Deciphering the cis-regulatory elements for XYR1 and CRE1 regulators in Trichoderma reesei

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Silva Rocha, Rafael ^a   Castro, Lilian Dos Santos ^a   Antoniêto, Amanda Cristina Campos ^a   Guazzaroni, María Eugenia ^a   Persinoti, Gabriela Felix ^a   Silva, Roberto Nascimento ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN CRE1; PROTEIN XYR1; REGULATOR PROTEIN; UNCLASSIFIED DRUG; FUNGAL DNA; FUNGAL PROTEIN;

ARTICLE; BINDING SITE; CEL3C GENE; CEL3D GENE; CEL61A GENE; CEL61B GENE; CEL6A GENE; CEL7A GENE; CEL7B GENE; FUNGAL STRAIN; FUNGUS MUTANT; GENE; GENOME; HYPOCREA JECORINA; MOLECULAR MECHANICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN MOTIF; REGULATORY SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SWO GENE; XYN1 GENE; XYN3 GENE; CONSENSUS SEQUENCE; DNA SEQUENCE; FUNGAL GENE; GENE EXPRESSION REGULATION; GENETICS; TRICHODERMA;

BASE SEQUENCE; BINDING SITES; CONSENSUS SEQUENCE; DNA, FUNGAL; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; PROMOTER REGIONS, GENETIC; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SEQUENCE ANALYSIS, DNA; TRICHODERMA;

EID: 84903289493     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099366     Document Type: Article

References (61)

1. Tomme P, Van Tilbeurgh H, Pettersson G, Van Damme J, Vandekerckhove J, et al. (1988) Studies of the cellulolytic system of Trichoderma reesei QM 9414. Analysis of domain function in two cellobiohydrolases by limited proteolysis. European journal of biochemistry/FEBS 170: 575-581.
2. Sternberg D, Mandels GR (1979) Induction of cellulolytic enzymes in Trichoderma reesei by sophorose. Journal of bacteriology 139: 761-769. (Pubitemid 10234086)
3. Minty JJ, Singer ME, Scholz SA, Bae CH, Ahn JH, et al. (2013) Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proceedings of the National Academy of Sciences of the United States of America 110: 14592-14597.
4. Maurya DP, Singh D, Pratap D, Maurya JP (2012) Optimization of solid state fermentation conditions for the production of cellulase by Trichoderma reesei. Journal of environmental biology/Academy of Environmental Biology, India 33: 5-8.
5. Schuster A, Schmoll M (2010) Biology and biotechnology of Trichoderma. Applied microbiology and biotechnology 87: 787-799.
6. Amore A, Giacobbe S, Faraco V (2013) Regulation of cellulase and hemicellulase gene expression in fungi. Current genomics 14: 230-249.
7. Adav SS, Chao LT, Sze SK (2012) Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation. Molecular & cellular proteomics : MCP 11: M111 012419.
8. Stricker AR, Mach RL, de Graaff LH (2008) Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei). Applied microbiology and biotechnology 78: 211-220.
9. Ouyang J, Yan M, Kong D, Xu L (2006) A complete protein pattern of cellulase and hemicellulase genes in the filamentous fungus Trichoderma reesei. Biotechnology journal 1: 1266-1274.
10. Portnoy T, Margeot A, Linke R, Atanasova L, Fekete E, et al. (2011) The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation. BMC genomics 12: 269.
11. Furukawa T, Shida Y, Kitagami N, Mori K, Kato M, et al. (2009) Identification of specific binding sites for XYR1, a transcriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei. Fungal genetics and biology : FG & B 46: 564-574.
12. Wang S, Liu G, Wang J, Yu J, Huang B, et al. (2013) Enhancing cellulase production in Trichoderma reesei RUT C30 through combined manipulation of activating and repressing genes. Journal of industrial microbiology & biotechnology 40: 633-641.
13. Herold S, Bischof R, Metz B, Seiboth B, Kubicek CP (2013) Xylanase gene transcription in Trichoderma reesei is triggered by different inducers representing different hemicellulosic pentose polymers. Eukaryotic cell 12: 390-398.
14. Gyalai-Korpos M, Nagy G, Mareczky Z, Schuster A, Reczey K, et al. (2010) Relevance of the light signaling machinery for cellulase expression in Trichoderma reesei (Hypocrea jecorina). BMC research notes 3: 330.
15. Seiboth B, Karimi RA, Phatale PA, Linke R, Hartl L, et al. (2012) The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei. Molecular microbiology 84: 1150-1164.
16. Nitta M, Furukawa T, Shida Y, Mori K, Kuhara S, et al. (2012) A new Zn(II)(2)Cys(6)-type transcription factor BglR regulates beta-glucosidase expression in Trichoderma reesei. Fungal genetics and biology : FG & B 49: 388-397.
17. Portnoy T, Margeot A, Seidl-Seiboth V, Le Crom S, Ben Chaabane F, et al. (2011) Differential regulation of the cellulase transcription factors XYR1, ACE2, and ACE1 in Trichoderma reesei strains producing high and low levels of cellulase. Eukaryotic cell 10: 262-271.
18. Ling M, Qin Y, Li N, Liang Z (2009) Binding of two transcriptional factors, Xyr1 and ACEI, in the promoter region of cellulase cbh1 gene. Biotechnology letters 31: 227-231.
19. Stricker AR, Grosstessner-Hain K, Wurleitner E, Mach RL (2006) Xyr1 (xylanase regulator 1) regulates both the hydrolytic enzyme system and D-xylose metabolism in Hypocrea jecorina. Eukaryotic cell 5: 2128-2137. (Pubitemid 44956824)
20. Ilmen M, Thrane C, Penttila M (1996) The glucose repressor gene cre1 of Trichoderma: isolation and expression of a full-length and a truncated mutant form. Molecular & general genetics : MGG 251: 451-460.
21. Clapier CR, Cairns BR (2009) The biology of chromatin remodeling complexes. Annual review of biochemistry 78: 273-304.
22. Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447: 407-412.
23. Narlikar GJ, Fan HY, Kingston RE (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108: 475-487. (Pubitemid 34260873)
24. Struhl K (1999) Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98: 1-4.
25. Ries L, Belshaw NJ, Ilmen M, Penttila ME, Alapuranen M, et al. (2014) The role of CRE1 in nucleosome positioning within the cbh1 promoter and coding regions of Trichoderma reesei. Applied microbiology and biotechnology 98: 749-762.
26. 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. Molecular genetics and genomics : MGG 270: 46-55. (Pubitemid 37267103)
27. Mach RL, Strauss J, Zeilinger S, Schindler M, Kubicek CP (1996) Carbon catabolite repression of xylanase I (xyn1) gene expression in Trichoderma reesei. Molecular microbiology 21: 1273-1281. (Pubitemid 26313253)
28. Messner R, Kubicek CP (1991) Carbon Source Control of Cellobiohydrolase I and II Formation by Trichoderma reesei. Applied and environmental microbiology 57: 630-635.
29. Rauscher R, Wurleitner E, Wacenovsky C, Aro N, Stricker AR, et al. (2006) Transcriptional regulation of xyn1, encoding xylanase I, in Hypocrea jecorina. Eukaryotic cell 5: 447-456.
30. Sun J, Tian C, Diamond S, Glass NL (2012) Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa. Eukaryotic cell 11: 482-493.
31. van Peij NN, Visser J, de Graaff LH (1998) Isolation and analysis of xlnR, encoding a transcriptional activator co-ordinating xylanolytic expression in Aspergillus niger. Molecular microbiology 27: 131-142. (Pubitemid 28022583)
32. Aro N, Ilmen M, Saloheimo A, Penttila M (2003) ACEI of Trichoderma reesei is a repressor of cellulase and xylanase expression. Applied and environmental microbiology 69: 56-65. (Pubitemid 36077457)
33. Saloheimo A, Aro N, Ilmen M, Penttila M (2000) Isolation of the ace1 gene encoding a Cys(2)-His(2) transcription factor involved in regulation of activity of the cellulase promoter cbh1 of Trichoderma reesei. The Journal of biological chemistry 275: 5817-5825. (Pubitemid 30115227)
34. Klein CJ, Olsson L, Nielsen J (1998) Glucose control in Saccharomyces cerevisiae: the role of Mig1 in metabolic functions. Microbiology 144 (Pt 1): 13-24. (Pubitemid 28045209)
35. Ogasawara W, Shida Y, Furukawa T, Shimada R, Nakagawa S, et al. (2006) Cloning, functional expression and promoter analysis of xylanase III gene from Trichoderma reesei. Applied microbiology and biotechnology 72: 995-1003. (Pubitemid 44477378)
36. Wurleitner E, Pera L, Wacenovsky C, Cziferszky A, Zeilinger S, et al. (2003) Transcriptional regulation of xyn2 in Hypocrea jecorina. Eukaryotic cell 2: 150-158. (Pubitemid 36770385)
37. Aro N, Saloheimo A, Ilmen M, Penttila M (2001) ACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei. The Journal of biological chemistry 276: 24309-24314.
38. Glass NL, Schmoll M, Cate JH, Coradetti S (2013) Plant cell wall deconstruction by ascomycete fungi. Annual review of microbiology 67: 477-498.
39. Takashima S, Iikura H, Nakamura A, Masaki H, Uozumi T (1996) Analysis of Cre1 binding sites in the Trichoderma reesei cbh1 upstream region. FEMS microbiology letters 145: 361-366. (Pubitemid 26422875)
40. Gorsche R, Jovanovic B, Gudynaite-Savitch L, Mach RL, Mach-Aigner AR (2014) A highly sensitive in vivo footprinting technique for condition-dependent identification of cis elements. Nucleic acids research 42: e1.
41. Cubero B, Scazzocchio C (1994) 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. The EMBO journal 13: 407-415. (Pubitemid 24034224)
42. Rahman Z, Shida Y, Furukawa T, Suzuki Y, Okada H, et al. (2009) Evaluation and characterization of Trichoderma reesei cellulase and xylanase promoters. Applied microbiology and biotechnology 82: 899-908.
43. Mach RL, Zeilinger S (2003) Regulation of gene expression in industrial fungi: Trichoderma. Applied microbiology and biotechnology 60: 515-522. (Pubitemid 36169525)
44. Lockington RA, Rodbourn L, Barnett S, Carter CJ, Kelly JM (2002) Regulation by carbon and nitrogen sources of a family of cellulases in Aspergillus nidulans. Fungal genetics and biology : FG & B 37: 190-196. (Pubitemid 35333775)
45. Dos Santos Castro L, Pedersoli WR, Antonieto AC, Steindorff AS, Silva-Rocha R, et al. (2014) Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reesei using high-throughput genomic and proteomic analyses. Biotechnology for biofuels 7: 41.
46. Castro LD, Antonieto AC, Pedersoli WR, Rocha RS, Persinoti GF, et al. (2014) Expression pattern of cellulolytic and xylanolytic genes regulated by transcriptional factors XYR1 and CRE1 are affected by carbon source in Trichoderma reesei. Gene expression patterns : GEP.
47. Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic acids research 34: W369-373. (Pubitemid 44529795)
48. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic acids research 18: 6097-6100.
49. Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, et al. (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature biotechnology 26: 553-560. (Pubitemid 351668043)
50. Murray PG, Collins CM, Grassick A, Tuohy MG (2003) Molecular cloning, transcriptional, and expression analysis of the first cellulase gene (cbh2), encoding cellobiohydrolase II, from the moderately thermophilic fungus Talaromyces emersonii and structure prediction of the gene product. Biochemical and biophysical research communications 301: 280-286. (Pubitemid 36279234)
51. Zeilinger S, Mach RL, Kubicek CP (1998) 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. The Journal of biological chemistry 273: 34463-34471.
52. Furukawa T, Shida Y, Kitagami N, Ota Y, Adachi M, et al. (2008) Identification of the cis-acting elements involved in regulation of xylanase III gene expression in Trichoderma reesei PC-3-7. Fungal genetics and biology : FG & B 45: 1094-1102.
53. Wasserman WW, Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nature reviews Genetics 5: 276-287. (Pubitemid 38435623)
54. Hallikas O, Palin K, Sinjushina N, Rautiainen R, Partanen J, et al. (2006) Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124: 47-59. (Pubitemid 43069309)
55. Shida Y, Furukawa T, Ogasawara W, Kato M, Kobayashi T, et al. (2008) Functional analysis of the egl3 upstream region in filamentous fungus Trichoderma reesei. Applied microbiology and biotechnology 78: 515-524.
56. MacPherson S, Larochelle M, Turcotte B (2006) A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiology and molecular biology reviews : MMBR 70: 583-604. (Pubitemid 44484686)
57. Stangl H, Gruber F, Kubicek CP (1993) Characterization of the Trichoderma reesei cbh2 promoter. Current genetics 23: 115-122. (Pubitemid 23045011)
58. Mach-Aigner AR, Pucher ME, Steiger MG, Bauer GE, Preis SJ, et al. (2008) Transcriptional regulation of xyr1, encoding the main regulator of the xylanolytic and cellulolytic enzyme system in Hypocrea jecorina. Applied and environmental microbiology 74: 6554-6562.
59. Guelzim N, Bottani S, Bourgine P, Kepes F (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nature genetics 31: 60-63.
60. Carle-Urioste JC, Escobar-Vera J, El-Gogary S, Henrique-Silva F, Torigoi E, et al. (1997) Cellulase induction in Trichoderma reesei by cellulose requires its own basal expression. The Journal of biological chemistry 272: 10169-10174. (Pubitemid 27171694)
61. el-Gogary S, Leite A, Crivellaro O, Eveleigh DE, el-Dorry H (1989) Mechanism by which cellulose triggers cellobiohydrolase I gene expression in Trichoderma reesei. Proceedings of the National Academy of Sciences of the United States of America 86: 6138-6141. (Pubitemid 19210616)