title: The impact of chromatin remodelling on cellulase expression in Trichoderma reesei.
abstract: BACKGROUND
  Trichoderma reesei is used for industry-scale production of plant cell wall-degrading enzymes, in particular cellulases, but also xylanases. The expression of the encoding genes was so far primarily investigated on the level of transcriptional regulation by regulatory proteins. Otherwise, the impact of chromatin remodelling on gene expression received hardly any attention. In this study we aimed to learn if the chromatin status changes in context to the applied conditions (repressing/inducing), and if the presence or absence of the essential transactivator, the Xylanase regulator 1 (Xyr1), influences the chromatin packaging.
  
  
  RESULTS
  Comparing the results of chromatin accessibility real-time PCR analyses and gene expression studies of the two prominent cellulase-encoding genes, cbh1 and cbh2, we found that the chromatin opens during sophorose-mediated induction compared to D-glucose-conferred repression. In the strain bearing a xyr1 deletion the sophorose mediated induction of gene expression is lost and the chromatin opening is strongly reduced. In all conditions the chromatin got denser when Xyr1 is absent. In the case of the xylanase-encoding genes, xyn1 and xyn2, the result was similar concerning the condition-specific response of the chromatin compaction. However, the difference in chromatin status provoked by the absence of Xyr1 is less pronounced. A more detailed investigation of the DNA accessibility in the cbh1 promoter showed that the deletion of xyr1 changed the in vivo footprinting pattern. In particular, we detected increased hypersensitivity on Xyr1-sites and stronger protection of Cre1-sites. Looking for the players directly causing the observed chromatin remodelling, a whole transcriptome shotgun sequencing revealed that 15 genes encoding putative chromatin remodelers are differentially expressed in response to the applied condition and two amongst them are differentially expressed in the absence of Xyr1.
  
  
  CONCLUSIONS
  The regulation of xylanase and cellulase expression in T. reesei is not only restricted to the action of transcription factors but is clearly related to changes in the chromatin packaging. Both the applied condition and the presence of Xyr1 influence chromatin status.
authors.affiliation: Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria. tdemello@mail.tuwien.ac.at.
authors.forename: Thiago M
authors.initials: TM
authors.lastname: Mello-de-Sousa
authors.affiliation: Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria. alice.rassinger@tuwien.ac.at.
authors.forename: Alice
authors.initials: A
authors.lastname: Rassinger
authors.affiliation: Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria. Marion.Pucher@gmx.at.
authors.forename: Marion E
authors.initials: ME
authors.lastname: Pucher
authors.affiliation: Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo 14049-900, Ribeirão Preto, SP, Brazil. liliancastro@usp.br.
authors.forename: Lilian
authors.initials: L
authors.lastname: dos Santos Castro
authors.affiliation: Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil. gabriela.persinoti@bioetanol.org.br.
authors.forename: Gabriela F
authors.initials: GF
authors.lastname: Persinoti
authors.affiliation: Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo 14049-900, Ribeirão Preto, SP, Brazil. silvarochar@gmail.com.
authors.forename: Rafael
authors.initials: R
authors.lastname: Silva-Rocha
authors.affiliation: Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasilia, Brasília, DF, Brazil. mpossas@unb.br.
authors.forename: Marcio J
authors.initials: MJ
authors.lastname: Poças-Fonseca
authors.affiliation: Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria. robert.mach@tuwien.ac.at.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Mach
authors.affiliation: Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo 14049-900, Ribeirão Preto, SP, Brazil. rsilva@fmrp.usp.br.
authors.forename: Roberto
authors.initials: R
authors.lastname: Nascimento Silva
authors.affiliation: Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Wien, Austria. astrid.mach-aigner@tuwien.ac.at.
authors.forename: Astrid R
authors.initials: AR
authors.lastname: Mach-Aigner
mesh_terms: D002480:Cellulase / Q000235:genetics*; D044602:Cellulases / Q000235:genetics; D002843:Chromatin / Q000235:genetics*; D042002:Chromatin Assembly and Disassembly / Q000235:genetics*; D005656:Fungal Proteins / Q000235:genetics; D015966:Gene Expression Regulation, Fungal / Q000235:genetics; D005947:Glucose / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D015534:Trans-Activators / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics; D059467:Transcriptome / Q000235:genetics; D014242:Trichoderma / Q000235:genetics*
chemical_list: D002843:Chromatin; D005656:Fungal Proteins; D015534:Trans-Activators; D044602:Cellulases; D002480:Cellulase; D005947:Glucose