The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome

Seidl, Verena; Gamauf, Christian; Druzhinina, Irina S.; Seiboth, Bernhard; Hartl, Lukas; Kubicek, Christian P.

doi:10.1186/1471-2164-9-327

The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome

Journal Article · Fri Jul 11 00:00:00 EDT 2008 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-9-327· OSTI ID:1626467

Seidl, Verena ^[1]; Gamauf, Christian ^[2]; Druzhinina, Irina S. ^[2]; Seiboth, Bernhard ^[2]; Hartl, Lukas ^[2]; Kubicek, Christian P. ^[2]

Vienna Univ. of Technology (Austria). Inst. of Chemical Engineering, Research Area Gene Technology and Applied Biochemistry; DOE/OSTI
Vienna Univ. of Technology (Austria). Inst. of Chemical Engineering, Research Area Gene Technology and Applied Biochemistry

Background: The hypercellulolytic mutant Hypocrea jecorina (anamorph Trichoderma reesei) RUT C30 is the H. jecorina strain most frequently used for cellulase fermentations and has also often been employed for basic research on cellulase regulation. This strain has been reported to contain a truncated carbon catabolite repressor gene cre1 and is consequently carbon catabolite derepressed. To date this and an additional frame-shift mutation in the glycoprotein-processing βglucosidase II encoding gene are the only known genetic differences in strain RUT C30. Results: In the present paper we show that H. jecorina RUT C30 lacks an 85 kb genomic fragment, and consequently misses additional 29 genes comprising transcription factors, enzymes of the primary metabolism and transport proteins. This loss is already present in the ancestor of RUT C30 – NG 14 – and seems to have occurred in a palindromic AT-rich repeat (PATRR) typically inducing chromosomal translocations, and is not linked to the cre1 locus. The mutation of the cre1 locus has specifically occurred in RUT C30. Some of the genes that are lacking in RUT C30 could be correlated with pronounced alterations in its phenotype, such as poor growth on α-linked oligoand polyglucosides (loss of maltose permease), or disturbance of osmotic homeostasis. Conclusion: Our data place a general caveat on the use of H. jecorina RUT C30 for further basic research.

View Accepted Manuscript (DOE)

Research Organization:: Vienna Univ. of Technology (Austria). Institute of Chemical Engineering

Sponsoring Organization:: Austrian Science Foundation (FWF); USDOE

OSTI ID:: 1626467

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 9; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 4 of Integrative transcriptome and proteome analyses of Trichoderma longibrachiatum LC and its cellulase hyper-producing mutants generated by heavy ion mutagenesis reveal the key genes involved in cellulolytic enzymes regulation Dong, Miaoyin; Wang, Shuyang; Xu, Fuqiang figshare https://doi.org/10.6084/m9.figshare.20003652.v1	dataset	January 2022
Additional file 5 of Integrative transcriptome and proteome analyses of Trichoderma longibrachiatum LC and its cellulase hyper-producing mutants generated by heavy ion mutagenesis reveal the key genes involved in cellulolytic enzymes regulation Dong, Miaoyin; Wang, Shuyang; Xu, Fuqiang figshare https://doi.org/10.6084/m9.figshare.20003655	dataset	January 2022
Additional file 6 of Integrative transcriptome and proteome analyses of Trichoderma longibrachiatum LC and its cellulase hyper-producing mutants generated by heavy ion mutagenesis reveal the key genes involved in cellulolytic enzymes regulation Dong, Miaoyin; Wang, Shuyang; Xu, Fuqiang figshare https://doi.org/10.6084/m9.figshare.20003658	image	January 2022
Additional file 7 of Integrative transcriptome and proteome analyses of Trichoderma longibrachiatum LC and its cellulase hyper-producing mutants generated by heavy ion mutagenesis reveal the key genes involved in cellulolytic enzymes regulation Dong, Miaoyin; Wang, Shuyang; Xu, Fuqiang figshare https://doi.org/10.6084/m9.figshare.20003661.v1	dataset	January 2022
Additional file 8 of Integrative transcriptome and proteome analyses of Trichoderma longibrachiatum LC and its cellulase hyper-producing mutants generated by heavy ion mutagenesis reveal the key genes involved in cellulolytic enzymes regulation Dong, Miaoyin; Wang, Shuyang; Xu, Fuqiang figshare https://doi.org/10.6084/m9.figshare.20003664.v1	dataset	January 2022
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Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing Le Crom, S.; Schackwitz, W.; Pennacchio, L. Proceedings of the National Academy of Sciences, Vol. 106, Issue 38 https://doi.org/10.1073/pnas.0905848106	journal	September 2009
Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa Tian, Chaoguang; Beeson, William T.; Iavarone, Anthony T. Proceedings of the National Academy of Sciences, Vol. 106, Issue 52 https://doi.org/10.1073/pnas.0906810106	journal	December 2009
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass Minty, Jeremy J.; Singer, Marc E.; Scholz, Scott A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 36 https://doi.org/10.1073/pnas.1218447110	journal	August 2013
Network of nutrient-sensing pathways and a conserved kinase cascade integrate osmolarity and carbon sensing in Neurospora crassa Huberman, Lori B.; Coradetti, Samuel T.; Glass, N. Louise Proceedings of the National Academy of Sciences, Vol. 114, Issue 41 https://doi.org/10.1073/pnas.1707713114	journal	September 2017
Quantitative Secretomic Analysis of Trichoderma reesei Strains Reveals Enzymatic Composition for Lignocellulosic Biomass Degradation Adav, Sunil S.; Chao, Lim Tze; Sze, Siu Kwan Molecular & Cellular Proteomics, Vol. 11, Issue 7 https://doi.org/10.1074/mcp.m111.012419	journal	February 2012
Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era McCluskey, Kevin; Baker, Scott E. Mycology, Vol. 8, Issue 2 https://doi.org/10.1080/21501203.2017.1281849	journal	January 2017
Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences Bacolla, Albino; Tainer, John A.; Vasquez, Karen M. Nucleic Acids Research, Vol. 44, Issue 12 https://doi.org/10.1093/nar/gkw261	journal	April 2016
Trichoderma reesei RUT-C30 - thirty years of strain improvement Peterson, R.; Nevalainen, H. Microbiology, Vol. 158, Issue 1, p. 58-68 https://doi.org/10.1099/mic.0.054031-0	journal	October 2011
Transformation System for Hypocrea jecorina ( Trichoderma reesei ) That Favors Homologous Integration and Employs Reusable Bidirectionally Selectable Markers Steiger, Matthias G.; Vitikainen, Marika; Uskonen, Pekka Applied and Environmental Microbiology, Vol. 77, Issue 1 https://doi.org/10.1128/aem.02100-10	journal	November 2010
The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species Schmoll, Monika; Dattenböck, Christoph; Carreras-Villaseñor, Nohemí Microbiology and Molecular Biology Reviews, Vol. 80, Issue 1 https://doi.org/10.1128/mmbr.00040-15	journal	February 2016
Targets of light signalling in Trichoderma reesei Tisch, Doris; Schmoll, Monika BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-657	journal	January 2013
Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae Udatha, D. B. R. K. Gupta; Topakas, Evangelos; Salazar, Margarita BMC Systems Biology, Vol. 9, Issue 1 https://doi.org/10.1186/s12918-015-0224-5	journal	November 2015
A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei Mello-de-Sousa, Thiago M.; Gorsche, Rita; Rassinger, Alice Biotechnology for Biofuels, Vol. 7, Issue 1 https://doi.org/10.1186/s13068-014-0129-3	journal	September 2014
Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes Jourdier, Etienne; Baudry, Lyam; Poggi-Parodi, Dante Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0837-6	journal	June 2017
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
Rational engineering of the Trichoderma reesei RUT-C30 strain into an industrially relevant platform for cellulase production Fonseca, Lucas Miranda; Parreiras, Lucas Salera; Murakami, Mario Tyago Biotechnology for Biofuels, Vol. 13, Issue 1 https://doi.org/10.1186/s13068-020-01732-w	journal	May 2020
Identification of the CRE-1 Cellulolytic Regulon in Neurospora crassa Sun, Jianping; Glass, N. Louise PLoS ONE, Vol. 6, Issue 9 https://doi.org/10.1371/journal.pone.0025654	journal	September 2011
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
The Promoter Toolbox for Recombinant Gene Expression in Trichoderma reesei Fitz, Elisabeth; Wanka, Franziska; Seiboth, Bernhard Frontiers in Bioengineering and Biotechnology, Vol. 6 https://doi.org/10.3389/fbioe.2018.00135	journal	October 2018
Strain improvement and process optimization of Trichderma reesei Rut C30 for enhanced cellulase production Wu, Gaihong; He, Ronglin; Jia, Wendi Biofuels, Vol. 2, Issue 5 https://doi.org/10.4155/bfs.11.124	journal	September 2011

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59 BASIC BIOLOGICAL SCIENCES
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The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome

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