I. Energies-nouvelles and D. Biotechnologie, Avenue de Bois- Préau, 92852 Rueil-Malmaison Cedex, France. 2 École normale supérieure, Institut de Biologie de l'ENS, IBENS, Austrian Center of Industrial Biotechnology, vol.8197166, issue.9 4, pp.1-4

B. Görke and J. Stülke, Carbon catabolite repression in bacteria: many ways to make the most out of nutrients, Nature Reviews Microbiology, vol.280, issue.8, pp.613-624, 2008.
DOI : 10.1038/nrmicro1932

J. Deutscher, The mechanisms of carbon catabolite repression in bacteria, Current Opinion in Microbiology, vol.11, issue.2, pp.87-93, 2008.
DOI : 10.1016/j.mib.2008.02.007

URL : https://hal.archives-ouvertes.fr/hal-00315464

J. Gancedo, Carbon catabolite repression in yeast, Microbiol Mol Biol Rev, vol.62, pp.334-361, 1998.

H. Ronne, Glucose repression in fungi, Trends in Genetics, vol.11, issue.1, pp.12-17, 1995.
DOI : 10.1016/S0168-9525(00)88980-5

J. Westholm, N. Nordberg, E. Murén, A. Ameur, J. Komorowski et al., Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3, BMC Genomics, vol.9, issue.1, p.601, 2008.
DOI : 10.1186/1471-2164-9-601

C. Dowzer and J. Kelly, Analysis of the creA gene, a regulator of carbon catabolite repression in Aspergillus nidulans., Molecular and Cellular Biology, vol.11, issue.11, pp.5701-5709, 1991.
DOI : 10.1128/MCB.11.11.5701

G. Ruijter and J. Visser, Carbon repression in aspergilli, FEMS Microbiology Letters, vol.151, issue.2, pp.103-114, 1997.
DOI : 10.1111/j.1574-6968.1997.tb12557.x

B. Felenbok, M. Flipphi, and I. Nikolaev, Ethanol catabolism in Aspergillus nidulans: A model system for studying gene regulation, Progress Nucleic Acid Res Mol Biol, vol.69, pp.149-204, 2001.
DOI : 10.1016/S0079-6603(01)69047-0

C. Panozzo, E. Cornillot, and B. Felenbok, The CreA Repressor Is the Sole DNA-binding Protein Responsible for Carbon Catabolite Repression of the alcA Gene in Aspergillus nidulans via Its Binding to a Couple of Specific Sites, Journal of Biological Chemistry, vol.273, issue.11, pp.6367-6372, 1998.
DOI : 10.1074/jbc.273.11.6367

R. Mach, J. Strauss, S. Zeilinger, M. Schindler, and C. Kubicek, Carbon catabolite repression of xylanase I (xyn1) gene expression in Trichoderma reesei, Molecular Microbiology, vol.21, issue.6, pp.1273-1281, 1996.
DOI : 10.1046/j.1365-2958.1996.00094.x

B. Cubero and C. Scazzocchio, 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, vol.13, pp.407-415, 1994.

S. Takashima, H. Iikura, A. Nakamura, H. Masaki, and T. Uozumi, upstream region, FEMS Microbiology Letters, vol.145, issue.3, pp.361-366, 1996.
DOI : 10.1111/j.1574-6968.1996.tb08601.x

A. Cziferszky, R. Mach, and C. Kubicek, Phosphorylation Positively Regulates DNA Binding of the Carbon Catabolite Repressor Cre1 of Hypocrea jecorina (Trichoderma reesei), Journal of Biological Chemistry, vol.277, issue.17, pp.14688-14699, 2002.
DOI : 10.1074/jbc.M200744200

C. Bailey, H. Arst, and . Jr, Carbon Catabolite Repression in Aspergillus nidulans, European Journal of Biochemistry, vol.121, issue.2, pp.573-577, 1975.
DOI : 10.1016/S0076-6879(57)03413-8

J. Strauss, H. Horvath, B. Abdallah, J. Kindermann, R. Mach et al., The function of CreA, the carbon catabolite repressor of Aspergillus Portnoy et al is regulated at the transcriptional and post-transcriptional level, BMC Genomics Mol Microbiol, vol.12, issue.32, pp.269169-178, 1999.

H. Ilyés, E. Fekete, L. Karaffa, E. Fekete, E. Sándor et al., CreA-mediated carbon catabolite repression of $beta;-galactosidase formation in Aspergillus nidulans is growth rate dependent, FEMS Microbiology Letters, vol.235, issue.1, pp.147-151, 2004.
DOI : 10.1016/j.femsle.2004.04.020

R. Shroff, O. Connor, S. Hynes, M. Lockington, R. Kelly et al., Null Alleles ofcreA,the Regulator of Carbon Catabolite Repression inAspergillus nidulans, Fungal Genetics and Biology, vol.22, issue.1, pp.28-38, 1997.
DOI : 10.1006/fgbi.1997.0989

T. Nakari-setälä, M. Paloheimo, J. Kallio, J. Vehmaanperä, M. Penttilä et al., Genetic Modification of Carbon Catabolite Repression in Trichoderma reesei for Improved Protein Production, Applied and Environmental Microbiology, vol.75, issue.14, pp.4853-4860, 2009.
DOI : 10.1128/AEM.00282-09

R. Mach, M. Schindler, and C. Kubicek, Transformation of Trichoderma reesei based on hygromycin B resistance using homologous expression signals, Current Genetics, vol.33, issue.6, pp.567-570, 1994.
DOI : 10.1007/BF00351679

G. Smyth, Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments, Statistical Applications in Genetics and Molecular Biology, vol.3, issue.1, 2004.
DOI : 10.2202/1544-6115.1027

P. Piper, C. Ortiz-calderon, C. Holyoak, P. Coote, and M. Cole, Hsp30, the integral plasma membrane heat shock protein of Saccharmyces cerevisiae, is a stress-inducible regulator of plasma membrane H+-ATPase, Cell Stress & Chaperones, vol.2, issue.1, pp.12-24, 1997.
DOI : 10.1379/1466-1268(1997)002<0012:HTIPMH>2.3.CO;2

C. Kubicek, M. Mikus, . Schuster, M. Schmoll, and B. Seiboth, Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina, Biotechnology for Biofuels, vol.2, issue.1, p.19, 2009.
DOI : 10.1186/1754-6834-2-19

N. Boase and J. Kelly, A role for creD, a carbon catabolite repression gene from Aspergillus nidulans, in ubiquitination, Molecular Microbiology, vol.21, issue.3, pp.929-940, 2004.
DOI : 10.1111/j.1365-2958.2004.04172.x

M. Thomas-chollier, O. Sand, J. Turatsinze, R. Janky, M. Defrance et al., RSAT: regulatory sequence analysis tools, Nucleic Acids Research, vol.36, issue.Web Server, pp.119-127, 2008.
DOI : 10.1093/nar/gkn304

J. Mogensen, H. Nielsen, G. Hofmann, and J. Nielsen, Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol, Fungal Genetics and Biology, vol.43, issue.8, pp.593-603, 2006.
DOI : 10.1016/j.fgb.2006.03.003

D. Martinez, R. Berka, B. Henrissat, M. Saloheimo, M. Arvas et al., Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina), Nature Biotechnology, vol.307, issue.5, pp.553-560, 2008.
DOI : 10.1038/nbt1403

D. Taatjes and R. Tjian, Structure and Function of CRSP/Med2, Molecular Cell, vol.14, issue.5, pp.675-683, 2004.
DOI : 10.1016/j.molcel.2004.05.014

D. Balciunas, M. Hallberg, S. Björklund, and H. Ronne, Functional Interactions within Yeast Mediator and Evidence of Differential Subunit Modifications, Journal of Biological Chemistry, vol.278, issue.6, pp.3831-3839, 2003.
DOI : 10.1074/jbc.M206946200

A. Maccabe, P. Miró, L. Ventura, and D. Ramón, Glucose uptake in germinating Aspergillus nidulans conidia: involvement of the creA and sorA genes, Microbiology, vol.149, issue.8, pp.2129-2136, 2003.
DOI : 10.1099/mic.0.26349-0

G. Peter, L. Düring, and A. Ahmed, Carbon Catabolite Repression Regulates Amino Acid Permeases in Saccharomyces cerevisiae via the TOR Signaling Pathway, Journal of Biological Chemistry, vol.281, issue.9, pp.5546-5552, 2006.
DOI : 10.1074/jbc.M513842200

L. Karaffa, E. Fekete, C. Gamauf, A. Szentirmai, C. Kubicek et al., Dgalactose induces cellulase gene expression in Hypocrea jecorina at low growth rates, pp.1507-1514, 2006.

S. Zeilinger, M. Schmoll, M. Pail, R. Mach, and C. Kubicek, Nucleosome transactions on the Hypocrea jecorina ( Trichoderma reesei ) cellulase promoter cbh2 associated with cellulase induction, Molecular Genetics and Genomics, vol.270, issue.1, pp.46-55, 2003.
DOI : 10.1007/s00438-003-0895-2

I. García, R. Gonzalez, D. Gómez, and C. Scazzocchio, Chromatin Rearrangements in the prnD-prnB Bidirectional Promoter: Dependence on Transcription Factors, Eukaryotic Cell, vol.3, issue.1, pp.144-56, 2004.
DOI : 10.1128/EC.3.1.144-156.2004

Y. Reyes-dominguez, F. Narendja, H. Berger, A. Gallmetzer, R. Fernandez-martin et al., Nucleosome Positioning and Histone H3 Acetylation Are Independent Processes in the Aspergillus nidulans prnD-prnB Bidirectional Promoter, Eukaryotic Cell, vol.7, issue.4, pp.656-63, 2008.
DOI : 10.1128/EC.00184-07

F. Holstege, E. Jennings, J. Wyrick, T. Lee, C. Hengartner et al., Dissecting the Regulatory Circuitry of a Eukaryotic Genome, Cell, vol.95, issue.5, pp.717-728, 1998.
DOI : 10.1016/S0092-8674(00)81641-4

P. Becker and W. Horz, ATP-Dependent Nucleosome Remodeling, Annual Review of Biochemistry, vol.71, issue.1, pp.247-273, 2002.
DOI : 10.1146/annurev.biochem.71.110601.135400

P. Sudarsanam, V. Iyer, P. Brown, and F. Winston, Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae, Proceedings of the National Academy of Sciences, vol.97, issue.7, pp.3364-3369, 2000.
DOI : 10.1073/pnas.97.7.3364

M. Dechassa, B. Zhang, R. Horowitz-scherer, J. Persinger, C. Woodcock et al., Architecture of the SWI/SNF-Nucleosome Complex, Molecular and Cellular Biology, vol.28, issue.19, pp.6010-6021, 2008.
DOI : 10.1128/MCB.00693-08

A. Kanauchi, C. Yamashiro, S. Tanabe, and T. Murayama, A ras homologue of Neurospora crassa regulates morphology, Mol Gen Genet, vol.254, pp.427-432, 1997.

J. Fortwendel, K. Fuller, T. Stephens, W. Bacon, D. Askew et al., Aspergillus fumigatus RasA Regulates Asexual Development and Cell Wall Integrity, Eukaryotic Cell, vol.7, issue.9, pp.1530-1539, 2008.
DOI : 10.1128/EC.00080-08

D. Breviario, A. Hinnebusch, and R. Dhar, Multiple regulatory mechanisms control the expression of the RAS1 and RAS2 genes of Saccharomyces cerevisiae, EMBO J, vol.7, pp.1805-1813, 1988.

L. Du and P. Novick, Pag1p, a Novel Protein Associated with Protein Kinase Cbk1p, Is Required for Cell Morphogenesis and Proliferation in Saccharomyces cerevisiae, Molecular Biology of the Cell, vol.13, issue.2, pp.503-514, 2002.
DOI : 10.1091/mbc.01-07-0365

T. Ohara, I. Inoue, F. Namiki, H. Kunoh, and T. Tsuge, REN1 Is Required for Development of Microconidia and Macroconidia, but Not of Chlamydospores, in the Plant Pathogenic Fungus Fusarium oxysporum, Genetics, vol.166, issue.1, pp.113-137, 2004.
DOI : 10.1534/genetics.166.1.113

J. Yu, Z. Hamari, K. Han, J. Seo, Y. Reyes-domínguez et al., Double-joint PCR: a PCR-based molecular tool for gene manipulations in filamentous fungi, Fungal Genetics and Biology, vol.41, issue.11, pp.973-81, 2004.
DOI : 10.1016/j.fgb.2004.08.001

L. Hartl, C. Kubicek, and B. Seiboth, Induction of the gal Pathway and Cellulase Genes Involves No Transcriptional Inducer Function of the Galactokinase in Hypocrea jecorina, Journal of Biological Chemistry, vol.282, issue.25, pp.18654-18659, 2008.
DOI : 10.1074/jbc.M700955200

F. Gruber, J. Visser, C. Kubicek, D. Graaff, and L. , Cloning of the Trichoderma reesei pyrG gene and its use as a homologous marker for a highfrequency transformation system, Curr Genet, vol.18, pp.451-456, 1990.

J. Kelly and M. Hynes, Transformation of Aspergillus niger by the amdS gene of Aspergillus nidulans, EMBO J, vol.4, pp.475-479, 1985.

L. Jourdren, A. Duclos, C. Brion, T. Portnoy, H. Mathis et al., Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments, Nucleic Acids Research, vol.38, issue.10, p.117, 2010.
DOI : 10.1093/nar/gkq110

S. Lemoine, F. Combes, N. Servant, L. Crom, and S. , Goulphar: Rapid access and expertise for standard two-color microarray normalization methods, BMC Bioinformatics, vol.7, issue.1, p.467, 2006.
DOI : 10.1186/1471-2105-7-467

URL : https://hal.archives-ouvertes.fr/inserm-00122139

M. Pfaffl, G. Horgan, and L. Dempfle, Relative expression software tool (REST © ) for group-wise comparison and statistical alaysis of relative expression results in real-time PCR. Nucleic Acid Research, p.36, 2002.

I. Druzhinina, M. Schmoll, B. Seiboth, and C. Kubicek, Global Carbon Utilization Profiles of Wild-Type, Mutant, and Transformant Strains of Hypocrea jecorina, Applied and Environmental Microbiology, vol.72, issue.3, pp.2126-2133, 2006.
DOI : 10.1128/AEM.72.3.2126-2133.2006

A. Saeed, V. Sharov, J. White, J. Li, W. Liang et al., TM4: a free, open-source system for microarray data management and analysis, Biotechniques, vol.34, pp.374-378, 2003.

P. Pavlidis and W. Noble, Analysis of strain and regional variation in gene expression in mouse brain, Genome Biol, vol.2, p.42, 2001.

A. Ben-dor, R. Shamir, and Z. Yakhini, Clustering Gene Expression Patterns, Journal of Computational Biology, vol.6, issue.3-4, pp.281-97, 1999.
DOI : 10.1089/106652799318274

M. Walter, T. Rattei, R. Arnold, U. Güldener, M. Münsterkötter et al., Frishman D: PEDANT covers all complete RefSeq genomes, Database, pp.37-408, 2009.