title: Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reesei using high-throughput genomic and proteomic analyses.
abstract: BACKGROUND
  The filamentous fungus Trichoderma reesei is a major producer of lignocellulolytic enzymes utilized by bioethanol industries. However, to achieve low cost second generation bioethanol production on an industrial scale an efficient mix of hydrolytic enzymes is required for the deconstruction of plant biomass. In this study, we investigated the molecular basis for lignocellulose-degrading enzyme production T. reesei during growth in cellulose, sophorose, and glucose.
  
  
  RESULTS
  We examined and compared the transcriptome and differential secretome (2D-DIGE) of T. reesei grown in cellulose, sophorose, or glucose as the sole carbon sources. By applying a stringent cut-off threshold 2,060 genes were identified as being differentially expressed in at least one of the respective carbon source comparisons. Hierarchical clustering of the differentially expressed genes identified three possible regulons, representing 123 genes controlled by cellulose, 154 genes controlled by sophorose and 402 genes controlled by glucose. Gene regulatory network analyses of the 692 genes differentially expressed between cellulose and sophorose, identified only 75 and 107 genes as being specific to growth in sophorose and cellulose, respectively. 2D-DIGE analyses identified 30 proteins exclusive to sophorose and 37 exclusive to cellulose. A correlation of 70.17% was obtained between transcription and secreted protein profiles.
  
  
  CONCLUSIONS
  Our data revealed new players in cellulose degradation such as accessory proteins with non-catalytic functions secreted in different carbon sources, transporters, transcription factors, and CAZymes, that specifically respond in response to either cellulose or sophorose.
authors.affiliation: Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900 Ribeirão Preto, SP, Brazil.
authors.forename: Lilian
authors.initials: L
authors.lastname: Dos Santos Castro
authors.affiliation: Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900 Ribeirão Preto, SP, Brazil.
authors.forename: Wellington Ramos
authors.initials: WR
authors.lastname: Pedersoli
authors.affiliation: Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900 Ribeirão Preto, SP, Brazil.
authors.forename: Amanda Cristina Campos
authors.initials: ACC
authors.lastname: Antoniêto
authors.affiliation: Departamento de Biologia Celular, Universidade de Brasília, Asa Norte, 70910-900 Brasília, DF, Brazil.
authors.forename: Andrei Stecca
authors.initials: AS
authors.lastname: Steindorff
authors.affiliation: Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900 Ribeirão Preto, SP, Brazil.
authors.forename: Rafael
authors.initials: R
authors.lastname: Silva-Rocha
authors.affiliation: Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, 14049-900 Ribeirão Preto, SP, Brazil.
authors.forename: Nilce M
authors.initials: NM
authors.lastname: Martinez-Rossi
authors.affiliation: Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900 Ribeirão Preto, SP, Brazil.
authors.forename: Antonio
authors.initials: A
authors.lastname: Rossi
authors.affiliation: Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, and Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Campinas, Brazil.
authors.forename: Neil Andrew
authors.initials: NA
authors.lastname: Brown
authors.affiliation: Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, and Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Campinas, Brazil.
authors.forename: Gustavo H
authors.initials: GH
authors.lastname: Goldman
authors.affiliation: Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900 Ribeirão Preto, SP, Brazil.
authors.forename: Vitor M
authors.initials: VM
authors.lastname: Faça
authors.affiliation: Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, 14049-900 Ribeirão Preto, SP, Brazil.
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.
authors.forename: Roberto Nascimento
authors.initials: RN
authors.lastname: Silva