Post-genomic approaches to understanding interactions between fungi and their environment

IMA Fungus

Volumn 2, Issue 1, 2011, Pages 81-86

  de Vries, Ronald P ^a,b   Benoit, Isabelle ^b   Doehlemann, Gunther ^c   Kobayashi, Tetsuo ^d   Magnuson, Jon K ^e   Panisko, Ellen A ^e   Baker, Scott E ^e   Lebrun, Marc Henri ^f  

^a CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

^b UTRECHT UNIVERSITY   (Netherlands)

^c MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^d NAGOYA UNIVERSITY   (Japan)

^e PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^f INRA Institut National de la Recherche Agronomique   (France)

Author keywords

(post )genomics; Aspergillus niger; Aspergillus oryzae; Phycomyces blakesleeanus; Thielavia terrestris; Ustilago maydis

Indexed keywords

EID: 84860382622     PISSN: 22106340     EISSN: 22106359     Source Type: Journal    
DOI: 10.5598/imafungus.2011.02.01.11     Document Type: Article

References (40)

1. Acero FJ, Carbu M, El-Akhal MR, Garrido C, Gonzalez-Rodriguez VE, Cantoral JM (2011) Development of proteomics-based fungicides: new strategies for environmentally friendly control of fungal plant diseases. International Journal of Molecular Sciences 12: 795-816
2. Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J (2008) A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proceedings of the National Academy of Sciences, USA 105: 4387-4392
3. Bhadauria V, Popescu L, Zhao WS, Peng YL (2007) Fungal transcriptomics. Microbiology Research 162: 285-298
4. Cuomo CA, Guldener U, Xu JR, Trail F, Turgeon BG, Di Pietro A, et al. (2007) The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317: 1400-1402
5. de Groot MJ, Daran-Lapujade P, van Breukelen B, Knijnenburg TA, de Hulster EA, Reinders MJ, et al. (2007) Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. Microbiology 153: 3864-3878
6. de Vries RP and Visser J (2001) Aspergillus enzymes involved in degradation of plant cell wall polysaccharides. Microbiology and Molecular Biology Reviews 65: 497-522
7. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, et al. (2005) The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434: 980-986
8. Doehlemann G, Wahl R, Horst RJ, Voll LM, Usadel B, Poree F, et al. (2008) Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. Plant Journal 56: 181-195
9. Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, et al. (2008) The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biology 9: R77 (71-22)
10. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868
11. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 1105-1115
12. Gasser B, Sauer M, Maurer M, Stadlmayr G, Mattanovich D (2007) Transcriptomics-based identification of novel factors enhancing heterologous protein secretion in yeasts. Applied and Environmental Microbiology 73: 6499-6507
13. Gowda M, Venu RC, Raghupathy MB, Nobuta K, Li H, Wing R, et al. (2006) Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods. BMC Genomics 7: 310
14. Grinyer J, McKay M, Nevalainen H, Herbert BR (2004) Fungal proteomics: initial mapping of biological control strain Trichoderma harzianum. Current Genetics 45: 163-169
15. Hauser NC, Dukalska M, Fellenberg K, Rupp S (2009) From experimental setup to data analysis in transcriptomics: copper metabolism in the human pathogen Candida albicans. Journal of Biophotonics 2: 262-268
16. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183
17. Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, et al. (2007) Genome sequence of the lignocellulosebioconverting and xylose-fermenting yeast Pichia stipitis. Nature Biotechnology 25: 319-326
18. Kämper J, Kahmann R, Bölker M, Ma L-J, Brefort T, Saville BJ, et al. (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444: 97-101
19. Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, et al. (2005) Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Researchs 33: 6469-6485
20. Kim ST, Cho KS, Yu S, Kim SG, Hong JC, Han CD, et al. (2003) Proteomic analysis of differentially expressed proteins induced by rice blast fungus and elicitor in suspension-cultured rice cells. Proteomics 3: 2368-2378
21. Kim ST, Yu S, Kim SG, Kim HJ, Kang SY, Hwang DH, et al. (2004) Proteome analysis of rice blast fungus (Magnaporthe grisea) proteome during appressorium formation. Proteomics 4: 3579-3587
22. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, et al. (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proceedings of the National Academy of Sciences, USA 94: 13057-13062
23. Levin AM, de Vries RP, Conesa A, de Bekker C, Talon M, Menke HH, et al. (2007a) Spatial differentiation in the vegetative mycelium of Aspergillus niger. Eukaryotic Cell 6: 2311-2322
24. Levin AM, de Vries RP and Wosten HA (2007b) Localization of protein secretion in fungal colonies using a novel culturing technique; the ring-plate system. Journal of Microbiological Methods 69: 399-401
25. Lim D, Hains P, Walsh B, Bergquist P, Nevalainen H (2001) Proteins associated with the cell envelope of Trichoderma reesei: a proteomic approach. Proteomics 1: 899-909
26. Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438: 1157-1161
27. Martin F, Aerts A, Ahren D, Brun A, Danchin EG, Duchaussoy F, et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452: 88-92
28. Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, et al. (2010) Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464: 1033-1038
29. Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, et al. (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology 26: 553-560
30. Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, et al. (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology 22: 695-700
31. Matis M, Zakelj-Mavric M, Peter-Katalinic J (2005) Mass spectrometry and database search in the analysis of proteins from the fungus Pleurotus ostreatus. Proteomics 5: 67-75
32. Mogensen J, Nielsen HB, Hofmann G, Nielsen J (2006) Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol. Fungal Genetics and Biology 43: 593-603
33. Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, et al. (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438: 1151-1156
34. Noguchi Y, Sano M, Kanamaru K, Ko T, Takeuchi M, Kato M, et al. (2009) Genes regulated by AoXlnR, the xylanolytic and cellulolytic transcriptional regulator, in Aspergillus oryzae. Applied Microbiology and Biotechnology 85: 141-154
35. Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, et al. (2010) Genome sequence of the model mushroom Schizophyllum commune. Nature Biotechnology. 28: 957-963
36. Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology 25: 221-231
37. Rossouw D, Naes T, Bauer FF (2008) Linking gene regulation and the exo-metabolome: a comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast. BMC Genomics 9: 530
38. Skibbe DS, Doehlemann G, Fernandes J, Walbot V (2010) Maize tumors caused by Ustilago maydis require organ-specific genes in host and pathogen. Science 328: 89-92
39. Wösten HAB, Mouhka SM, McLaughlin PMJ, Sietsma JH, Wessels JGH (1991) Localization of growth and excretion of proteins in Aspergillus niger. Journal of General Microbiology 137: 2017-2023
40. Yates JR, Morgan SF, Gatlin CL, Griffin PR, Eng JK (1998) Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis. Analytical Chemistry 70: 3557-3565