Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction

Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri; Frischmann, Alexa; Seiboth, Bernhard; Baker, Scott E.; Le Crom, Stéphane; Lemoine, Sophie; Margeot, Antoine; Bidard, Frédérique

doi:10.1186/s13068-017-0897-7

Title: Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction

Journal Article · Thu Sep 07 00:00:00 EDT 2017 · Biotechnology for Biofuels

DOI:https://doi.org/10.1186/s13068-017-0897-7· OSTI ID:1626985

^[1]; Ramoni, Jonas ^[2]; Aouam, Thiziri ^[3]; Frischmann, Alexa ^[2]; Seiboth, Bernhard ^[2]; Baker, Scott E. ^[4]; Le Crom, Stéphane ^[5]; Lemoine, Sophie ^[6]; Margeot, Antoine ^[3]; Bidard, Frédérique ^[3]

IFP Energies Nouvelles, Rueil-Malmaison (France); Institut Pasteur, Paris (France). Genetics of Biofilms. Dept. of Microbiology
Technische Univ. Wien (Austria). Inst. of Chemical Engineering. Research Division Biochemical Technology. Molecular Biotechnology
IFP Energies Nouvelles, Rueil-Malmaison (France)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Earth and Biological Sciences Directorate
Sorbonne Univ., Paris (France). Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS).
Ecole Normale Superieure, Paris (France). PSL Research Univ. CNRS. Inserm. Institut de Biologie de l’École normale supérieure (IBENS). Plateforme Génomique

Background: The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefneries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identifcation of mutations underlying this cellulase-negative phenotype. Results: Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identifed a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identifed 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confrming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no efect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions. Conclusion: We were able to establish a link between a chromosomal translocation in QM9978 and the cellulasenegative phenotype of the strain. We identifed the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specifc trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1626985

Journal Information:: Biotechnology for Biofuels, Vol. 10, Issue 1; ISSN 1754-6834

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Enhancement of cellulase production in Trichoderma reesei RUT-C30 by comparative genomic screening Liu, Pei; Lin, Aibo; Zhang, Guoxiu Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1131-z	journal	May 2019
The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus Wu, Vincent W.; Thieme, Nils; Huberman, Lori B. Proceedings of the National Academy of Sciences, Vol. 117, Issue 11 https://doi.org/10.1073/pnas.1915611117	journal	February 2020
Metabolic Engineering of Fungal Strains for Efficient Production of Cellulolytic Enzymes Zhao, Xin-Qing; Zhang, Xiao-Yue; Zhang, Fei Fungal Cellulolytic Enzymes https://doi.org/10.1007/978-981-13-0749-2_2	book	January 2018
The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles Novy, Vera; Nielsen, Fredrik; Seiboth, Bernhard Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1571-z	journal	October 2019
The role of PKAc1 in gene regulation and trichodimerol production in Trichoderma reesei Hinterdobler, Wolfgang; Schuster, André; Tisch, Doris Fungal Biology and Biotechnology, Vol. 6, Issue 1 https://doi.org/10.1186/s40694-019-0075-8	journal	September 2019
Protein hyperproduction in fungi by design Baker, Scott E. Applied Microbiology and Biotechnology, Vol. 102, Issue 20 https://doi.org/10.1007/s00253-018-9265-1	journal	August 2018
Regulation of plant cell wall degradation by light in Trichoderma Schmoll, Monika Fungal Biology and Biotechnology, Vol. 5, Issue 1 https://doi.org/10.1186/s40694-018-0052-7	journal	April 2018
The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles Novy, Vera; Nielsen, Fredrik; Seiboth, Bernhard BioMed Central https://doi.org/10.14288/1.0383323	text	January 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
09 BIOMASS FUELS
Biotechnology & Applied Microbiology
Energy & Fuels
Trichoderma reesei
Genome analysis
Transcriptome
vib1
Cellulase production
Promoter
Translocation

MOESM4 of Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri https://doi.org/10.6084/m9.figshare.c.3874429_d4.v1 The current record is supplemented by this text	text	January 2017
Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri https://doi.org/10.6084/M9.FIGSHARE.C.3874429 The current record is supplemented by this collection	collection	January 2017
MOESM2 of Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri https://doi.org/10.6084/m9.figshare.c.3874429_d2.v1 The current record is supplemented by this text	text	January 2017
MOESM3 of Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri https://doi.org/10.6084/m9.figshare.c.3874429_d3.v1 The current record is supplemented by this text	text	January 2017
MOESM3 of Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri https://doi.org/10.6084/m9.figshare.c.3874429_d3 The current record is supplemented by this text	text	January 2017
MOESM2 of Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri https://doi.org/10.6084/m9.figshare.c.3874429_d2 The current record is supplemented by this text	text	January 2017
MOESM4 of Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri https://doi.org/10.6084/m9.figshare.c.3874429_d4 The current record is supplemented by this text	text	January 2017
MOESM1 of Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri https://doi.org/10.6084/m9.figshare.c.3874429_d1.v1 The current record is supplemented by this image	image	January 2017
Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction Ivanova, Christa; Ramoni, Jonas; Aouam, Thiziri https://doi.org/10.6084/m9.figshare.c.3874429.v1 The current record is supplemented by this collection	collection	January 2017