The role of CRE1 in nucleosome positioning within the cbh1 promoter and coding regions of Trichoderma reesei

Applied Microbiology and Biotechnology

Volumn 98, Issue 2, 2014, Pages 749-762

  Ries, L ^a,e   Belshaw, N J ^b   Ilmen M ^c   Penttila M E ^c   Alapuranen, M ^d   Archer, D B ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b INSTITUTE OF FOOD RESEARCH   (United Kingdom)

^c VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

^d Roal Oy   (Finland)

^e UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Cellobiohydrolase I; Cellobiohydrolase II; CRE1; Nucleosome positioning; Trichoderma reesei

Indexed keywords

BINDING SITES; BIODEGRADATION; ENCODING (SYMBOLS); GENE ENCODING; SIGNAL ENCODING;

CELLOBIOHYDROLASE I; CELLOBIOHYDROLASES; CRE1; NUCLEOSOMES; TRICHODERMA REESEI;

TRANSCRIPTION;

BACTERIAL PROTEIN; CBH1 PROTEIN; CELL EXTRACT; CRE1 PROTEIN; SOPHOROSE; UNCLASSIFIED DRUG;

DNA; ENZYME ACTIVITY; FUNCTIONAL ROLE; FUNGUS; GENE EXPRESSION; GENOME; GENOMICS; MUTATION;

ARTICLE; BACTERIAL GROWTH; BINDING SITE; CARBON SOURCE; CHROMATIN STRUCTURE; DNA EXTRACTION; GEL MOBILITY SHIFT ASSAY; GENE DELETION; GENE MUTATION; GENETIC CODE; GENETIC TRANSCRIPTION; HYPOCREA JECORINA; NONHUMAN; NUCLEOSOME; PROMOTER REGION; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; SOUTHERN BLOTTING;

FUNGI; HYPOCREA JECORINA;

CELLULOSE 1,4-BETA-CELLOBIOSIDASE; GENE DELETION; GENE EXPRESSION REGULATION, FUNGAL; NUCLEOSOMES; PROMOTER REGIONS, GENETIC; TRANSCRIPTION FACTORS; TRICHODERMA;

EID: 84895072098     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-5354-3     Document Type: Article

References (38)

1. Aro N, Saloheimo A, Ilmén M, Penttilä M (2001) ACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei. J Biol Chem 276:24309-24314. doi: 10.1074/jbc.M003624200
2. Aro N, Ilmén M, Saloheimo A, Penttilä M (2003) ACE1 of Trichoderma reesei is a repressor of cellulase and xylanase expression. Appl Environ Microbiol 69:56-65. doi: 10.1128/AEM.69.1.56-65.2003 (Pubitemid 36077457)
3. Arya G, Maitra A, Grigoryev SA (2010) A structural perspective on the where, how, why and what of nucleosome positioning. J Biomol Struct Dyn 27:803-819. doi: 10.1080/07391102.2010.10508585
4. Brosch G, Loidl P, Graessle S (2008) Histone modifications and chromatin dynamics: a focus on filamentous fungi. FEMS Microbiol Rev 32:409-439. doi: 10.1111/j.1574-6976.2007.00100.x (Pubitemid 351538743)
5. Bustin SA (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25:169-193
6. Clark DJ (2010) Nucleosome positioning, nucleosome spacing and the nucleosome code. J Biomol Struct Dyn 27:781-791. doi: 10.1080/073911010010524945
7. Cockerill PN (2011) Structure and function of active chromatin and DNase I hypersensitive sites. FEBS J 278:2182-2210. doi: 10.1111/j.1742-4658.2011. 08128.x
8. Cziferszky A, Mach RL, Kubicek CP (2002) Phosphorylation positively regulates DNA binding of the carbon catabolite repressor CRE1 of Hypocrea jecorina (Trichoderma reesei). J Biol Chem 277:14688-14694. doi: 10.1074/jbc.M200744200 (Pubitemid 34952538)
9. Furukawa T, Shida Y, Kitagami N, Mori K, Kato M, Kobayashi T, Okada H, Ogasawara W, Morikawa Y (2009) Identification of specific binding sites for XYR1, a transcriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei. Fungal Genet Biol 46:564-574. doi: 10.1016/j.fgb.2009.04.001
10. García I, Gonzalez R, Gómez D, Scazzocchio C (2004) Chromatin rearrangements in the prnD-prnB bidirectional promoter: dependence on transcription factors. Eukaryot Cell 3:144-156. doi: 10.1128/EC.3.1.144-156.2004 (Pubitemid 38237306)
11. Gonzalez R, Scazzocchio C (1997) A rapid method for chromatin structure analysis in the filamentous fungus Aspergillus nidulans. Nucl Acids Res 25:3955-3956. doi: 10.1093/nar/25.19.3955 (Pubitemid 27420508)
12. Häkkinen M, Arvas M, Oja M, Aro N, Penttilä M, Saloheimo M, Pakula TM (2012) Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates. Microb Cell Fact 11:134-160. doi: 10.1186/1475-2859-11-134
13. Ilmén M, Thrane C, Penttilä M (1996) The glucose repressor gene cre1 of Trichoderma: isolation and expression of a full length and a truncated mutant form. Mol Gen Genet 251:451-460. doi: 10.1007/BF02172374
14. Ilmén M, Thrane C, Penttilä M (1998) The glucose repressor gene cre1 of Trichoderma: isolation and expression of a full length and a truncated mutant form. Mol Gen Genet 257(Corrigendum):386
15. Knob A, Terrasan CRF, Carmona EC (2010) β-Xylosidases from filamentous fungi: an overview. World J Microb Biotechnol 26:389-407. doi: 10.1007/s11274-009-0190-4
16. Kubicek CP, Mikus M, Schuster A, Schmoll M, Seiboth B (2009) Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina. Biotechnol Biofuels 2:6834-6848. doi: 10.1186/1754-6834-2-19
17. Le Crom S, Schackwitz W, Pennacchio L, Magnuson JK, Culley DE, Collett JR, Martin J, Druzhinina IS, Mathis H, Monot F, Seiboth B, Cherry B, Rey M, Berka R, Kubicek CP, Baker SE, Margeot A (2009) Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc Natl Acad Sci U S A 106:16151-16156. doi: 10.1073/pnas. 0905848106
18. Ling M, Qin Y, Li N, Liang Z (2009) Binding of two transcriptional factors, XYR1 and ACE1 in the promoter region of cellulase cbh1 gene. Biotechnol Lett 31:227-231. doi: 10.1007/s10529-008-9857-4
19. Liu T, Wang T, Li X, Liu X (2008) Improved heterologous gene expression in Trichoderma reesei by cellobiohydrolase I gene (cbh1) promoter optimisation. Acta Biochem Biophys Sin 40:158-165. doi: 10.1111/j.1745-7270.2008.00388.x (Pubitemid 351305791)
20. Mach RL, Zeilinger Z (2003) Regulation of gene expression in industrial fungi: Trichoderma. Appl Microbiol Biotechnol 60:515-522. doi: 10.1007/s00253-002-1162-x (Pubitemid 36169525)
21. Mach RL, Seiboth B, Myasnikov A, Gonzalez R, Strauss J, Harkki AM, Kubicek CP (1995) The bgl1 gene of Trichoderma reesei QM9414 encodes an extracellular, cellulose-inducible β-glucosidase involved in cellulase induction by sophorose. Mol Microbiol 16:687-697. doi: 10.1111/j.1365-2958.1995. tb02430.x
22. Mach-Aigner AR, Pucher ME, Steiger MG, Bauer GE, Preis SJ, Mach RL (2008) Transcriptional regulation of xyr1, encoding the main regulator of the xylanolytic and cellulolytic enzyme system in Hypocrea jecorina. Appl Environ Microbiol 74:6554-6562. doi: 10.1128/AEM.01143-08
23. Mandels M, Reese ET (1957) Induction of cellulase in Trichoderma viride as influenced by carbon sources and metals. J Bacteriol 73:269-278
24. Mandels M, Weber J, Parizek R (1971) Enhanced cellulase production by a mutant of Trichoderma viride. Appl Microbiol 21:152-154
25. Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EGJ, Grigoriev IV, Harris P, Jackson M, Kubicek C, Han CS, Ho I, Larrondo LF, Lopez de Leon A, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barbote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnol 26:553-560. doi: 10.1038/nbt1403 (Pubitemid 351668043)
26. Mathieu M, Nikolaev I, Scazzocchio C, Felenbok B (2005) Patterns of nucleosomal organisation in the alc regulon of Aspergillus nidulans: roles of the AlcR transcriptional activator and the CreA global repressor. Mol Microbiol 56:535-548. doi: 10.1111/j.1365-2958.2005.04559.x (Pubitemid 40516789)
27. Montenecourt BS, Eveleigh DE (1979) Selective isolation of high yielding cellulase mutants of Trichoderma reesei. Adv Chem Ser 181:289-301. doi: 10.1021/ba-1979-0181.ch014
28. Nakari-Setälä T, Paloheimo M, Kallio J, Vehmaanperä J, Penttilä M, Saloheimo M (2009) Genetic modification of carbon catabolite repression in Trichoderma reesei for improved protein production. Appl Environ Microbiol 75:4853-4860. doi: 10.1128/AEM.00282-09
29. Porciuncula JO, Furukawa T, Mori K, Shida Y, Hirakawa H, Tashiro K, Kuhara S, Nakagawa S, Morikawa Y, Ogasawara W (2013) Single nucleotide polymorphism analysis of a Trichoderma reesei hyper-cellulolytic mutant developed in Japan. Biosci Biotechnol Biochem 77:534-543. doi: 10.1271/bbb.129794
30. Portnoy T, Margeot A, Linke R, Atanasova L, Fekete E, Sandor E, Hartl L, Karaffa L, Druzhinina IS, Seiboth B, Le Crom S, Kubicek CP (2011) The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation. BMC Genomics 12:269-281. doi: 10.1186/1471-2164-12-269
31. Rahman Z, Shida Y, Furukawa T, Suzuki Y, Okada H, Ogasawara W, Morikawa Y (2009) Evaluation and characterisation of Trichoderma reesei cellulase and xylanase promoters. Appl Microbiol Biot 82:899-908. doi: 10.1007/s00253-008- 1841-3
32. Scazzocchio C, Ramón A (2008) Chromatin in the genus Aspergillus. In: Goldman GH, Osmani SA (eds) The aspergilli: genomics, medical aspects, biotechnology and research methods, vol 26. CRC, Boca Raton, pp 321-341
33. Schuster A, Schmoll M (2010) Biology and biotechnology of Trichoderma. Appl Microbiol Biotechnol 87:787-799. doi: 10.1007/s00253-010-2632-1
34. Sekinger EA, Moqtaderi Z, Struhl K (2005) Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell 18:735-748. doi: 10.1016/j.molcel.2005.05.003 (Pubitemid 40804808)
35. Stricker AR, Grosstessner-Hain K, Würleiter E, Mach RL (2006) XYR1 (Xylanase Regulator 1) regulates both the hydrolytic enzyme system and D-xylose metabolism in Hypocrea jecorina. Eukaryot Cell 5:2128-2137. doi: 10.1128/EC.00211-06 (Pubitemid 44956824)
36. Stricker AR, Mach RL, de Graaff HL (2008) Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei). Appl Microbiol Biotechnol 78:211-220. doi: 10.1007/s00253-007-1322-0
37. Takashima S, Jikura H, Nakamura A, Masaki H, Uozumi T (1996) Analysis of CRE1 binding sites in the Trichoderma reesei cbh1 upstream region. FEMS Microbiol Lett 145:361-366. doi: 10.1111/j.1574-6968.1996.tb08601.x (Pubitemid 26422875)
38. Zeilinger S, Schmoll M, Pail M, Mach RL, Kubicek CP (2003) Nucleosome transactions on the Hypocrea jecorina (Trichoderma reesei) cellulase promoter cbh2 associated with cellulase induction. Mol Genet Gen 270:46-55. doi: 10.1007/s00438-003-0895-2 (Pubitemid 37267103)