Dix NJ, Webster J: Fungal Ecology. 1994, Chapman & Hall Ltd
Google Scholar
Zhang N, Castlebury LA, Miller AN, Huhndorf SM, Schoch CL, Seifert KA, Rossman AY, Rogers JD, Kohlmeyer J, Volkmann-Kohlmeyer B, Sung GH: An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny. Mycologia. 2006, 98: 1076-1087. 10.3852/mycologia.98.6.1076.
Article
CAS
PubMed
Google Scholar
Cook R-J: Making greater use of introduced microorganisms for biological control of plant pathogens. Annu Rev Phytopathol. 1993, 31: 53-80. 10.1146/annurev.py.31.090193.000413.
Article
CAS
PubMed
Google Scholar
Benitez T, Rincon AM, Limon MC, Codon AC: Biocontrol mechanisms of Trichoderma strains. Int Microbiol. 2004, 7: 249-260.
CAS
PubMed
Google Scholar
Harman GE, Howell CR, Viterbo A, Chet I, Lorito M: Trichoderma spp. - opportunistic avirulent plant symbionts. Nature Rev Microbiol. 2004, 2: 43-56. 10.1038/nrmicro797.
Article
CAS
Google Scholar
Bailey B-A, Lumsden R-D: Direct effects of Trichoderma and Gliocladium on plant growth and resistance to plant pathogens. Trichoderma and Gliocladium. Enzymes, biological control and commercial applications. Edited by: Harman G-E, Kubicek C-P. 1998, Taylor & Francis, London, 2: 185-204.
Google Scholar
Carpenter MA, Stewart A, Ridgway HJ: Identification of novel Trichoderma hamatum genes expressed during mycoparasitism using subtractive hybridisation. FEMS Microbiol Letts. 2005, 251: 105-112. 10.1016/j.femsle.2005.07.035.
Article
CAS
Google Scholar
Liu PG, Yang Q: Identification of genes with a biocontrol function in Trichoderma harzianum mycelium using the expressed sequence tag approach. Res Microbiol. 2005, 156: 416-423. 10.1016/j.resmic.2004.10.007.
Article
CAS
PubMed
Google Scholar
Scherm B, Schmoll M, Balmas V, Kubicek CP, Migheli Q: Identification of potential marker genes for Trichoderma harzianum strains with high antagonistic potential against Rhizoctonia solani by a rapid subtraction hybridization approach. Curr Genet. 2009, 55: 81-91. 10.1007/s00294-008-0226-6.
Article
CAS
PubMed
Google Scholar
Vizcaíno JA, González FJ, Suárez MB, Redondo J, Heinrich J, Delgado-Jarana J, Hermosa R, Gutiérrez S, Monte E, Llobell A, Rey M: Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. BMC Genomics. 2006, 7: 193-10.1186/1471-2164-7-193.
Article
PubMed Central
PubMed
Google Scholar
Vizcaíno JA, Redondo J, Suárez MB, Cardoza RE, Hermosa R, González FJ, Rey M, Monte E: Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol. Appl Microbiol Biotechnol. 2007, 75: 853-862. 10.1007/s00253-007-0885-0.
Article
PubMed
Google Scholar
Trichoderma atroviride genome sequence. [http://genome.jgi-psf.org/Triat1/Triat1.home.html]
Casas-Flores S, Rios-Momberg M, Bibbins M, Ponce-Noyola P, Herrera-Estrella A: BLR-1 and BLR-2, key regulatory elements of photoconidiation and mycelial growth in Trichoderma atroviride. Microbiology UK. 2004, 150: 3561-3569. 10.1099/mic.0.27346-0.
Article
CAS
Google Scholar
Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R: Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev. 2004, 68: 1-108. 10.1128/MMBR.68.1.1-108.2004.
Article
PubMed Central
CAS
PubMed
Google Scholar
Arvas M, Pakula T, Lanthaler K, Saloheimo M, Valkonen M, Suortti T, Robson G, Penttilä M: Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae. BMC Genomics. 2006, 7: 32-10.1186/1471-2164-7-32.
Article
PubMed Central
PubMed
Google Scholar
Hinnebusch AT: Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol. 2005, 59: 407-50. 10.1146/annurev.micro.59.031805.133833.
Article
CAS
PubMed
Google Scholar
Andersen MR, Lehmann L, Nielsen J: Systemic analysis of the response of Aspergillus niger to ambient pH. Genome Biol. 2009, 10: R47-10.1186/gb-2009-10-5-r47.
Article
PubMed Central
PubMed
Google Scholar
Murillo LA, Newport G, Lan CY, Habelitz S, Dungan J, Agabian NM: Genome-wide transcription profiling of the early phase of biofilm formation by Candida albicans. Eukaryot Cell. 2005, 4: 1562-1573. 10.1128/EC.4.9.1562-1573.2005.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tian C, Kasuga T, Sachs MS, Glass NL: Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons. Eukaryot Cell. 2007, 6: 1018-1029. 10.1128/EC.00078-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Westergaard SL, Oliveira AP, Bro C, Olsson L, Nielsen J: A systems biology approach to study glucose repression in the yeast Saccharomyces cerevisiae. Biotechnol Bioeng. 2007, 96: 134-145. 10.1002/bit.21135.
Article
CAS
PubMed
Google Scholar
Zhao R, Houry WA: Hsp90: a chaperone for protein folding and gene regulation. Biochem Cell Biol. 2005, 83: 703-710. 10.1139/o05-158.
Article
CAS
PubMed
Google Scholar
Cowen LE, Lindquist S: Hsp90 potentiates the rapid evolution of new traits: drug resistance in diverse fungi. Science. 2005, 309: 2185-2189. 10.1126/science.1118370.
Article
CAS
PubMed
Google Scholar
Bösl B, Grimminger V, Walter S: The molecular chaperone Hsp104--a molecular machine for protein disaggregation. J Struct Biol. 2006, 156: 139-148.
Article
PubMed
Google Scholar
Kliebenstein DJ, Rowe HC, Denby KJ: Secondary metabolites influence Arabidopsis/Botrytis interactions: variation in host production and pathogen sensitivity. Plant J. 2005, 44: 25-36. 10.1111/j.1365-313X.2005.02508.x.
Article
CAS
PubMed
Google Scholar
Rhizoctonia solani: whole genome sequencing project. [http://rsolani.org/genome.html]
Botrytis cinerea database. [http://www.broad.mit.edu/annotation/genome/botrytis_cinerea/Home.html]
Hinnebusch AT, Natarajan K: Gcn4p, a master regulator of gene expression, is controlled at multiple levels by diverse signals of starvation and stress. Eukaryot Cell. 2002, 1: 22-32. 10.1128/EC.01.1.22-32.2002.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hoffmann B, Valerius O, Andermann M, Braus GH: Transcriptional autoregulation and inhibition of mRNA translation of amino acid regulator gene cpcA of filamentous fungus Aspergillus nidulans. Mol Biol Cell. 2001, 12: 2846-2857.
Article
PubMed Central
CAS
PubMed
Google Scholar
Viterbo A, Ramot O, Chemin L, Chet I: Significance of lytic enzymes from Trichoderma spp. in the biocontrol of fungal plant pathogens. Antonie Van Leeuwenhoek. 2002, 81: 549-556. 10.1023/A:1020553421740.
Article
CAS
PubMed
Google Scholar
Sims AH, Gent ME, Lanthaler K, Dunn-Coleman NS, Oliver SG, Robson GD: Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo. Appl Environ Microbiol. 2005, 71: 2737-2747. 10.1128/AEM.71.5.2737-2747.2005.
Article
PubMed Central
CAS
PubMed
Google Scholar
Krappmann S, Bignell EM, Reichard U, Rogers T, Haynes K, Braus GH: The Aspergillus fumigatus transcriptional activator CpcA contributes significantly to the virulence of this fungal pathogen. Mol Microbiol. 2004, 52: 785-799. 10.1111/j.1365-2958.2004.04015.x.
Article
CAS
PubMed
Google Scholar
Rohde JR, Bastidas R, Puria R, Cardenas ME: Nutritional control via Tor signaling in Saccharomyces cerevisiae. Curr Opin Microbiol. 2008, 11: 153-160. 10.1016/j.mib.2008.02.013.
Article
PubMed Central
CAS
PubMed
Google Scholar
Teichert S, Wottawa M, Schönig B, Tudzynski B: Role of the Fusarium fujikuroi TOR kinase in nitrogen regulation and secondary metabolism. Eukaryot Cell. 2006, 5: 1807-1819. 10.1128/EC.00039-06.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chung KS, Won M, Lee SB, Jang YJ, Hoe KL, Kim DU, Lee JW, Kim KW, Yoo HS: Isolation of a novel gene from Schizosaccharomyces pombe: stm1+ encoding a seventransmembrane loop protein that may couple with the heterotrimeric Galpha 2 protein, Gpa2. J Biol Chem. 2001, 276: 40190-40201.
Article
CAS
PubMed
Google Scholar
Zeilinger S, Reithner B, Scala V, Peissl I, Lorito M, Mach RL: Signal transduction by Tga3, a novel G protein alpha subunit of Trichoderma atroviride. Appl Environ Microbiol. 2005, 71: 1591-1597. 10.1128/AEM.71.3.1591-1597.2005.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dijksterhuis J, Veenhuis M, Harder W, Nordbring-Hertz B: Nematophagous fungi: physiological aspects and structure-function relationships. Adv Microb Physiol. 1994, 36: 111-143. full_text.
Article
CAS
PubMed
Google Scholar
Delgado-Jarana J, Sousa S, González F, Rey M, Llobell A: ThHog1 controls the hyperosmotic stress response in Trichoderma harzianum. Microbiology UK. 2006, 152: 1687-1700. 10.1099/mic.0.28729-0.
Article
CAS
Google Scholar
Brunner K, Omann M, Pucher ME, Delic M, Lehner SM, Domnanich P, Kratochwill K, Druzhinina I, Denk D, Zeilinger S: Trichoderma G protein-coupled receptors: functional characterisation of a cAMP receptor-like protein from Trichoderma atroviride. Curr Genet. 2008, 54: 283-299. 10.1007/s00294-008-0217-7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mendoza-Mendoza A, Pozo MJ, Grzegorski D, Martínez P, García JM, Olmedo-Monfil V, Cortés C, Kenerley C, Herrera-Estrella A: Enhanced biocontrol activity of Trichoderma through inactivation of a mitogen-activated protein kinase. Proc Natl Acad Sci USA. 2003, 100: 15965-15970. 10.1073/pnas.2136716100.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mukherjee M, Mukherjee PK, Kale SP: cAMP signalling is involved in growth, germination, mycoparasitism and secondary metabolism in Trichoderma virens. Microbiology UK. 2007, 153: 1734-1742. 10.1099/mic.0.2007/005702-0.
Article
CAS
Google Scholar
Mukherjee PK, Latha J, Hadar R, Horwitz BA: Role of two G-protein alpha subunits, TgaA and TgaB, in the antagonism of plant pathogens by Trichoderma virens. Appl Environ Microbiol. 2004, 70: 542-549. 10.1128/AEM.70.1.542-549.2004.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mukherjee PK, Latha J, Hadar R, Horwitz BA: TmkA, a mitogen-activated protein kinase of Trichoderma virens, is involved in biocontrol properties and repression of conidiation in the dark. Eukaryot Cell. 2003, 2: 446-455. 10.1128/EC.2.3.446-455.2003.
Article
PubMed Central
CAS
PubMed
Google Scholar
Reithner B, Brunner K, Schuhmacher R, Peissl I, Seidl V, Krska R, Zeilinger S: The G protein alpha subunit Tga1 of Trichoderma atroviride is involved in chitinase formation and differential production of antifungal metabolites. Fungal Genet Biol. 2005, 42: 749-760. 10.1016/j.fgb.2005.04.009.
Article
CAS
PubMed
Google Scholar
Reithner B, Schuhmacher R, Stoppacher N, Pucher M, Brunner K, Zeilinger S: Signalling via the Trichoderma atroviride mitogen-activated protein kinase Tmk 1 differentially affects mycoparasitism and plant protection. Fungal Genet Biol. 2007, 44: 1123-1133. 10.1016/j.fgb.2007.04.001.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rocha-Ramirez V, Omero C, Chet I, Horwitz BA, Herrera-Estrella A: Trichoderma atroviride G-protein alpha-subunit gene tga1 is involved in mycoparasitic coiling and conidiation. Eukaryot Cell. 2002, 1: 594-605. 10.1128/EC.1.4.594-605.2002.
Article
PubMed Central
CAS
PubMed
Google Scholar
Murakami Y, Tatebayashi K, Saito H: Two adjacent docking sites in the yeast Hog1 mitogen-activated protein (MAP) kinase differentially interact with the Pbs2 MAP kinase kinase and the Ptp2 protein tyrosine phosphatase. Mol Cell Biol. 2008, 28: 2481-2494. 10.1128/MCB.01817-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Suárez MB, Vizcaíno JA, Llobell A, Monte E: Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach. Curr Genet. 2007, 51: 331-342. 10.1007/s00294-007-0130-5.
Article
PubMed
Google Scholar
Hu G, Leger RJ: A phylogenomic approach to reconstructing the diversification of serine proteases in fungi. J Evol Biol. 2004, 17: 1204-1214. 10.1111/j.1420-9101.2004.00786.x.
Article
CAS
PubMed
Google Scholar
Olmedo-Monfil V, Mendoza-Mendoza A, Gómez I, Cortés C, Herrera-Estrella A: Multiple environmental signals determine the transcriptional activation of the mycoparasitism related gene prb1 in Trichoderma atroviride. Mol Genet Genomics. 2002, 267: 703-712. 10.1007/s00438-002-0703-4.
Article
CAS
PubMed
Google Scholar
Flores A, Chet I, Herrera-Estrella A: Improved biocontrol activity of Trichoderma harzianum by over-expression of the proteinase-encoding gene prb1. Curr Genet. 1997, 31: 30-37. 10.1007/s002940050173.
Article
CAS
PubMed
Google Scholar
Benhamou N, Chet I: Cellular and Molecular Mechanisms Involved in the Interaction between Trichoderma harzianum and Pythium ultimum. Appl EnvironMicrobiol. 1997, 63: 2095-2099.
CAS
Google Scholar
Oh Y, Donofrio N, Pan H, Coughlan S, Brown DE, Meng S, Mitchell T, Dean RA: Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae. Genome Biol. 2008, 9: R85-10.1186/gb-2008-9-5-r85.
Article
PubMed Central
PubMed
Google Scholar
Fungal Genetics Stock Center. [http://www.fgsc.net/methods/vogels.html]
Berrocal-Tito G, Sametz-Baron L, Eichenberg K, Horwitz BA, Herrera-Estrella A: Rapid blue light regulation of a Trichoderma harzianum photolyase gene. J Biol Chem. 1999, 274: 14288-14294. 10.1074/jbc.274.20.14288.
Article
CAS
PubMed
Google Scholar
Chomczynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987, 162: 156-159. 10.1016/0003-2697(87)90021-2.
Article
CAS
PubMed
Google Scholar
Detter JC, Jett JM, Lucas SM, Dalin E, Arellano AR, Wang M, Nelson JR, Chapman J, Lou Y, Rokhsar D, Hawkins TL, Richardson PM: Isothermal strand displacement amplification applications for high-throughput genomics. Genomics. 2002, 80: 691-698. 10.1006/geno.2002.7020.
Article
CAS
PubMed
Google Scholar
Huang X, Madan A: CAP3: A DNA Sequence Assembling Program. Genome Research. 1999, 9: 868-877. 10.1101/gr.9.9.868.
Article
PubMed Central
CAS
PubMed
Google Scholar
HMMER User's Guide: Biological sequence analysis using profile hidden Markov models. [http://hmmer.janelia.org/]
Kumar S, Tamura K, Nei M: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 2004, 5: 150-163. 10.1093/bib/5.2.150.
Article
CAS
PubMed
Google Scholar
Sun J, Lu X, Rinas U, Zeng AP: Metabolic pecularities of Aspergillus niger disclosed by comparative metabolic genomics. Genome Biology. 2007, 8: R182-10.1186/gb-2007-8-9-r182.
Article
PubMed Central
PubMed
Google Scholar
Ma H, Zeng AP: Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics. 2003, 19: 270-277. 10.1093/bioinformatics/19.2.270.
Article
CAS
PubMed
Google Scholar
The Software Cytoscape. [http://www.cytoscape.org]
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13: 2498-2504. 10.1101/gr.1239303.
Article
PubMed Central
CAS
PubMed
Google Scholar
Horie T, Tatebayashi K, Yamada R, Saito H: Phosphorylated Ssk1 prevents unphosphorylated Ssk1 from activating the Ssk2 mitogen-activated protein kinase kinase kinase in the yeast high-osmolarity glycerol osmoregulatory pathway. Mol Cell Biol. 2008, 28: 5172-5183. 10.1128/MCB.00589-08.
Article
PubMed Central
CAS
PubMed
Google Scholar