ClassII peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi

ISME Journal

Volumn 3, Issue 12, 2009, Pages 1387-1395

  Bödeker, Inga T M ^a   Nygren, Cajsa M R ^a   Taylor, Andy F S ^b   Olson, Åke ^a   Lindahl, Björn D ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

Author keywords

ClassII peroxidases; Decomposition; Degenerate primer; Ectomycorrhiza; nutrient cycling; Soil organic matter

Indexed keywords

FUNGAL DNA; FUNGAL PROTEIN; PEROXIDASE; PRIMER DNA;

ARTICLE; CLUSTER ANALYSIS; DNA SEQUENCE; ENZYME ACTIVE SITE; ENZYMOLOGY; GENETICS; METHODOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; MYCORRHIZA; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY;

CATALYTIC DOMAIN; CLONING, MOLECULAR; CLUSTER ANALYSIS; CONSERVED SEQUENCE; DNA PRIMERS; DNA, FUNGAL; FUNGAL PROTEINS; MOLECULAR SEQUENCE DATA; MYCORRHIZAE; PEROXIDASE; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID;

BASIDIOMYCOTA; CORTINARIUS; FUNGI; HOMOBASIDIOMYCETES; LACTARIUS; RUSSULA;

EID: 72649085431     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2009.77     Document Type: Article

References (41)

1. Aerts R. (1995). The advantages of being evergreen. Trends Ecol Evol 10: 402-407.
2. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, MillerWet al. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
3. Baldrian P. (2006). Fungal laccases-occurrence and properties. FEMS Microbio Rev 30: 215-242.
4. Bao W, Omalley DM, Whettn R, Sederoff RR. (1993). A laccase associated with lignification in loblolly-pine xylem. Science 260: 672-674.
5. Bending GD, Read DJ. (1996). Nitrogen mobilization from protein polyphenol complex by ericoid and ectomycorrhizal fungi. Soil Biol Biochem 28: 1603-1612.
6. Bending GD, Read DJ. (1997). Lignin and soluble phenolic degradation by ectomycorrhizal and ericoid mycorrhizal fungi. Mycol Res 101: 1348-1354.
7. Binder M, Hibbet DS, Larsson KH, Larsson E, Langer E, Langer G. (2005). The phylogenetic distribution of resupinate forms across the major clades of mushroom- forming fungi (Homobasidiomycetes). System Biodivers 3: 113-157.
8. Chambers SM, Burke RM, Brooks PR, Cairney JWG. (1999). Molecular and biochemical evidence for manganesedependent peroxidase activity in Tylospora fibrillosa. Mycol Res 103: 1098-1102.
9. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG et al. (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
10. Dijkstra FA, Cheng WX. (2007). Interactions between soil and tree roots accelerate long-term soil carbon decomposition. Ecol Lett 10: 1046-1053.
11. Haselwandter K, Bobleter O, Read DJ. (1990). Degradation of C-14 labeled lignin and dehydropolymer of coniferyl alcohol by ericoid and ectomycorrhizal fungi. Arch Microbiol 153: 352-354.
12. Hatakka A. (1994). Ligin-modifying enzymes from selected white-rot fungi-production and role in lignin degradation. FEMS Microbiol Rev 13: 125-135.
13. Hibbett DS, Gilbert LB, Donoghue MJ. (2000). Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 407: 506-508.
14. Kirk TD, Farrell RL. (1987). Enzymatic combustion-the microbial degradation of lignin. Ann Rev Microbiol 41: 465-505.
15. Knudsen H, Versterholt J. (2008). Funga Nordica. Nordsvamp. Copenhagen, Denmark.
16. Koide RT, Sharda JN, Herr JR, Malcom GM. (2008). Ectomycorrhizal fungi and the biotrophy-saprotrophy continuum. New Phytol 178: 230-233.
17. Lindahl BD, Ihrmark K, Boberg J, Trumboe SE, Hogberg P, Stenlid J et al. (2007). Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. New Phytol 173: 611-620.
18. Lindahl BD, Taylor AFS. (2004). Occurrence of Nacetylhexosaminidase- encoding genes in ectomycorrhizal basidiomycetes. New Phytol 164: 193-199.
19. Lindahl BD, Taylor AFS, Finlay RD. (2002). Defining nutritional constraints on carbon cycling in boreal forests-towards a less 'phytocentric' perspective. Plant Soil 242: 123-135.
20. Lynch M, Conery JS. (2000). The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
21. Maijala P, Harrington TC, Raudaskoski M. (2003). A peroxidase gene family and gene trees in Heterobasidion and related genera. Mycologia 95: 209-211.
22. Martin F, Aerts A, Ahren D, Brun A, Danchin EGJ, Duchaussoy F et al. (2008). The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452: 88-92, U7.
23. Martinez AT. (2002). Molecular biology and structure- function of lignin-degrading heme peroxidases. Enzyme Microb Technol 30: 425-444.
24. Morgenstern I, Klopman S, Hibbett DS. (2008). Molecular evolution and diversity of lignin degrading heme peroxidases in the agaricomycetes. J Mol Evol 66: 243-257.
25. Myneni RB, Dong J, Tucker CJ, Kaufmann RK, Kauppi PE, Liski J et al. (2001). A large carbon sink in the woody biomass of Northern forests. Proc Natl Acad Sci USA 98: 14784-14789.
26. Northup RR, Yu ZS, Dahlgren RA, Vogt KA. (1995). Polyphenol control of nitrogen release from pine litter. Nature 377: 227-229.
27. Nygren CMR, Eberhardt U, Karlsson M, Parrent JL, Lindahl BD, Taylor AFS. (2008). Growth on nitrate and occurrence of nitrate reductase-encoding genes in a phylogenetically diverse range of ectomycorrhizal fungi. New Phytol 180: 875-889.
28. Passardi F, Bakalovic N, Teixeira FK, Margis-Pinheiro M, Penel C, Dunand C. (2007a). Prokaryotic origins of the non-animal peroxidase superfamily and organellemediated transmission to eukaryotes. Genomics 89: 567-579.
29. Passardi F, Theiler G, Zamocky M, Cosio C, Rouhier N, Teixeira F et al. (2007b). PeroxiBase: The peroxidase database. Phytochemistry 68: 1605-1611.
30. Pérez-Boada M, Ruiz-Duenas FJ, Pogni R, Basosi R, Choinowski T, Martinez MJ et al. (2005). Versatile peroxidase oxidation of high redox potential aromatic compounds: Site-directed mutagenesis, spectroscopic and crystallographic investigation of three long-ranged electron transfer pathways. J Mol Biol 354: 385-402.
31. Rayner ADM, Boddy L, Dowson CG. (1987). Genetic interactions and developmental versatility during establishment of decomposer basidiomycetes in wood and tree litter. In: Fletcher M, Gray TRG, Jones JG (eds). Symposium of the Society for General Microbiology, 41.
32. Ecology of Microbial Communities. Cambridge University Press: New York, USA, Cambridge, UK
33. Read DJ. (1991). Mycorrhizas in ecosystems. Experientia 47: 376-391.
34. Robinson JM. (1996). Atmospheric bulk chemistry and evolutionary megasymbiosis. Chemosphere 33: 1641-1653.
35. Ruiz-Duenas FJ, Martinez MJ, Martinez AT. (1999). Molecular characterization of a novel peroxidase isolated from the ligninolytic fungus Pleurotus eryngii. Mol Microbiol 31: 223-235.
36. Sinsabaugh RL. (2005). Fungal enzymes at the community scale. In: Dighton J, White JF, Oudemans P (eds). The Fungal Community. Its Organization and Role in the Ecosystem, 3rd edn. Taylor & Francis: Boca Raton, FL. pp 349-360.
37. Steffen KT, Hatakka A, Hofrichter M. (2002). Degradation of humic acids by the litter-decomposing basidiomycetes Collybia dryophila. Appl Environ Microbiol 68: 3442-3448.
38. Swofford DL. (2003). PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinaur Associates: Sunderland, MA.
39. Talbot JM, Allison SD, Treseder KK. (2008). Decomposers in disguise: mycorrhizal fungi as regulators of soil C dynamics in ecosystems under global change. Funct Ecol 22: 955-963.
40. Trojanowski J, Haider K, Huttermann A. (1984). Decomposition of C-14 labeled lignin, holocellulose and lignocellulose by mycorrhizal fungi. Arch Microbiol 139: 202-206.
41. Wapinski I, Pfeffer A, Friedman N, Regev A. (2007). Natural history and evolutionary principles of gene duplication in fungi. Nature 449: 54-61.