Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose

Biotechnology for Biofuels

Volumn 6, Issue 1, 2013, Pages

  Bischof, Robert ^a   Fourtis, Lukas ^a   Limbeck, Andreas ^a   Gamauf, Christian ^b   Seiboth, Bernhard ^a   Kubicek, Christian P ^a  

^a VIENNA UNIVERSITY OF TECHNOLOGY   (Austria)

^b CLARIANT PRODUKTE DEUTSCHLAND GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOREFINERY PRODUCTS; CELLULASE PRODUCTION; COMPARATIVE ANALYSIS; ENZYME FORMATION; ENZYME PRODUCTION; LIGNOCELLULOSIC BIOMASS; SECOND GENERATION; TRICHODERMA REESEI;

BIOCHEMISTRY; CARBON; ENZYMES; GENE EXPRESSION; PHOSPHOLIPIDS; REPAIR; SUGARS;

STRAW;

CARBON; CHEMOSYNTHESIS; COMPARATIVE STUDY; DNA; ENZYME; FUNGUS; GENE EXPRESSION; HOMEOSTASIS; IRON; METABOLISM; PHOSPHOLIPID; STRAW; SUBSTRATE; WHEAT;

HYPOCREA JECORINA; TRITICUM AESTIVUM;

EID: 84883620601     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/1754-6834-6-127     Document Type: Article

References (50)

1. Kubicek CP, Fungi and lignocellulosic biomass New York: Wiley 2012
2. Production of bioethanol from wheat straw: an overview on pretreatment, hydrolysis and fermentation. Talebnia F, Karakashev D, Angelidaki I, Bioresour Technol 2010 101 4744 4753 10.1016/j.biortech.2009.11.080 20031394
3. Biology and biotechnology of Trichoderma. Schuster A, Schmoll M, Appl Microbiol Biotechnol 2010 87 787 799 10.1007/s00253-010-2632-1 20461510
4. Transcriptional regulation of plant cell wall degradation by filamentous fungi. Aro N, Pakula T, Penttilä M, FEMS Microbiol Rev 2005 29 719 739 10.1016/j.femsre.2004.11.006 16102600 (Pubitemid 41139180)
5. Fungal cellulolytic enzyme production: A review. Persson I, Tjerneld F, Hahn-Hägerdal B, Proc Biochem 1991 26 65 74 10.1016/0032-9592(91)80019-L
6. Studies on Quantitative Physiology of Trichoderma reesei with Two-Stage Continuous Culture for Cellulase Production. Ryu D, Andreotti R, Mandels M, Reese ET, Biotechnol Bioengin 1979 21 1887 1903 10.1002/bit.260211102
7. An accurate normalization strategy for RT-qPCR in Hypocrea jecorina (Trichoderma reesei). Steiger MG, Mach RL, Mach-Aigner AR, J Biotechnol 2010 145 30 37 10.1016/j.jbiotec.2009.10.012 19861137
8. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Güldener U, Mannhaupt G, Münsterkötter M, Mewes HW, Nucleic Acids Res 2004 32 5539 5545 10.1093/nar/gkh894 15486203 (Pubitemid 39545671)
9. Isotope-assisted screening for iron-containing metabolites reveals a high degree of diversity among known and unknown siderophores produced by Trichoderma spp. Lehner SM, Atanasova L, Neumann NK, Krska R, Lemmens M, Druzhinina IS, Schuhmacher R, Appl Environ Microbiol 2013 79 18 31 10.1128/AEM.02339-12 23064341
10. Novel traits of Trichoderma predicted through the analysis of its secretome. Druzhinina IS, Shelest E, Kubicek CP, FEMS Microbiol Lett 2012 337 1 9 10.1111/j.1574-6968.2012.02665.x 22924408
11. Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates. Häkkinen M, Arvas M, Oja M, Aro N, Penttilä M, Saloheimo M, Pakula TM, Microb Cell Fact. 2012 11 134 10.1186/1475-2859-11-134 23035824
12. A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases. Seidl V, Huemer B, Seiboth B, Kubicek CP, FEBS J 2005 272 5923 5939 10.1111/j.1742-4658.2005.04994.x 16279955 (Pubitemid 41689363)
13. Xyr1 (xylanase regulator 1) regulates both the hydrolytic enzyme system and D-xylose metabolism in Hypocrea jecorina. Stricker AR, Grosstessner-Hain K, Würleitner E, Mach RL, Eukaryot Cell. 2006 5 2128 2137 10.1128/EC.00211-06 17056741 (Pubitemid 44956824)
14. Identification of specific binding sites for XYR1, atranscriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei. Furukawa T, Shida Y, Kitagami N, Mori K, Kato M, Kobayashi T, Okada H, Ogasawara W, Morikawa Y, Fungal Genet Biol 2009 46 564 574 10.1016/j.fgb.2009.04.001 19393758
15. Genome Sequence Analysis of the Cellulolytic Fungus Trichoderma reesei (syn. Hypocrea jecorina) Reveals a Surprisingly Limited Inventory of Carbohydrate Active Enzymes. Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, et al. Nat Biotechnol 2008 26 553 560 10.1038/nbt1403 18454138 (Pubitemid 351668043)
16. Corder GW, Foreman DI, Nonparametric Statistics for Non-Statisticians: A Step-by-Step Approach NY: Wiley 2009
17. The role of macroautophagy in development of filamentous fungi. Bartoszewska M, Kiel JAKW, Antioxid Redox Signaling 2011 14 2271 2287 10.1089/ars.2010.3528
18. Regulation of macroautophagy in S. cerevisiae. Inoue Y, Klionsky DJ, Semin Cell Dev Biol 2010 21 664 670 10.1016/j.semcdb.2010.03.009 20359542
19. Systems analysis of lactose metabolism in Trichoderma reesei identifies a lactose permease that is essential for cellulase induction. Ivanova C, Baath J, Seiboth B, Kubicek CP, PLOS One. 2013 8 62631 10.1371/journal.pone.0062631 23690947
20. Differential induction of two xylanases in Trichoderma reesei. Zeilinger S, Mach RL, Schindler M, Herzog P, Kubicek CP, J Biol Chem 1996 271 25624 25629 10.1074/jbc.271.41.25624 8810338 (Pubitemid 26337942)
21. Prepared for the possible: xylanase gene transcription in Trichoderma reesei is triggered by different inducers representing different hemicellulosic pentose polymers. Herold S, Bischof R, Metz B, Seiboth B, Kubicek CP, Eukaryot Cell 2013 12 390 398 10.1128/EC.00182-12 23291620
22. Molecular regulation of arabinan and L-arabinose metabolism in Hypocrea jecorina (Trichoderma reesei). Akel E, Metz B, Seiboth B, Kubicek CP, Eukaryot Cell 2009 8 1837 1844 10.1128/EC.00162-09 19801419
23. The phosducin-like protein PhLP1 impacts regulation of glycoside hydrolases and light response in Trichoderma reesei. Tisch D, Kubicek CP, Schmoll M, BMC Genomics 2012 12 613
24. Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa. Sun J, Tian C, Diamond S, Glass NL, Eukaryot Cell. 2012 11 482 493 10.1128/EC.05327-11 22345350
25. Role of Ace2 (Activator of Cellulases 2) within the xyn2 transcriptosome of Hypocrea jecorina. Stricker AR, Trefflinger P, Aro N, Penttilä M, Mach RL, Fungal Genet Biol 2008 45 436 445 10.1016/j.fgb.2007.08.005 17920314 (Pubitemid 351296468)
26. ACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei. Aro N, Saloheimo A, Ilmén M, Penttilä M, J Biol Chem 2001 276 24309 24314 10.1074/jbc.M003624200 11304525
27. Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi. Coradetti ST, Craig JP, Xiong Y, Shock T, Tian C, Glass NL, Proc Natl Acad Sci U S A 2012 109 7397 7402 10.1073/pnas.1200785109 22532664
28. ManR, a novel Zn(II)(2)Cys(6) transcriptional activator, controls the β-mannan utilization system in Aspergillus oryzae. Ogawa M, Kobayashi T, Koyama Y, Fungal Genet Biol 2012 49 987 995 10.1016/j.fgb.2012.09.006 23063954
29. Genes regulated by AoXlnR, the xylanolytic and cellulolytic transcriptional regulator, in Aspergillus oryzae. Noguchi Y, Sano M, Kanamaru K, Ko T, Takeuchi M, Kato M, Kobayashi T, Appl Microbiol Biotechnol 2009 85 141 154 10.1007/s00253-009-2236-9 19777228
30. Xyr1 receives the lactose induction signal and regulates metabolism in Hypocrea jecorina. Stricker AR, Steiger MG, Mach RL, FEBS Lett 2007 581 3915 3920 10.1016/j.febslet.2007.07.025 17662982 (Pubitemid 47212095)
31. The cell wall: a carbohydrate armour for the fungal cell. Latgé JP, Mol Microbiol 2007 66 279 290 10.1111/j.1365-2958.2007.05872.x 17854405 (Pubitemid 47482373)
32. Choline stimulates synthesis of extracellular proteins in Trichoderma reesei. Schreiber G, Kolar H, Foisner R, Kubicek CP, Arch Microbiol 1986 144 41 47 10.1007/BF00454954 (Pubitemid 16158404)
33. Subcellular fractionation of a hypercellulolytic mutant, Trichoderma reesei Rut-C30: localization of endoglucanase in microsomal fraction. Glenn M, Ghosh A, Ghosh BK, Appl Environ Microbiol 1985 50 1137 1143 4091550 (Pubitemid 16235094)
34. Mitochondria autophagy in yeast. Kanki T, Klionsky DJ, Okamoto K, Antioxid Redox Signaling. 2011 14 1989 2011 10.1089/ars.2010.3762
35. Autophagosome formation: core machinery and adaptions. Xie Z, Klionsky DJ, Nat Cell Biol 2007 9 1102 1109 10.1038/ncb1007-1102 17909521 (Pubitemid 47500484)
36. The Atg1 kinase complex is involved in the regulation of protein recruitment to initiate sequestering vesicle formation for nonspecific autophagy in Saccharomyces cerevisiae. Cheong H, Nair U, Geng J, Klionsky DJ, Mol Biol Cell 2008 19 668 681 18077553 (Pubitemid 351272154)
37. Atg 17 functions in cooperation with Atg1 and Atg13 in yeast autophagy. Kabeya Y, Kamada Y, Baba M, Takikawa H, Sasaki M, Ohsumi Y, Mol Biol Cell 2005 16 2544 2553 10.1091/mbc.E04-08-0669 15743910 (Pubitemid 40632233)
38. Autophagy promotes survival in aging submerged cultures of the filamentous fungus Aspergillus niger. Nitsche BM, Burggraaf-van Welzen AM, Lamers G, Meyer V, Ram AF, Appl Microbiol Biotechnol 2013 Epub ahead of print
39. Autophagy is required for trap formation in the nematode trapping fungus Arthrobotrys oligospora. Chen YL, Gao Y, Zhang KQ, Zou CG, Environ Microbiol Rep 2013 5 511 517 10.1111/1758-2229.12054 23864564
40. Linkage of autophagy to fungal development, lipid storage and virulence in Metarhizium robertsii. Duan Z, Chen Y, Huang W, Shang Y, Chen P, Wang C, Autophagy 2013 9 538 549 10.4161/auto.23575 23380892
41. Reactive oxygen species in phytopathogenic fungi: signaling, development, and disease. Heller J, Tudzynski P, Annu Rev Phytopathol 2011 49 369 90 10.1146/annurev-phyto-072910-095355 21568704
42. Functions and regulation of the Nox family in the filamentous fungus Podospora anserina: a new role in cellulose degradation. Brun S, Malagnac F, Bidard F, Lalucque H, Silar P, Mol Microbiol 2009 74 480 496 10.1111/j.1365-2958.2009.06878.x 19775249
43. Functional analysis of the Trichoderma harzianum nox1 gene, encoding an NADPH oxidase, relates production of reactive oxygen species to specific biocontrol activity against Pythium ultimum. Montero-Barrientos M, Hermosa R, Cardoza RE, Gutiérrez S, Monte E, Appl Environ Microbiol 2011 77 3009 3016 10.1128/AEM.02486-10 21421791
44. Mechanisms of wood degradation by brown-rot fungi: chelator-mediated cellulose degradation and binding of iron by cellulose. Xu G, Goodell B, J Biotechnol 2001 87 43 57 10.1016/S0168-1656(00)00430-2 11267698 (Pubitemid 32232224)
45. Lignocellulosic polysaccharides and lignin degradation by wood decay fungi: the relevance of nonenzymatic Fenton-based reactions. Arantes V, Milagres AM, Filley TR, Goodell B, J Ind Microbiol Biotechnol 2011 38 541 555 10.1007/s10295-010-0798-2 20711629
46. Expression of Biomass-Degrading Enzymes Is a Major Event during Conidium Development in Trichoderma reesei. Metz B, Seidl-Seiboth V, Haarmann T, Kopchinskiy A, Lorenz P, Seiboth B, Kubicek CP, Eukaryot Cell 2011 10 1527 1735 10.1128/EC.05014-11 21890820
47. RSAT regulatory sequence analysis tools. Thomas-Chollier M, Sand O, Turatsinze JV, Janky R, Defrance M, Vervisch E, Brohée S, van Helden J, Nucleic Acids Res 2008 1 119 127
48. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Pfaffl MW, Horgan GW, Dempfle L, Nucleic Acids Res 2002 30 36 10.1093/nar/30.9.e36 11972351
49. The unequal variance t-test is an underused alternative to Student's t-test and the Mann-Whitney U test. Ruxton GD, Behav Ecol 2006 17 688 690 10.1093/beheco/ark016 (Pubitemid 43992440)
50. Release of carboxymethyl-cellulase and β-glucosidase from cell walls of Trichoderma reesei. Kubicek CP, Eur J Appl Microbiol Biotechnol 1981 13 226 231 10.1007/BF00500103