Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei, the hyper-cellulolytic filamentous fungus

References

• Gilbert HJ, Hazlewood GP. Bacterial cellulases and xylanases. J. Gen. Microbiol. 1993;139:187–194.10.1099/00221287-139-2-187
   Google Scholar
• Goyal A, Ghosh B. Characteristics of fungal cellulases. Biores. Technol. 1991;36:37–50.10.1016/0960-8524(91)90098-5
   Web of Science ®Google Scholar
• Watanabe H, Noda H, Tokuda G, et al. A cellulase gene of termite origin. Nature. 1998;394:330–331.10.1038/28527
   PubMed Web of Science ®Google Scholar
• Harris PV, Welner D, McFarland KC, et al. Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family. Biochemistry. 2010;49:3305–3316.10.1021/bi100009p
   PubMed Web of Science ®Google Scholar
• Morgenstern I, Powlowski J, Tsang A. Fungal cellulose degradation by oxidative enzymes: from dysfunctional GH61 family to powerful lytic polysaccharide monooxygenase family. Brief. Funct. Genomics. 2014;13:471–481.10.1093/bfgp/elu032
   PubMed Web of Science ®Google Scholar
• Mandels M, Reese ET. Induction of cellulase in Trichoderma viride as influenced by carbon sources and metals. J. Bacteriol. 1957;73:269–278.
   PubMed Web of Science ®Google Scholar
• Bisaria VS, Mishra S. Regulatory aspects of cellulase biosynthesis and secretion. Crit. Rev. Biotechnol. 1989;9:61–103.10.3109/07388558909040616
   PubMed Web of Science ®Google Scholar
• Kubicek CP, Messner R, Gruber F, et al. The trichoderma cellulase regulatory puzzle: from the interior life of a secretory fungus. Enz. Microb. Technol. 1993;15:90–99.10.1016/0141-0229(93)90030-6
   PubMed Web of Science ®Google Scholar
• Ilmén M, Saloheimo A, Onnela M-L, et al. Regulation of cellulase gene expression in the filamentous fungus Trichoderma reesei. Appl. Environ. Microbiol. 1997;63:1298–1306.
   PubMed Web of Science ®Google Scholar
• Nogawa M, Goto M, Okada H, et al. L-Sorbose induces cellulase gene transcription in the cellulolytic fungus Trichoderma reesei. Curr. Genet. 2001;38:329–334.10.1007/s002940000165
   PubMed Web of Science ®Google Scholar
• Stricker AR, Grosstessner-Hain K, Würleitner E, et al. Xyr1 (Xylanase Regulator 1) regulates both the hydrolytic enzyme system and D-xylose metabolism in Hypocrea jecorina. Eukaryot. Cell. 2006;5:2128–2137.10.1128/EC.00211-06
   PubMed Web of Science ®Google Scholar
• Rauscher R, Würleitner E, Wacenovsky C, et al. Transcriptional regulation of xyn1, encoding xylanase I, in Hypocrea jecorina. Eukaryot. Cell. 2006;5:447–456.10.1128/EC.5.3.447-456.2006
   PubMed Web of Science ®Google Scholar
• Aro N, Saloheimo A, Ilmén M, et al. ACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei. J. Biol. Chem. 2001;276:24309–24314.10.1074/jbc.M003624200
   PubMed Web of Science ®Google Scholar
• Häkkinen M, Valkonen MJ, Westerholm-Parvinen A, et al. Screening of candidate regulators for cellulase and hemicellulase production in Trichoderma reesei and identification of a factor essential for cellulase production. Biotechnol. Biofuels. 2014;7:14.10.1186/1754-6834-7-14
   PubMed Web of Science ®Google Scholar
• Saloheimo A, Aro N, Ilmén M, et al. Isolation of the ace1 gene encoding a Cys2-His2 transcription factor involved in regulation of activity of the cellulase promoter cbh1 of Trichoderma reesei. J. Biol. Chem. 2000;275:5817–5825.10.1074/jbc.275.8.5817
   PubMed Web of Science ®Google Scholar
• Aro N, Ilmen M, Saloheimo A, et al. ACEI of Trichoderma reesei is a repressor of cellulase and xylanase expression. Appl. Environ. Microbiol. 2003;69:56–65.10.1128/AEM.69.1.56-65.2003
   PubMed Web of Science ®Google Scholar
• Nitta M, Furukawa T, Shida Y, et al. A new Zn(II)2Cys6-type transcription factor BglR regulates β-glucosidase expression in Trichoderma reesei. Fungal Genet. Biol. 2012;49:388–397.10.1016/j.fgb.2012.02.009
   PubMed Web of Science ®Google Scholar
• Strauss J, Mach RL, Zeilinger S, et al. Crel, the carbon catabolite repressor protein from Trichoderma reesei. FEBS Lett. 1995;376:103–107.10.1016/0014-5793(95)01255-5
   PubMed Web of Science ®Google Scholar
• Takashima S, Iikura H, Nakamura A, et al. Analysis of Cre1 binding sites in the Trichoderma reesei cbh1 upstream region. FEMS Microbiol. Lett. 1996;145:361–366.10.1111/fml.1996.145.issue-3
   PubMed Web of Science ®Google Scholar
• Ilmén M, Thrane C, Penttilä M. The glucose repressor gene cre1 of Trichoderma: isolation and expression of a full-length and a truncated mutant form. Mol. Gen. Genet. 1996;251:451–460.
   PubMedGoogle Scholar
• Herpoël-Gimbert I, Margeot A, Dolla A, et al. Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains. Biotechnol. Biofuels. 2008;1:18.10.1186/1754-6834-1-18
   PubMed Web of Science ®Google Scholar
• Mandels M. Microbial sources of cellulase. Biotechnol Bioeng. 1975;5:81–105.
   Google Scholar
• Mäntylä AL, Rossi KH, Vanhanen SA, et al. Electrophoretic karyotyping of wild-type and mutant Trichoderma longibrachiatum (reesei) strains. Curr. Genet. 1992;21:471–477.10.1007/BF00351657
   PubMed Web of Science ®Google Scholar
• Kawamori M, Morikawa Y, Takasawa S. Induction and production of cellulases by L-sorbose in Trichoderma reesei. Appl. Microbiol. Biotechnol. 1986;24:449–453.
   Web of Science ®Google Scholar
• Xu J, Takakuwa N, Nogawa M, et al. A third xylanase from Trichoderma reesei PC-3-7. Appl. Microbiol. Biotechnol. 1998;49:718–724.10.1007/s002530051237
   Web of Science ®Google Scholar
• Porciuncula JDO, Furukawa T, Mori K, et al. Single nucleotide polymorphism analysis of a Trichoderma reesei hyper-cellulolytic mutant developed in Japan. Biosci. Biotechnol. Biochem. 2013;77:534–543.10.1271/bbb.120794
   PubMed Web of Science ®Google Scholar
• Shida Y, Yamaguchi K, Nitta M, et al. The impact of a single-nucleotide mutation of bgl2 on cellulase induction in a Trichoderma reesei mutant. Biotechnol. Biofuels. 2015;8:3305.10.1186/s13068-015-0420-y
   Web of Science ®Google Scholar
• Demain AL. Biosolutions to the energy problem. J. Ind. Microbiol. Biotechnol. 2009;36:319–332.10.1007/s10295-008-0521-8
   PubMed Web of Science ®Google Scholar
• Gray KA, Zhao L, Emptage M. Bioethanol. Curr. Opin. Chem. Biol. 2006;10:141–146.10.1016/j.cbpa.2006.02.035
   PubMed Web of Science ®Google Scholar
• Mussatto SI, Dragone G, Guimarã PM, et al. Technological trends, global market, and challenges of bio-ethanol production. Biotechnol. 2010;28:817–e830.
   Google Scholar
• Saloheimo M, Kuja-Panula J, Ylosmaki E, et al. Enzymatic properties and intracellular localization of the novel Trichoderma reesei beta-glucosidase BGLII (Cel1A). Appl. Environ. Microbiol. 2002;68:4546–4553.10.1128/AEM.68.9.4546-4553.2002
   PubMed Web of Science ®Google Scholar
• Du F, Wolger E, Wallace L, et al. Determination of product inhibition of CBH1, CBH2, and EG1 using a novel cellulase activity assay. Appl. Biochem. Biotechnol. 2010;161:313–317.10.1007/s12010-009-8796-4
   PubMed Web of Science ®Google Scholar
• Kubicek CP, Penttilä M. Regulation of production of plant polysaccharide degrading enzymes by Trichoderma. In: Harman GE, Kubicek CP, editors. Trichoderma and Gliocladium, Enzymes, biological control and commercial applications. Vol 2, Gunpowder Square: London; 1998. p. 49–72.
   Google Scholar
• Margolles-Clark E, Tenkanen M, Nakari-Setala T, et al. Cloning of genes encoding alpha-L-arabinofuranosidase and beta-xylosidase from Trichoderma reesei by expression in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 1996;62:3840–3846.
   PubMed Web of Science ®Google Scholar
• el-Gogary S, Leite A, Crivellaro O, et al. Mechanism by which cellulose triggers cellobiohydrolase I gene expression in Trichoderma reesei. Proc. Natl. Acad. Sci. 1989;86:6138–6141.10.1073/pnas.86.16.6138
   PubMed Web of Science ®Google Scholar
• Carle-Urioste JC, Escobar-Vera J, El-Gogary S, et al. Cellulase induction in Trichoderma reesei by cellulose requires its own basal expression. J. Biol. Chem. 1997;272:10169–10174.
   PubMed Web of Science ®Google Scholar
• Aro N, Pakula T, Penttilä M. Transcriptional regulation of plant cell wall degradation by filamentous fungi. FEMS Microbiol. Rev. 2005;29:719–739.10.1016/j.femsre.2004.11.006
   PubMed Web of Science ®Google Scholar
• Kubicek CP, Messner R, Gruber F, et al. Triggering of cellulase biosynthesis by cellulose in Trichoderma reesei. Involvement of a constitutive, sophorose-inducible, glucose-inhibited beta-diglucoside permease. J. Biol. Chem. 1993;268:19364–19368.
   PubMed Web of Science ®Google Scholar
• Fowler T, Brown RD. The bgl1 gene encoding extracellular beta-glucosidase from Trichoderma reesei is required for rapid induction of the cellulase complex. Mol. Microbiol. 1992;6:3225–3235.10.1111/mmi.1992.6.issue-21
   PubMed Web of Science ®Google Scholar
• Fritscher C, Messner R. Cellobiose metabolism and cellobiohydrolase I biosynthesis by Trichoderma reesei. Exp. Mycol. 1990;14:405–415.10.1016/0147-5975(90)90063-Y
   Google Scholar
• Sternberg D, Mandels GR. Induction of cellulolytic enzymes in Trichoderma reesei by sophorose. J. Bacteriol. 1979;139:761–769.
   PubMed Web of Science ®Google Scholar
• Vaheri M, Leisola M, Kauppinen V. Transglycosylation products of cellulase system of Trichoderma reesei. Biotechnol. Lett. 1979;1:41–46.10.1007/BF01395789
   Web of Science ®Google Scholar
• Mach RL, Seiboth B, Myasnikov A, et al. The bgl1 gene of Trichoderma reesei QM9414 encodes an extracellular, cellulose-inducible beta-glucosidase involved in cellulase induction by sophorose. Mol. Microbiol. 1995;16:687–697.10.1111/mmi.1995.16.issue-4
   PubMed Web of Science ®Google Scholar
• Furukawa T, Shida Y, Kitagami N, et al. Identification of specific binding sites for XYR1, a transcriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei. Fungal Genet. Biol. 2009;46:564–574.10.1016/j.fgb.2009.04.001
   PubMed Web of Science ®Google Scholar
• Zhou Q, Xu J, Kou Y, et al. Differential involvement of β-glucosidases from Hypocrea jecorina in rapid induction of cellulase genes by cellulose and cellobiose. Eukaryot. Cell. 2012;11:1371–1381.10.1128/EC.00170-12
   PubMed Web of Science ®Google Scholar
• Xu J, Nogawa M, Okada H, Morikawa Y. Regulation of xyn3 gene expression in Trichoderma reesei PC-3-7. Appl. Microbiol. Biotechnol. 2000;54:370–375.10.1007/s002530000410
   PubMed Web of Science ®Google Scholar
• Mach RL, Strauss J, Zeilinger S, et al. Carbon catabolite repression of xylanase I (xyn1) gene expression in Trichoderma reesei. Mol. Microbiol. 1996;21:1273–1281.10.1046/j.1365-2958.1996.00094.x
   PubMed Web of Science ®Google Scholar
• Zeilinger S, Mach RL, Schindler M, et al. Different inducibility of expression of the two xylanase genes xyn1 and xyn2 in Trichoderma reesei. J. Biol. Chem. 1996;271:25624–25629.10.1074/jbc.271.41.25624
   PubMed Web of Science ®Google Scholar
• Mach RL, Zeilinger S. Regulation of gene expression in industrial fungi: Trichoderma. Appl. Microbiol. Biotechnol. 2003;60:515–522.10.1007/s00253-002-1162-x
   PubMed Web of Science ®Google Scholar
• Stricker AR, Steiger MG, Mach RL. Xyr1 receives the lactose induction signal and regulates lactose metabolism in Hypocrea jecorina. FEBS Lett. 2007;581:3915–3920.10.1016/j.febslet.2007.07.025
   PubMed Web of Science ®Google Scholar
• Stricker AR, Trefflinger P, Aro N, et al. Role of Ace2 (Activator of Cellulases 2) within the xyn2 transcriptosome of Hypocrea jecorina. Fungal Genet. Biol. 2008;45:436–445.10.1016/j.fgb.2007.08.005
   PubMed Web of Science ®Google Scholar
• Lichius A, Bidard F, Buchholz F, et al. Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics. 2015;16:326.10.1186/s12864-015-1526-0
   PubMed Web of Science ®Google Scholar
• Derntl C, Gudynaite-Savitch L, Calixte S, et al. Mutation of the Xylanase regulator 1 causes a glucose blind hydrolase expressing phenotype in industrially used Trichoderma strains. Biotechnol. Biofuels. 2013;6:62.10.1186/1754-6834-6-62
   PubMed Web of Science ®Google Scholar
• Mach-Aigner AR, Pucher ME, Steiger MG, et al. Transcriptional Regulation of xyr1, encoding the main regulator of the xylanolytic and cellulolytic enzyme system in Hypocrea jecorina. Appl. Environ. Microbiol. 2008;74:6554–6562.10.1128/AEM.01143-08
   PubMed Web of Science ®Google Scholar
• Mach-Aigner AR, Grosstessner-Hain K, Poças-Fonseca MJ, et al. From an electrophoretic mobility shift assay to isolated transcription factors: a fast genomic-proteomic approach. BMC Genomics. 2010;11:1–10.
   PubMed Web of Science ®Google Scholar
• Derntl C, Rassinger A, Srebotnik E, et al. Xpp1 regulates the expression of xylanases, but not of cellulases in Trichoderma reesei. Biotechnol. Biofuels. 2015;8:1–11.
   PubMed Web of Science ®Google Scholar
• Aro N, Saloheimo A, Ilmén M, et al. ACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei. J. Biol. Chem. 2001;276:24309–24314.10.1074/jbc.M003624200
   PubMed Web of Science ®Google Scholar
• MacPherson S, Larochelle M, Turcotte B. A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol. Mol. Biol. Rev. 2006;70:583–604.10.1128/MMBR.00015-06
   PubMed Web of Science ®Google Scholar
• Chilton IJ, Delaney CE, Barham-Morris J, et al. The Aspergillus nidulans stress response transcription factor StzA is ascomycete-specific and shows species-specific polymorphisms in the C-terminal region. Mycol. Res. 2008;112:1435–1446.10.1016/j.mycres.2008.06.028
   PubMed Web of Science ®Google Scholar
• O'Neil JD, Bugno M, Stanley MS, et al. Cloning of a novel gene encoding a C2H2 zinc finger protein that alleviates sensitivity to abiotic stresses in Aspergillus nidulans. Mycol. Res. 2002;106:491–498.10.1017/S0953756202005701
   Web of Science ®Google Scholar
• Cziferszky A, Mach RL, Kubicek CP. Phosphorylation positively regulates DNA binding of the carbon catabolite repressor Cre1 of Hypocrea jecorina (Trichoderma reesei). J. Biol. Chem. 2002;277:14688–14694.10.1074/jbc.M200744200
   PubMed Web of Science ®Google Scholar
• Espeso EA, Peñalva MA. In vitro binding of the two-finger repressor CreA to several consensus and non-consensus sites at the ipnA upstream region is context dependent. FEBS Lett. 1994;342:43–48.10.1016/0014-5793(94)80581-4
   PubMed Web of Science ®Google Scholar
• Kulmburg P, Mathieu M, Dowzer C, et al. Specific binding sites in the alcR and alcA promoters of the ethanol regulon for the CREA repressor mediating carbon catabolite repression in Aspergillus nidulans. Mol. Microbiol. 1993;7:847–857.10.1111/mmi.1993.7.issue-6
   PubMed Web of Science ®Google Scholar
• Cubero B, Scazzocchio C. Two different, adjacent and divergent zinc finger binding sites are necessary for CREA-mediated carbon catabolite repression in the proline gene cluster of Aspergillus nidulans. EMBO J. 1994;13:407–415.
   PubMed Web of Science ®Google Scholar
• Zeilinger S, Mach RL, Kubicek CP. Two adjacent protein binding motifs in the cbh2 (cellobiohydrolase II-encoding) promoter of the fungus Hypocrea jecorina (Trichoderma reesei) cooperate in the induction by cellulose. J. Biol. Chem. 1998;273:34463–34471.10.1074/jbc.273.51.34463
   PubMed Web of Science ®Google Scholar
• Würleitner E, Pera L, Wacenovsky C, et al. Transcriptional Regulation of xyn2 in Hypocrea jecorina. Eukaryot. Cell. 2003;2:150–158.10.1128/EC.2.1.150-158.2003
   PubMed Web of Science ®Google Scholar
• Ilmén M, Onnela ML, Klemsdal S, et al. Functional analysis of the cellobiohydrolase I promoter of the filamentous fungus Trichoderma reesei. Mol. Gen. Genet. 1996;253:303–314.
   PubMedGoogle Scholar
• Margolles-clark E, Ilmén M, Penttilä M. Expression patterns of ten hemicellulase genes of the filamentous fungus Trichoderma reesei on various carbon sources. J. Biotechnol. 1997;57:167–179.10.1016/S0168-1656(97)00097-7
   Web of Science ®Google Scholar
• Denton JA, Kelly JM. Disruption of Trichoderma reesei cre2, encoding an ubiquitin C-terminal hydrolase, results in increased cellulase activity. BMC Biotechnol. 2011;11:103.10.1186/1472-6750-11-103
   PubMed Web of Science ®Google Scholar
• Brakhage AA, Andrianopoulos A, Kato M, et al. HAP-Like CCAAT-binding complexes in filamentous fungi: implications for biotechnology. Fungal Genet. Biol. 1999;27:243–252.10.1006/fgbi.1999.1136
   PubMed Web of Science ®Google Scholar
• Tsukagoshi N, Kobayashi T, Kato M. Regulation of the amylolytic and(hemi-)cellulolytic genes in aspergilli. J. Gen. Appl. Microbiol. 2001;47:1–19.10.2323/jgam.47.1
   PubMed Web of Science ®Google Scholar
• Kato M, Aoyama A, Kobayashi T., et al. An Aspergillus nidulans nuclear protein, AnCP, involved in enhancement of Taka-amylase A gene expression, binds to the CCAAT-containing taaG2, amdS, and gatA promoters. Mol. Gen. Genet. 1997;254:119–126.10.1007/s004380050399
   PubMedGoogle Scholar
• Zeilinger S, Ebner A, Marosits T, et al. The Hypocrea jecorina HAP 2/3/5 protein complex binds to the inverted CCAAT-box (ATTGG) within the cbh2 (cellobiohydrolase II-gene) activating element. Mol. Genet. Genomics. 2001;266:56–63.
   PubMed Web of Science ®Google Scholar
• Périer RC, Praz V, Junier T, et al. The eukaryotic promoter database (EPD). Nucleic Acids. Res. 2000;28:302–303.10.1093/nar/28.1.302
   PubMed Web of Science ®Google Scholar
• Pinkham JL, Guarente L. Cloning and molecular analysis of the HAP2 locus: a global regulator of respiratory genes in Saccharomyces cerevisiae. Mol Cell Biol. 1985;5:3410–3416.10.1128/MCB.5.12.3410
   PubMed Web of Science ®Google Scholar
• McNabb DS, Xing Y, Guarente L. Cloning of yeast HAP5: a novel subunit of a heterotrimeric complex required for CCAAT binding. Genes. Dev. 1995;9:47–58.10.1101/gad.9.1.47
   PubMed Web of Science ®Google Scholar
• Narendja FM, Davis MA, Hynes MJ. AnCF, the CCAAT binding complex of Aspergillus nidulans, is essential for the formation of a DNase I-hypersensitive site in the 5′ region of the amdS gene. Mol. Cell Biol. 1999;19:6523–6531.10.1128/MCB.19.10.6523
   PubMed Web of Science ®Google Scholar
• Zeilinger S, Schmoll M, Pail M, et al. Nucleosome transactions on the Hypocrea jecorina (Trichoderma reesei) cellulase promoter cbh2 associated with cellulase induction. Mol. Genet. Genomics. 2003;270:46–55.10.1007/s00438-003-0895-2
   PubMed Web of Science ®Google Scholar
• Negrete-Urtasun S, Denison SH, Arst HN Jr. Characterization of the pH signal transduction pathway gene palA of Aspergillus nidulans and identification of possible homologs. J. Bacteriol. 1997;179:1832–1835.
   PubMed Web of Science ®Google Scholar
• Trevisan GL, Oliveira EH, Peres NT, et al. Transcription of Aspergillus nidulans pacC is modulated by alternative RNA splicing of palB. FEBS Lett. 2011;585:3442–3445.10.1016/j.febslet.2011.09.037
   PubMed Web of Science ®Google Scholar
• Galindo A, Hervás-Aguilar A, Rodríguez-Galán O, et al. PalC, one of two Bro1 domain proteins in the fungal pH signalling pathway, localizes to cortical structures and binds Vps32. Traffic. 2007;8:1346–1364.10.1111/j.1600-0854.2007.00620.x
   PubMed Web of Science ®Google Scholar
• Hervás-Aguilar A, Galindo A, Peñalva MA. Receptor-independent Ambient pH signaling by ubiquitin attachment to fungal arrestin-like PalF. J. Biol. Chem. 2010;285:18095–18102.10.1074/jbc.M110.114371
   PubMed Web of Science ®Google Scholar
• Calcagno-Pizarelli AM, Negrete-Urtasun S, Denison SH, et al. Establishment of the Ambient pH signaling complex in Aspergillus nidulans: PalI assists plasma membrane localization of PalH. Eukaryot. Cell. 2007;6:2365–2375.10.1128/EC.00275-07
   PubMed Web of Science ®Google Scholar
• Tilburn J, Sarkar S, Widdick DA, et al. The Aspergillus PacC zinc finger transcription factor mediates regulation of both acid- and alkaline-expressed genes by ambient pH. EMBO J. 1995;14:779–790.
   PubMed Web of Science ®Google Scholar
• He R, Ma L, Li C, et al. Trpac1, a pH response transcription regulator, is involved in cellulase gene expression in Trichoderma reesei. Enz. Microb. Technol. 2014;67:17–26.10.1016/j.enzmictec.2014.08.013
   PubMed Web of Science ®Google Scholar
• Häkkinen M, Sivasiddarthan D, Aro N, et al. The effects of extracellular pH and of the transcriptional regulator PACI on the transcriptome of Trichoderma reesei. Microb. Cell Fact. 2015;14:63.10.1186/s12934-015-0247-z
   PubMed Web of Science ®Google Scholar
• Henrique-Silva F, El-Gogary S, Carle-Urioste JC, et al. Two regulatory regions controlling basal and cellulose-induced expression of the gene encoding cellobiohydrolase I of Trichoderma reesei are adjacent to its TATA box. Biochem. Biophys. Res. Commun. 1996;228:229–237.10.1006/bbrc.1996.1646
   PubMed Web of Science ®Google Scholar
• Ling M, Qin Y, Li N, et al. Binding of two transcriptional factors, Xyr1 and ACEI, in the promoter region of cellulase cbh1 gene. Biotechnol. Lett. 2009;31:227–231.10.1007/s10529-008-9857-4
   PubMed Web of Science ®Google Scholar
• Stangl H, Gruber F, Kubicek CP. Characterization of the Trichoderma reesei cbh2 promoter. Curr. Genet. 1993;23:115–122.10.1007/BF00352009
   PubMed Web of Science ®Google Scholar
• Schmoll M, Kubicek CP. Regulation of Trichoderma cellulase formation: lessons in molecular biology from an industrial fungus. A review. Acta Microbiol. Immunol. Hung. 2003;50:125–145.10.1556/AMicr.50.2003.2-3.3
   PubMedGoogle Scholar
• Shida Y, Furukawa T, Ogasawara W, et al. Functional analysis of the egl3 upstream region in filamentous fungus Trichoderma reesei. Appl. Microbiol. Biotechnol. 2008;78:515–524.10.1007/s00253-007-1338-5
   PubMed Web of Science ®Google Scholar
• Ogasawara W, Shida Y, Furukawa T, et al. Cloning, functional expression and promoter analysis of xylanase III gene from Trichoderma reesei. Appl. Microbiol. Biotechnol. 2006;72:995–1003.10.1007/s00253-006-0365-y
   PubMed Web of Science ®Google Scholar
• Furukawa T, Shida Y, Kitagami N, et al. Identification of the cis-acting elements involved in regulation of xylanase III gene expression in Trichoderma reesei PC-3-7. Fungal Genet. Biol. 2008;45:1094–1102.10.1016/j.fgb.2008.03.006
   PubMed Web of Science ®Google Scholar
• Nevalainen H, Suominen P, Taimisto K. On the safety of Trichoderma reesei. J. Biotechnol. 1994;37:193–200.10.1016/0168-1656(94)90126-0
   PubMed Web of Science ®Google Scholar
• Wang TH, Liu T, Wu ZH, et al. Novel cellulase profile of Trichoderma reesei strains constructed by cbh1 gene replacement with eg3 gene expression cassette. Acta Biochim. Biophys. Sin. 2004;36:667–672.10.1093/abbs/36.10.667
   Google Scholar
• Miettinen-Oinonen A, Suominen P. Enhanced production of Trichoderma reesei endoglucanases and use of the new cellulase preparations in producing the stonewashed effect on denim fabric. Appl. Environ. Microbiol. 2002;68:3956–3964.10.1128/AEM.68.8.3956-3964.2002
   PubMed Web of Science ®Google Scholar
• Miettinen-Oinonen A, Paloheimo M, Lantto R, et al. Enhanced production of cellobiohydrolase in Trichoderma reesei and evaluation of the new preparations in biofinishing of cotton. J. Biotechnol. 2004;116:305–317.
   PubMed Web of Science ®Google Scholar
• Mäntylä A, Paloheimo M, Hakola S, et al. Production in Trichoderma reesei of three xylanases from Chaetomium thermophilum: a recombinant thermoxylanase for biobleaching of kraft pulp. Appl. Microbiol. Biotechnol. 2007;76:377–386.10.1007/s00253-007-1020-y
   PubMed Web of Science ®Google Scholar
• Paloheimo M, Mäntylä A, Kallio J, et al. Increased production of xylanase by expression of a truncated version of the xyn11A gene from Nonomuraea flexuosa in Trichoderma reesei. Appl. Environ. Microbiol. 2007;73:3215–3224.10.1128/AEM.02967-06
   PubMed Web of Science ®Google Scholar
• Keränen S, Penttilä M. Production of recombinant proteins in the filamentous fungus Trichoderma reesei. Curr. Opin. Biotechnol. 1995;6:534–537.10.1016/0958-1669(95)80088-3
   PubMed Web of Science ®Google Scholar
• Penttilä M. Heterologous protein production in the Trichoderma. In: Harman GE, Kubicek CP, editors. Trichoderma and Gliocladium. Gunpowder Square: London; 1998. p. 365–382.
   Google Scholar
• Rahman Z, Shida Y, Furukawa T, et al. Evaluation and characterization of Trichoderma reesei cellulase and xylanase promoters. Appl. Microbiol. Biotechnol. 2009;82:899–908.10.1007/s00253-008-1841-3
   PubMed Web of Science ®Google Scholar
• Duff SJB, Murray WD. Bioconversion of forest products industry waste cellulosics to fuel ethanol: a review. Biores. Technol. 1996;55:1–33.10.1016/0960-8524(95)00122-0
   Web of Science ®Google Scholar
• Nieves RA, Ehrman CI, Adney WS, et al. Survey and analysis of commercial cellulase preparations suitable for biomass conversion to ethanol. World J. Microbiol. Biotechnol. 1998;14:301–304.
   Web of Science ®Google Scholar
• Rahman Z, Shida Y, Furukawa T, et al. Application of Trichoderma reesei cellulase and xylanase promoters through homologous recombination for enhanced production of extracellular β-glucosidase I. Biosci Biotechnol Biochem. 2009;73:1083–1089.10.1271/bbb.80852
   PubMed Web of Science ®Google Scholar
• Nitta M, Shida Y, Okada H, et al. Hyphal surface architecture and cell morphology of Trichoderma reesei. J. Electron Microsc. (Tokyo). 2012;61:187–192.
   PubMedGoogle Scholar
• Osumi M, Yamada N, Yaguchi H, et al. Ultrahigh-resolution low-voltage SEM reveals ultrastructure of the glucan network formation from fission yeast protoplast. J. Electron Microsc. 1995;44:198–206.
   PubMedGoogle Scholar
• Chapman CM, Loewenberg JR, Schaller MJ, et al. Ultrastructural localization of cellulase in Trichoderma reesei using immunocytochemistry and enzyme cytochemistry. J. Histochem. Cytochem. 1983;31:1363–1366.10.1177/31.12.6195212
   PubMed Web of Science ®Google Scholar
• Sprey B. Localisation of β-glucosidase in Trichoderma reesei cell walls with immunoelectron microscopy. FEMS Microbiol. Lett. 1986;36:287–292.
   Web of Science ®Google Scholar
• Sprey B. Cellular and extracellular localization of endocellulase in Trichoderma reesei. FEMS Microbiol. Lett. 1988;55:283–294.10.1111/fml.1988.55.issue-3
   Web of Science ®Google Scholar
• Ghosh A, Ghosh BK, Trimino-Vazquez H, et al. Cellulase secretion from a hyper-cellulolytic mutant of Trichoderma reesei Rut-C30. Arch. Microbiol. 1984;140:126–133.10.1007/BF00454914
   Web of Science ®Google Scholar
• Kurzątkowski W, Solecka J, Filipek J, et al. Ultrastructural localization of cellular compartments involved in secretion of the low molecular weight, alkaline xylanase by Trichoderma reesei. Arch. Microbiol. 1993;159:417–422.10.1007/BF00288587
   Web of Science ®Google Scholar
• Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008;24:133–141.10.1016/j.tig.2007.12.007
   PubMed Web of Science ®Google Scholar
• Spatz SJ, Rue CA. Sequence determination of a mildly virulent strain (CU-2) of Gallid herpesvirus type 2 using 454 pyrosequencing. Virus Genes. 2008;36:479–489.10.1007/s11262-008-0213-5
   PubMed Web of Science ®Google Scholar
• Holt KE, Parkhill J, Mazzoni CJ, et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat. Genet. 2008;40:987–993.10.1038/ng.195
   PubMed Web of Science ®Google Scholar
• Kotewicz ML, Mammel MK, LeClerc JE, et al. Optical mapping and 454 sequencing of Escherichia coli O157: H7 isolates linked to the US 2006 spinach-associated outbreak. Microbiology. 2008;154:3518–3528.10.1099/mic.0.2008/019026-0
   PubMed Web of Science ®Google Scholar
• Manning SD, Motiwala AS, Springman AC, et al. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc. Natl. Acad. Sci. USA. 2008;105:4868–4873.10.1073/pnas.0710834105
   PubMed Web of Science ®Google Scholar
• Novaes E, Drost DR, Farmerie WG, et al. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics. 2008;9:312.10.1186/1471-2164-9-312
   PubMed Web of Science ®Google Scholar
• Sadia B, Craig J, Hudson M, et al. Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing. Mol. Genet. Genomics. 2008;279:535–543.
   PubMed Web of Science ®Google Scholar
• Qi W, Käser M, Röltgen K, et al. Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing. PLoS Pathog. 2009;5:e1000580.10.1371/journal.ppat.1000580
   Google Scholar
• Wang J, Wang W, Li R, et al. The diploid genome sequence of an Asian individual. Nature. 2008;456:60–65.10.1038/nature07484
   PubMed Web of Science ®Google Scholar
• Wheeler DA, Srinivasan M, Egholm M, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008;452:872–876.10.1038/nature06884
   PubMed Web of Science ®Google Scholar
• Marie-Nelly H, Marbouty M, Cournac A, et al. High-quality genome (re)assembly using chromosomal contact data. Nat. Commun. 2014;5:5695.10.1038/ncomms6695
   PubMed Web of Science ®Google Scholar
• Le Crom S, Schackwitz W, Pennacchio L, et al. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc. Natl. Acad. Sci. USA. 2009;106:16151–16156.10.1073/pnas.0905848106
   PubMed Web of Science ®Google Scholar
• Koike H, Aerts A, LaButti K, et al. Comparative genomics analysis of Trichoderma reesei strains. Ind. Biotechnol. 2013;9:352–367.10.1089/ind.2013.0015
   Google Scholar
• Ries L, Pullan ST, Delmas S, et al. Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger. BMC Genomics. 2013;14:541.10.1186/1471-2164-14-541
   PubMed Web of Science ®Google Scholar
• Kang K, Zhong J, Jiang L, et al. Identification of microRNA-Like RNAs in the filamentous fungus Trichoderma reesei by solexa sequencing. PLoS ONE. 2013;8:e76288.10.1371/journal.pone.0076288
   PubMed Web of Science ®Google Scholar
• Nakazawa H, Kawai T, Ida N, et al. Construction of a recombinant Trichoderma reesei strain expressing Aspergillus aculeatus β-glucosidase 1 for efficient biomass conversion. Biotechnol. Bioeng. 2012;109:92–99.10.1002/bit.v109.1
   PubMed Web of Science ®Google Scholar
• Nakazawa H, Kawai T, Ida N, et al. A high performance Trichoderma reesei strain that reveals the importance of xylanase III in cellulosic biomass conversion. Enzyme Microb. Technol. 2016;82:89–95.10.1016/j.enzmictec.2015.08.019
   PubMed Web of Science ®Google Scholar