Differential gene expression in pycnoporus coccineus during interspecific mycelial interactions with different competitors

Applied and Environmental Microbiology

Volumn 79, Issue 21, 2013, Pages 6626-6636

  Arfi, Yonathan ^a,b   Levasseur, Anthony ^a   Record, Eric ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BOTRYTIS CINEREA; BROWN ROT FUNGI; CONIOPHORA PUTEANA; DIFFERENTIAL GENE EXPRESSIONS; ENVIRONMENTAL RESOURCES; PYCNOPORUS COCCINEUS; SECONDARY METABOLITES; WHITE ROT FUNGI;

DETOXIFICATION; TRANSCRIPTION;

FUNGI;

COMPETITION (ECOLOGY); DETOXIFICATION; ENVIRONMENTAL MONITORING; FUNGAL DISEASE; FUNGUS; GENE EXPRESSION; METABOLITE; POLYMERASE CHAIN REACTION;

FUNGAL PROTEIN;

ARTICLE; BOTRYTIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; MYCELIUM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PYCNOPORUS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

BASE SEQUENCE; BOTRYTIS; FUNGAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; MOLECULAR SEQUENCE DATA; MYCELIUM; PYCNOPORUS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, RNA; SPECIES SPECIFICITY;

EID: 84886905920     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02316-13     Document Type: Article

References (63)

1. Boddy L. 2000. Interspecific combative interactions between wooddecaying basidiomycetes. FEMS Microbiol. Ecol. 31:185-194.
2. Woodward S, Boddy L. 2008. Interactions between saprotrophic fungi, p 123-139. In Boddy L, Frankland JC, Van West P (ed), Ecology of saprotrophic basidiomycetes. Elsevier, Amsterdam, Netherlands.
3. Owens EM, Reddy CA, Grethlein HE. 1994. Outcome of interspecific interactions among brown-rot and white-rot wood decay fungi. FEMS Microbiol. Ecol. 14:19-24.
4. Boddy L, Heilmann-Clausen J. 2008. Basidiomycete community development in temperate angiosperm wood, p 211-239. In Boddy L, Frankland JC, Van West P (ed), Ecology of saprotrophic basidiomycetes. Elsevier, Amsterdam, Netherlands.
5. Song Z, Vail A, Sadowsky MJ, Schilling JS. 2012. Competition between two wood-degrading fungi with distinct influences on residues. FEMS Microbiol. Ecol. 79:109-117.
6. Weindling R. 1932. Trichoderma lignorum as a parasite of other soil fungi. Phytopathology 22:832-845.
7. Bruce A, Highley TL. 1991. Control of growth of wood decay basidiomycetes by Trichoderma spp. and other potentially antagonistic fungi. Forest Prod. J. 41:63-67.
8. Rayner AD, Boddy L. 1988. Decomposition of wood: its biology and ecology. John Wiley, Chichester, United Kingdom.
9. Griffith GS, Rayner ADM, Wildman HG. 1994. Interspecific interactions and mycelial morphogenesis of Hypholoma fasciculare (Agaricaceae). Nova Hedwigia 59:47-75.
10. Baldrian P. 2004. Increase of laccase activity during interspecific interactions of white-rot fungi. FEMS Microbiol. Ecol. 50:245-253.
11. Iakovlev A, Olson Å Elfstrand M, Stenlid J. 2004. Differential gene expression during interactions between Heterobasidion annosum and Physisporinus sanguinolentus. FEMS Microbiol. Lett. 241:79-85.
12. Hiscox J, Baldrian P, Rogers HJ, Boddy L. 2010. Changes in oxidative enzyme activity during interspecific mycelial interactions involving the white-rot fungus Trametes versicolor. Fungal Genet. Biol. 47:562-571.
13. White NA, Boddy L. 1992. Extracellular enzyme localization during interspecific fungal interactions. FEMS Microbiol. Lett. 98:75-79.
14. Iakovlev A, Stenlid J. 2000. Spatiotemporal patterns of laccase activity in interacting mycelia of wood-decaying basidiomycete fungi. Microb. Ecol. 39:236-245.
15. Chi Y, Hatakka A, Maijala P. 2007. Can co-culturing of two white-rot fungi increase lignin degradation and the production of lignin-degrading enzymes? Int. Biodeterior. Biodegradation 59:32-39.
16. Ferreira Gregorio AP, Da Silva IR, Sedarati MR, Hedger JN. 2006. Changes in production of lignin degrading enzymes during interactions between mycelia of the tropical decomposer basidiomycetes Marasmiellus troyanus and Marasmius pallescens. Microbiol. Res. 110:161-168.
17. De Vries OMH, Kooistra WHCF, Wessels JGH. 1986. Formation of an extracellular laccase by a Schizophyllum commune dikaryon. Microbiology 132:2817-2826.
18. Hynes J, Müller CT, Jones TH, Boddy L. 2007. Changes in volatile production during the course of fungal mycelial interactions between Hypholoma fasciculare and Resinicium bicolor. J. Chem. Ecol. 33:43-57.
19. Evans JA, Eyre CA, Rogers HJ, Boddy L, Müller CT. 2008. Changes in volatile production during interspecific interactions between four wood rotting fungi growing in artificial media. Fungal Ecol. 1:57-68.
20. Savoie J-M, Mata G. 2003. Trichoderma harzianum metabolites preadapt mushrooms to Trichoderma aggressivum antagonism. Mycologia 95:191-199.
21. Peiris D, Dunn W, Brown M, Kell D, Roy I, Hedger J. 2008. Metabolite profiles of interacting mycelial fronts differ for pairings of the wood decay basidiomycete fungus, Stereum hirsutum with its competitors Coprinus micaceus and Coprinus disseminatus. Metabolomics 4:52-62.
22. Freitag M, Morrell JJ. 1992. Changes in selected enzyme activities during growth of pure and mixed cultures of the white-rot decay fungus Trametes versicolor and the potential biocontrol fungus Trichoderma harzianum. Can. J. Microbiol. 38:317-323.
23. Reyes F, Villanueva P, Alfonso C. 1990. Comparative study of acid and alkaline phosphatase during the autolysis of filamentous fungi. Lett. Appl. Microbiol. 10:175-177.
24. Patil R, Ghormade V, Deshpande M. 2000. Chitinolytic enzymes: an exploration. Enzyme Microb. Technol. 26:473-483.
25. Lindahl BD, Finlay RD. 2006. Activities of chitinolytic enzymes during primary and secondary colonization of wood by basidiomycetous fungi. New Phytol. 169:389-397.
26. Eyre C, Muftah W, Hiscox J, Hunt J, Kille P, Boddy L, Rogers HJ. 2010. Microarray analysis of differential gene expression elicited in Trametes versicolor during interspecific mycelial interactions. Fungal Biol. 114: 646-660.
27. Jonkers W, Rodriguez Estrada AE, Lee K, Breakspear A, May G, Kistler HC. 2012. Metabolome and transcriptome of the interaction between Ustilago maydis and Fusarium verticillioides in vitro. Appl. Environ. Microbiol. 78:3656-3667.
28. Ujor VC, Monti M, Peiris DG, Clements MO, Hedger JN. 2012. The mycelial response of the white-rot fungus, Schizophyllum commune to the biocontrol agent, Trichoderma viride. Fungal Biol. 116:332-341.
29. Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier J-M, Quévillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun M-H, Dickman M. 2011. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet. 7(8): e1002230. doi:10.1371/journal.pgen.1002230.
30. Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Górecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kües U, Kumar TKA, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Dueñas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS. 2012. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719.
31. Ainsworth C. 1994. Isolation of RNA from floral tissue of Rumex acetosa (sorrel). Plant Mol. Biol. Rep. 12:198-203.
32. Tomsovskỳ M, Kolaøík M, Pažoutová S, Homolka L. 2006. Molecular phylogeny of European Trametes (Basidiomycetes, Polyporales) species based on LSU and ITS (nrDNA) sequences. Nova Hedwigia 82:269-280.
33. Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, Obendorf D, Conlan C, Bahlo M, Blizzard CA, Pyecroft S, Kreiss A, Kellis M, Stark A, Harkins TT, Marshall Graves JA, Woods GM, Hannon GJ, Papenfuss AT. 2010. The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science 327:84-87.
34. Delmas S, Pullan ST, Gaddipati S, Kokolski M, Malla S, Blythe MJ, Ibbett R, Campbell M, Liddell S, Aboobaker A, Tucker GA, Archer DB. 2012. Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genet. 8(8):e1002875. doi:10.1371/journal.pgen.1002875.
35. Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140.
36. Anderson IC, Parkin PI. 2007. Detection of active soil fungi by RT-PCR amplification of precursor rRNA molecules. J. Microbiol. Methods 68: 248-253.
37. White TJ, Bruns TD, Lee SB, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p 315-322. In Innis MA, Gelfand DH, Sninsky JJ, White TJ (ed), PCR protocols: a guide to methods and applications. Academic Press, Inc., New York, NY.
38. Wilson CL, Wisniewski ME, Biles CL, McLaughlin R, Chalutz E, Droby S. 1991. Biological control of post-harvest diseases of fruits and vegetables: alternatives to synthetic fungicides. Crop Prot. 10:172-177.
39. Tripathi P, Dubey N. 2004. Exploitation of natural products as an alternative strategy to control postharvest fungal rotting of fruit and vegetables. Postharvest Biol. Technol. 32:235-245.
40. Brown ME, Beringer JE. 1983. The potential of antagonists for fungal control. Agric. Ecosyst. Environ. 10:127-141.
41. Lim T-K, Rohrbach KG. 1980. Role of Penicillium funiculosum strains in the development of pineapple fruit diseases. Phytopathology 70:663.
42. Droby S, Chalutz E, Wilson CL, Wisniewski M. 1989. Characterization of the biocontrol activity of Debaryomyces hansenii in the control of Penicillium digitatum on grapefruit. Can. J. Microbiol. 35:794-800.
43. Lima G, Arru S, De Curtis F, Arras G. 1999. Influence of antagonist, host fruit and pathogen on the biological control of postharvest fungal diseases by yeasts. J. Ind. Microbiol. Biotechnol. 23:223-229.
44. Pusey PL. 1984. Postharvest biological control of stone fruit brown rot by Bacillus subtilis. Plant Dis. 68:753.
45. Sumarah MW, Kesting JR, Sørensen D, Miller JD. 2011. Antifungal metabolites from fungal endophytes of Pinus strobus. Phytochemistry 72:1833-1837.
46. Wicklow DT, Joshi BK, Gamble WR, Gloer JB, Dowd PF. 1998. Antifungal metabolites (monorden, monocillin IV, and cerebrosides) from Humicola fuscoatra Traaen NRRL 22980, a mycoparasite of Aspergillus flavus sclerotia. Appl. Environ. Microbiol. 64:4482-4484.
47. Lomascolo A, Uzan-Boukhris E, Herpoël-Gimbert I, Sigoillot J-C, Lesage-Meessen L. 2011. Peculiarities of Pycnoporus species for applications in biotechnology. Appl. Microbiol. Biotechnol. 92:1129-1149.
48. Stepanova EV, Koroleva OV, Vasil'chenko LG, Karapetian KN, Landesman EO, Iavmetdinov IS, Kozlov IP, Rabinovich ML. Fungal decomposition of oat straw during liquid and solid state fermentation. Prikl. Biokhim. Mikrobiol. 39:74-84.
49. Viniegra-González G, Favela-Torres E, Aguilar CN, Rómero-Gomez SDJ , Díaz-Godínez JG, Augur C. 2003. Advantages of fungal enzyme production in solid state over liquid fermentation systems. Biochem. Eng. J. 13:157-167.
50. Gottlieb D, Van Etten JL. 1964. Biochemical changes during the growth of fungi. I. Nitrogen compounds and carbohydrate changes in Penicillium atrovenetum. J. Bacteriol. 88:114-121.
51. Van Etten JL, Gottlieb D. 1965. Biochemical changes during the growth of fungi. II. Ergosterol and fatty acids in Penicillium atrovenetum. J. Bacteriol. 89:409-414.
52. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. 2008. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18:1509-1517.
53. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5:621-628.
54. MacDonald J, Doering M, Canam T, Gong Y, Guttman DS, Campbell MM, Master ER. 2011. Transcriptomic responses of the softwooddegrading white-rot fungus Phanerochaete carnosa during growth on coniferous and deciduous wood. Appl. Environ. Microbiol. 77:3211-3218.
55. Yuan T, Ren Y, Meng K, Feng Y, Yang P, Wang S, Shi P, Wang L, Xie D, Yao B. 2011. RNA-Seq of the xylose-fermenting yeast Scheffersomyces stipitis cultivated in glucose or xylose. Appl. Microbiol. Biotechnol. 92: 1237-1249.
56. Wassarman DA, Steitz JA. 1991. RNA splicing. Alive with DEAD proteins. Nature 349:463-464.
57. Score AJ, Palfreyman JW, White NA. 1997. Extracellular phenoloxidase and peroxidase enzyme production during interspecific fungal interactions. Int. Biodeterior. Biodegradation 39:225-233.
58. Barski OA, Tipparaju SM, Bhatnagar A. 2008. The aldo-keto reductase superfamily and its role in drug metabolism and detoxification. Drug Metab. Rev. 40:553-624.
59. Qiu M, Xie R, Shi Y, Zhang H, Chen H. 2010. Isolation and identification of two flavonoid-producing endophytic fungi from Ginkgo biloba L. Ann. Microbiol. 60:143-150.
60. Örner MW, Jha HC. 1993. Antifungal activity of flavonoids and their mixtures against different fungi occurring on grain. Pestic. Sci. 38:347-351.
61. Wang J, Ogata M, Hirai H, Kawagishi H. 2011. Detoxification of aflatoxin B1 by manganese peroxidase from the white-rot fungus Phanerochaete sordida YK-624. FEMS Microbiol. Lett. 314:164-169.
62. Harms H, Schlosser D, Wick LY. 2011. Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nat. Rev. Microbiol. 9:177-192.
63. Georis J, Lomascolo A, Camarero S, Dorgeo V, Herpoël I, Asther M, Martinez AT, Dauvrin T. 2003. Pycnoporus cinnabarinus laccases: an interesting tool for food or non-food applications. Commun. Agric. Appl. Biol. Sci. 68:263-266.