, D.; Rokhsar, D. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78 Nat. Biotechnol. 2004, 22 (6) 695-700
11. Ohm, R. A.; de Jong, J. F.; Lugones, L. G.; Aerts, A.; Kothe, E.; Stajich, J. E.; de Vries, R. P.; Record, E.; Levasseur, A.; Baker, S. E.; Bartholomew, K. A.; Coutinho, P. M.; Erdmann, S.; Fowler, T. J.; Gathman, A. C.; Lombard, V.; Henrissat, B.; Knabe, N.; Kues, U.; Lilly, W. W.; Lindquist, E.; Lucas, S.; Magnuson, J. K.; Piumi, F.; Raudaskoski, M.; Salamov, A.; Schmutz, J.; Schwarze, F. W.; vanKuyk, P. A.; Horton, J. S.; Grigoriev, I. V.; Wosten, H. A. Genome sequence of the model mushroom Schizophyllum commune Nat. Biotechnol. 2010, 28 (9) 957-63
12. Stajich, J. E.; Wilke, S. K.; Ahren, D.; Au, C. H.; Birren, B. W.; Borodovsky, M.; Burns, C.; Canback, B.; Casselton, L. A.; Cheng, C. K.; Deng, J.; Dietrich, F. S.; Fargo, D. C.; Farman, M. L.; Gathman, A. C.; Goldberg, J.; Guigo, R.; Hoegger, P. J.; Hooker, J. B.; Huggins, A.; James, T. Y.; Kamada, T.; Kilaru, S.; Kodira, C.; Kues, U.; Kupfer, D.; Kwan, H. S.; Lomsadze, A.; Li, W.; Lilly, W. W.; Ma, L. J.; Mackey, A. J.; Manning, G.; Martin, F.; Muraguchi, H.; Natvig, D. O.; Palmerini, H.; Ramesh, M. A.; Rehmeyer, C. J.; Roe, B. A.; Shenoy, N.; Stanke, M.; Ter-Hovhannisyan, V.; Tunlid, A.; Velagapudi, R.; Vision, T. J.; Zeng, Q.; Zolan, M. E.; Pukkila, P. J. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) Proc. Natl. Acad. Sci. 2010, 107 (26) 11889
13. Abbas, A.; Koc, H.; Liu, F.; Tien, M. Fungal degradation of wood: initial proteomic analysis of extracellular proteins of Phanerochaete chrysosporium grown on oak substrate Curr. Genet. 2005, 47 (1) 49-56
14. Shimizu, M.; Yuda, N.; Nakamura, T.; Tanaka, H.; Wariishi, H. Metabolic regulation at the tricarboxylic acid and glyoxylate cycles of the lignin-degrading basidiomycete Phanerochaete chrysosporium against exogenous addition of vanillin Proteomics 2005, 5 (15) 3919-31
15. Ravalason, H.; Jan, G.; Molle, D.; Pasco, M.; Coutinho, P. M.; Lapierre, C.; Pollet, B.; Bertaud, F.; Petit-Conil, M.; Grisel, S.; Sigoillot, J. C.; Asther, M.; Herpoel-Gimbert, I. Secretome analysis of Phanerochaete chrysosporium strain CIRM-BRFM41 grown on softwood Appl. Microbiol. Biotechnol. 2008, 80 (4) 719-33
16. Horie, K.; Rakwal, R.; Hirano, M.; Shibato, J.; Nam, H. W.; Kim, Y. S.; Kouzuma, Y.; Agrawal, G. K.; Masuo, Y.; Yonekura, M. Proteomics of two cultivated mushrooms Sparassis crispa and Hericium erinaceum provides insight into their numerous functional protein components and diversity J. Proteome Res. 2008, 7 (5) 1819-35
17. Plett, J. M.; Kemppainen, M.; Kale, S. D.; Kohler, A.; Legue, V.; Brun, A.; Tyler, B. M.; Pardo, A. G.; Martin, F. A secreted effector protein of Laccaria bicolor is required for symbiosis development Curr. Biol. 2011, 21 (14) 1197-203
18. Vincent, D.; Kohler, A.; Claverol, S.; Solier, E.; Joets, J.; Gibon, J.; Lebrun, M. H.; Plomion, C.; Martin, F. Secretome of the free-living mycelium from the ectomycorrhizal basidiomycete Laccaria bicolor J. Proteome Res. 2012, 11 (1) 157-71
19. Cox, K. D.; Scherm, H.; Riley, M. B. Characterization of Armillaria spp. from peach orchards in the southeastern United States using fatty acid methyl ester profiling Mycol. Res. 2006, 110 (Pt 4) 414-22
20. Schrettl, M.; Carberry, S.; Kavanagh, K.; Haas, H.; Jones, G. W.; O'Brien, J.; Nolan, A.; Stephens, J.; Fenelon, O.; Doyle, S. Self-protection against gliotoxin - a component of the gliotoxin biosynthetic cluster, GliT, completely protects Aspergillus fumigatus against exogenous gliotoxin PLoS Pathog. 2010, 6 (6) e1000952
21. Yang, H. C.; Mikami, Y.; Imai, T.; Taguchi, H.; Nishimura, K.; Miyaji, M.; Branchini, M. L. Extrusion of fluorescein diacetate by multidrug-resistant Candida albicans Mycoses 2001, 44 (9-10) 368-74
22. Sicoli, G.; Fatehi, J. Development of species-specific PCR primers on rDNA for the identification of European Armillaria species Forest Pathol. 2003, 33 (5) 287-297
23. Misiek, M.; Hoffmeister, D. Processing sites involved in intron splicing of Armillaria natural product genes Mycol. Res. 2008, 112 (Pt 2) 216-24
24. Kozarewa, I.; Turner, D. J. Amplification-free library preparation for paired-end Illumina sequencing Methods Mol. Biol. 2009, 733, 257-66
25. Li, H.; Ruan, J.; Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores Genome Res. 2008, 18 (11) 1851-8
26. Bentley, D. R.; Balasubramanian, S.; Swerdlow, H. P.; Smith, G. P.; Milton, J.; Brown, C. G.; Hall, K. P.; Evers, D. J.; Barnes, C. L.; Bignell, H. R.; Boutell, J. M.; Bryant, J.; Carter, R. J.; Keira Cheetham, R.; Cox, A. J.; Ellis, D. J.; Flatbush, M. R.; Gormley, N. A.; Humphray, S. J.; Irving, L. J.; Karbelashvili, M. S.; Kirk, S. M.; Li, H.; Liu, X.; Maisinger, K. S.; Murray, L. J.; Obradovic, B.; Ost, T.; Parkinson, M. L.; Pratt, M. R.; Rasolonjatovo, I. M.; Reed, M. T.; Rigatti, R.; Rodighiero, C.; Ross, M. T.; Sabot, A.; Sankar, S. V.; Scally, A.; Schroth, G. P.; Smith, M. E.; Smith, V. P.; Spiridou, A.; Torrance, P. E.; Tzonev, S. S.; Vermaas, E. H.; Walter, K.; Wu, X.; Zhang, L.; Alam, M. D.; Anastasi, C.; Aniebo, I. C.; Bailey, D. M.; Bancarz, I. R.; Banerjee, S.; Barbour, S. G.; Baybayan, P. A.; Benoit, V. A.; Benson, K. F.; Bevis, C.; Black, P. J.; Boodhun, A.; Brennan, J. S.; Bridgham, J. A.; Brown, R. C.; Brown, A. A.; Buermann, D. H.; Bundu, A. A.; Burrows, J. C.; Carter, N. P.; Castillo, N.; Chiara, E. C. M.; Chang, S.; Neil Cooley, R.; Crake, N. R.; Dada, O. O.; Diakoumakos, K. D.; Dominguez-Fernandez, B.; Earnshaw, D. J.; Egbujor, U. C.; Elmore, D. W.; Etchin, S. S.; Ewan, M. R.; Fedurco, M.; Fraser, L. J.; Fuentes Fajardo, K. V.; Scott Furey, W.; George, D.; Gietzen, K. J.; Goddard, C. P.; Golda, G. S.; Granieri, P. A.; Green, D. E.; Gustafson, D. L.; Hansen, N. F.; Harnish, K.; Haudenschild, C. D.; Heyer, N. I.; Hims, M. M.; Ho, J. T.; Horgan, A. M.; Hoschler, K.; Hurwitz, S.; Ivanov, D. V.; Johnson, M. Q.; James, T.; Huw Jones, T. A.; Kang, G. D.; Kerelska, T. H.; Kersey, A. D.; Khrebtukova, I.; Kindwall, A. P.; Kingsbury, Z.; Kokko-Gonzales, P. I.; Kumar, A.; Laurent, M. A.; Lawley, C. T.; Lee, S. E.; Lee, X.; Liao, A. K.; Loch, J. A.; Lok, M.; Luo, S.; Mammen, R. M.; Martin, J. W.; McCauley, P. G.; McNitt, P.; Mehta, P.; Moon, K. W.; Mullens, J. W.; Newington, T.; Ning, Z.; Ling, Ng, B.; Novo, S. M.; O'Neill, M. J.; Osborne, M. A.; Osnowski, A.; Ostadan, O.; Paraschos, L. L.; Pickering, L.; Pike, A. C.; Pike, A. C.; Chris Pinkard, D.; Pliskin, D. P.; Podhasky, J.; Quijano, V. J.; Raczy, C.; Rae, V. H.; Rawlings, S. R.; Chiva Rodriguez, A.; Roe, P. M.; Rogers, J.; Rogert Bacigalupo, M. C.; Romanov, N.; Romieu, A.; Roth, R. K.; Rourke, N. J.; Ruediger, S. T.; Rusman, E.; Sanches-Kuiper, R. M.; Schenker, M. R.; Seoane, J. M.; Shaw, R. J.; Shiver, M. K.; Short, S. W.; Sizto, N. L.; Sluis, J. P.; Smith, M. A.; Ernest Sohna Sohna, J.; Spence, E. J.; Stevens, K.; Sutton, N.; Szajkowski, L.; Tregidgo, C. L.; Turcatti, G.; Vandevondele, S.; Verhovsky, Y.; Virk, S. M.; Wakelin, S.; Walcott, G. C.; Wang, J.; Worsley, G. J.; Yan, J.; Yau, L.; Zuerlein, M.; Rogers, J.; Mullikin, J. C.; Hurles, M. E.; McCooke, N. J.; West, J. S.; Oaks, F. L.; Lundberg, P. L.; Klenerman, D.; Durbin, R.; Smith, A. J. Accurate whole human genome sequencing using reversible terminator chemistry Nature 2008, 456 (7218) 53-9
27. Zerbino, D. R.; Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs Genome Res. 2008, 18 (5) 821-9
28. Stanke, M.; Waack, S. Gene prediction with a hidden Markov model and a new intron submodel Bioinformatics 2003, 19 (Suppl 2) II215-25
29. Conesa, A.; Gotz, S.; Garcia-Gomez, J. M.; Terol, J.; Talon, M.; Robles, M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Bioinformatics 2005, 21 (18) 3674-6
30. Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat. Genet. 2000, 25 (1) 25-9
31. Bendtsen, J. D.; Nielsen, H.; von Heijne, G.; Brunak, S. Improved prediction of signal peptides: SignalP 3.0 J. Mol. Biol. 2004, 340 (4) 783-95
32. Altschul, S. F.; Madden, T. L.; Schaffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 1997, 25 (17) 3389-402
33. Enright, A. J.; Van Dongen, S.; Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families Nucleic Acids Res. 2002, 30 (7) 1575
34. Fitzpatrick, D. A.; Logue, M. E.; Stajich, J. E.; Butler, G. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis BMC Evol. Biol. 2006, 6 (1) 99
35. Creevey, C. J.; Fitzpatrick, D. A.; Philip, G. K.; Kinsella, R. J.; O'Connell, M. J.; Pentony, M. M.; Travers, S. A.; Wilkinson, M.; McInerney, J. O. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc. Biol. Sci. 2004, 271 (1557) 2551-8
36. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Research 2004, 32 (5) 1792
37. Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol. Biol. Evol. 2000, 17 (4) 540-52
38. Archie, J. W. A randomization test for phylogenetic information in systematic data Syst. Zool. 1989, 38, 251-278
39. Faith, D. P.; Cranston, P. S. Could a cladogram this short have arisen by chance alone? On permutation tests for cladistic structure Cladistics 1991, 7, 1-28
40. Keane, T. M.; Creevey, C. J.; Pentony, M. M.; Naughton, T. J.; McLnerney, J. O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified BMC Evol. Biol. 2006, 6, 29
41. Guindon, S.; Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol. 2003, 52 (5) 696
42. Page, R. D. GeneTree: comparing gene and species phylogenies using reconciled trees Bioinformatics 1998, 14 (9) 819-20
43. Slowinski, J. B.; Page, R. D. How should species phylogenies be inferred from sequence data? Syst. Biol. 1999, 48 (4) 814-25
44. Wehe, A.; Bansal, M. S.; Burleigh, J. G.; Eulenstein, O. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony Bioinformatics 2008, 24 (13) 1540-1
45. Fragner, D.; Zomorrodi, M.; Kues, U.; Majcherczyk, A. Optimized protocol for the 2-DE of extracellular proteins from higher basidiomycetes inhabiting lignocellulose Electrophoresis 2009, 30 (14) 2431-41
46. Imanaka, H.; Tanaka, S.; Feng, B.; Imamura, K.; Nakanishi, K. Cultivation characteristics and gene expression profiles of Aspergillus oryzae by membrane-surface liquid culture, shaking-flask culture, and agar-plate culture J. Biosci. Bioeng. 2010, 109 (3) 267-73
47. Kim, M.-S.; Klopfenstein, N. B.; McDonald, G. I.; Arumuganathan, K.; Vidaver, A. K. Characterization of North American Armillaria species by nuclear DNA content and RFLP analysis Mycologia 2000, 92 (5) 874-883
48. Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 1982, 157 (1) 105-32
49. Hunter, S.; Jones, P.; Mitchell, A.; Apweiler, R.; Attwood, T. K.; Bateman, A.; Bernard, T.; Binns, D.; Bork, P.; Burge, S.; de Castro, E.; Coggill, P.; Corbett, M.; Das, U.; Daugherty, L.; Duquenne, L.; Finn, R. D.; Fraser, M.; Gough, J.; Haft, D.; Hulo, N.; Kahn, D.; Kelly, E.; Letunic, I.; Lonsdale, D.; Lopez, R.; Madera, M.; Maslen, J.; McAnulla, C.; McDowall, J.; McMenamin, C.; Mi, H.; Mutowo-Muellenet, P.; Mulder, N.; Natale, D.; Orengo, C.; Pesseat, S.; Punta, M.; Quinn, A. F.; Rivoire, C.; Sangrador-Vegas, A.; Selengut, J. D.; Sigrist, C. J.; Scheremetjew, M.; Tate, J.; Thimmajanarthanan, M.; Thomas, P. D.; Wu, C. H.; Yeats, C.; Yong, S. Y. InterPro in 2011: new developments in the family and domain prediction database Nucleic Acids Res. 2011, 40 (Database issue) D306-12
50. Doerks, T.; Huber, S.; Buchner, E.; Bork, P. BSD: a novel domain in transcription factors and synapse-associated proteins Trends Biochem. Sci. 2002, 27 (4) 168-70
51. Fernandez-Fueyo, E.; Ruiz-Duenas, F. J.; Ferreira, P.; Floudas, D.; Hibbett, D. S.; Canessa, P.; Larrondo, L. F.; James, T. Y.; Seelenfreund, D.; Lobos, S.; Polanco, R.; Tello, M.; Honda, Y.; Watanabe, T.; Watanabe, T.; Ryu, J. S.; Kubicek, C. P.; Schmoll, M.; Gaskell, J.; Hammel, K. E.; St John, F. J.; Vanden Wymelenberg, A.; Sabat, G.; Splinter BonDurant, S.; Syed, K.; Yadav, J. S.; Doddapaneni, H.; Subramanian, V.; Lavin, J. L.; Oguiza, J. A.; Perez, G.; Pisabarro, A. G.; Ramirez, L.; Santoyo, F.; Master, E.; Coutinho, P. M.; Henrissat, B.; Lombard, V.; Magnuson, J. K.; Kues, U.; Hori, C.; Igarashi, K.; Samejima, M.; Held, B. W.; Barry, K. W.; LaButti, K. M.; Lapidus, A.; Lindquist, E. A.; Lucas, S. M.; Riley, R.; Salamov, A. A.; Hoffmeister, D.; Schwenk, D.; Hadar, Y.; Yarden, O.; de Vries, R. P.; Wiebenga, A.; Stenlid, J.; Eastwood, D.; Grigoriev, I. V.; Berka, R. M.; Blanchette, R. A.; Kersten, P.; Martinez, A. T.; Vicuna, R.; Cullen, D. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis Proc. Natl. Acad. Sci. U.S.A. 2012, 109 (14) 5458-63
52. Zhou, Q.; Rutland, M. W.; Teeri, T. T.; Brumer, H. Xyloglucan in cellulose modification Cellulose 2007, 14 (6) 625-641
53. Rose, J. K.; Braam, J.; Fry, S. C.; Nishitani, K. The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis: current perspectives and a new unifying nomenclature Plant Cell Physiol. 2002, 43 (12) 1421-35
54. Thompson, J. E.; Fry, S. C. Restructuring of wall-bound xyloglucan by transglycosylation in living plant cells Plant J. 2001, 26 (1) 23-34
55. Neer, E. J. Heterotrimeric G proteins: organizers of transmembrane signals Cell 1995, 80 (2) 249-57
56. Liu, Q. P.; Sulzenbacher, G.; Yuan, H.; Bennett, E. P.; Pietz, G.; Saunders, K.; Spence, J.; Nudelman, E.; Levery, S. B.; White, T.; Neveu, J. M.; Lane, W. S.; Bourne, Y.; Olsson, M. L.; Henrissat, B.; Clausen, H. Bacterial glycosidases for the production of universal red blood cells Nat. Biotechnol. 2007, 25 (4) 454-64
57. Boraston, A. B.; Bolam, D. N.; Gilbert, H. J.; Davies, G. J. Carbohydrate-binding modules: fine-tuning polysaccharide recognition Biochem. J. 2004, 382 (Pt 3) 769-81
58. Mehmood, M. A.; Xiao, X.; Hafeez, F. Y.; Gai, Y.; Wang, F. Molecular characterization of an endochitinase from Bacillus thuringiensis subsp. konkukian World J. Microbiol. Biotechnol. 2010, 26 (12) 2171-8
59. Zhang, J.; Siika-Aho, M.; Tenkanen, M.; Viikari, L. The role of acetyl xylan esterase in the solubilization of xylan and enzymatic hydrolysis of wheat straw and giant reed Biotechnol. Biofuels 2011, 4 (1) 60
60. Caufrier, F.; Martinou, A.; Dupont, C.; Bouriotis, V. Carbohydrate esterase family 4 enzymes: substrate specificity Carbohydr. Res. 2003, 338 (7) 687-92
61. Tsigos, I.; Bouriotis, V. Purification and characterization of chitin deacetylase from Colletotrichum lindemuthianum J. Biol. Chem. 1995, 270 (44) 26286-91
62. Jolie, R. P.; Duvetter, T.; Van Loey, A. M.; Hendrickx, M. E. Pectin methylesterase and its proteinaceous inhibitor: a review Carbohydr. Res. 2010, 345 (18) 2583-95
63. Yamada-Okabe, T.; Sakamori, Y.; Mio, T.; Yamada-Okabe, H. Identification and characterization of the genes for N-acetylglucosamine kinase and N-acetylglucosamine-phosphate deacetylase in the pathogenic fungus Candida albicans Eur. J. Biochem. 2001, 268 (8) 2498-505
64. Singh, P.; Ghosh, S.; Datta, A. Attenuation of virulence and changes in morphology in Candida albicans by disruption of the N-acetylglucosamine catabolic pathway Infect. Immun. 2001, 69 (12) 7898-903
65. Deli, A.; Koutsioulis, D.; Fadouloglou, V. E.; Spiliotopoulou, P.; Balomenou, S.; Arnaouteli, S.; Tzanodaskalaki, M.; Mavromatis, K.; Kokkinidis, M.; Bouriotis, V. LmbE proteins from Bacillus cereus are de-N-acetylases with broad substrate specificity and are highly similar to proteins in Bacillus anthracis FEBS J. 2010, 277 (13) 2740-53
66. Tanaka, T.; Fukui, T.; Fujiwara, S.; Atomi, H.; Imanaka, T. Concerted action of diacetylchitobiose deacetylase and exo-beta-D-glucosaminidase in a novel chitinolytic pathway in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 J. Biol. Chem. 2004, 279 (29) 30021-7
67. Watanabe, R.; Ohishi, K.; Maeda, Y.; Nakamura, N.; Kinoshita, T. Mammalian PIG-L and its yeast homologue Gpi12p are N- acetylglucosaminylphosphatidylinositol de-N-acetylases essential in glycosylphosphatidylinositol biosynthesis Biochem. J. 1999, 339 (Pt 1) 185-92
68. Kumar, S. V.; Phale, P. S.; Durani, S.; Wangikar, P. P. Combined sequence and structure analysis of the fungal laccase family Biotechnol. Bioeng. 2003, 83 (4) 386-94
69. Courty, P. E.; Hoegger, P. J.; Kilaru, S.; Kohler, A.; Buee, M.; Garbaye, J.; Martin, F.; Kues, U. Phylogenetic analysis, genomic organization, and expression analysis of multi-copper oxidases in the ectomycorrhizal basidiomycete Laccaria bicolor New Phytol. 2009, 182 (3) 736-50
70. Martinez, A. T.; Speranza, M.; Ruiz-Duenas, F. J.; Ferreira, P.; Camarero, S.; Guillen, F.; Martinez, M. J.; Gutierrez, A.; del Rio, J. C. Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin Int. Microbiol. 2005, 8 (3) 195-204
71. Kersten, P.; Cullen, D. Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium Fungal Genet. Biol. 2007, 44 (2) 77-87
72. Gold, M. H.; Youngs, H. L.; Gelpke, M. D. Manganese peroxidase Met. Ions Biol. Syst. 2000, 37, 559-86
73. Hammel, K. E.; Cullen, D. Role of fungal peroxidases in biological ligninolysis Curr. Opin. Plant Biol. 2008, 11 (3) 349-55
74. Bordoli, L.; Kiefer, F.; Arnold, K.; Benkert, P.; Battey, J.; Schwede, T. Protein structure homology modeling using SWISS-MODEL workspace Nat. Protoc. 2009, 4 (1) 1-13
75. Blodig, W.; Smith, A. T.; Doyle, W. A.; Piontek, K. Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism J. Mol. Biol. 2001, 305 (4) 851-61
76. Wood, Z. A.; Schroder, E.; Robin Harris, J.; Poole, L. B. Structure, mechanism and regulation of peroxiredoxins Trends Biochem. Sci. 2003, 28 (1) 32-40
77. Aran, M.; Ferrero, D. S.; Pagano, E.; Wolosiuk, R. A. Typical 2-Cys peroxiredoxins - modulation by covalent transformations and noncovalent interactions FEBS J. 2009, 276 (9) 2478-93
78. Sato, T.; Saito, H.; Swensen, J.; Olifant, A.; Wood, C.; Danner, D.; Sakamoto, T.; Takita, K.; Kasumi, F.; Miki, Y. The human prohibitin gene located on chromosome 17q21 is mutated in sporadic breast cancer Cancer Res. 1992, 52 (6) 1643-6
79. Nuell, M. J.; Stewart, D. A.; Walker, L.; Friedman, V.; Wood, C. M.; Owens, G. A.; Smith, J. R.; Schneider, E. L.; Dell' Orco, R.; Lumpkin, C. K. Prohibitin, an evolutionarily conserved intracellular protein that blocks DNA synthesis in normal fibroblasts and HeLa cells Mol. Cell. Biol. 1991, 11 (3) 1372-81
80. Lin, Y.-L.; Wen, T.-N.; Chang, S.-T.; Chu, F.-H. Proteomic Analysis of Differently Cultured Endemic Medicinal Mushroom Antrodia cinnamomea T.T. Chang et W.N. Chou from Taiwan Int. J. Med. Mushrooms 2011, 13 (5) 473-81
81. Costachel, C.; Coddeville, B.; Latge, J. P.; Fontaine, T. Glycosylphosphatidylinositol-anchored fungal polysaccharide in Aspergillus fumigatus J. Biol. Chem. 2005, 280 (48) 39835-42
82. Szeto, C. Y.; Leung, G. S.; Kwan, H. S. Le.MAPK and its interacting partner, Le.DRMIP, in fruiting body development in Lentinula edodes Gene 2007, 393 (1-2) 87-93
83. Herath, H. M.; Jacob, M.; Wilson, A. D.; Abbas, H. K.; Nanayakkara, N. P. New secondary metabolites from bioactive extracts of the fungus Armillaria tabescens Nat. Prod. Res. 2012, 10.1080/14786419.2012.738206
84. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 2004, 32 (5) 1792-7
85. Guindon, S.; Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol. 2003, 52 (5) 696-704