title: Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain.
abstract: BACKGROUND
  The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour.
  
  
  RESULTS
  We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance.
  
  
  CONCLUSIONS
  This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.
authors.affiliation: IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.|Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France.
authors.forename: Dante
authors.initials: D
authors.lastname: Poggi-Parodi
authors.affiliation: IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Bidard
authors.affiliation: IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Pirayre
authors.affiliation: IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.|Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Plateforme Génomique, Paris, F-75005 France.|Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, Paris, F-75005 France.|Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, CNRS, UMR 8197, Paris, F-75005 France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Portnoy
authors.affiliation: Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Plateforme Génomique, Paris, F-75005 France.|Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, Paris, F-75005 France.|Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, CNRS, UMR 8197, Paris, F-75005 France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Blugeon
authors.affiliation: Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Technische Universität Wien, Getreidemarkt 9/166, A- 1060 Vienna, Austria.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Seiboth
authors.affiliation: Austrian Center of Industrial Biotechnology, 8010 Graz, Austria.
authors.forename: Christian P
authors.initials: CP
authors.lastname: Kubicek
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France.|Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Plateforme Génomique, Paris, F-75005 France.|Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, Paris, F-75005 France.|Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, CNRS, UMR 8197, Paris, F-75005 France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Le Crom
authors.affiliation: IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Margeot
keywords: Biofuels; Cellulase; Fed-batch; Systems biology; Transcriptome; Trichoderma reesei