Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype

Journal Article · Mon Apr 20 00:00:00 EDT 2015 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-015-1526-0· OSTI ID:1242698

Lichius, Alexander ^[1]; Bidard, Frédérique ^[2]; Buchholz, Franziska ^[1]; Le Crom, Stéphane ^[3]; Martin, Joel ^[4]; Schackwitz, Wendy ^[4]; Austerlitz, Tina ^[1]; Grigoriev, Igor V. ^[4]; Baker, Scott E. ^[5]; Margeot, Antoine ^[2]; Seiboth, Bernhard ^[1]; Kubicek, Christian P. ^[1]

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1. Vienna Univ. of Technology (Austria). Inst. of Chemical Engineering
2. French Inst. of Petroleum (IFP), Rueil-Mamaison (France)
3. Univ. of Paris, Sorbonne (France)
4. U.S. Joint Genome Inst., Walnut Creek, CA (United States)
5. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Here, Trichoderma reesei is the main industrial source of cellulases and hemicellulases required for the hydrolysis of biomass to simple sugars, which can then be used in the production of biofuels and biorefineries. The highly productive strains in use today were generated by classical mutagenesis. As byproducts of this procedure, mutants were generated that turned out to be unable to produce cellulases. In order to identify the mutations responsible for this inability, we sequenced the genome of one of these strains, QM9136, and compared it to that of its progenitor T. reesei QM6a. In QM9136, we detected a surprisingly low number of mutagenic events in the promoter and coding regions of genes, i.e. only eight indels and six single nucleotide variants. One of these indels led to a frame-shift in the Zn₂Cys₆ transcription factor XYR1, the general regulator of cellulase and xylanase expression, and resulted in its C-terminal truncation by 140 amino acids. Retransformation of strain QM9136 with the wild-type xyr1 allele fully recovered the ability to produce cellulases, and is thus the reason for the cellulase-negative phenotype. Introduction of an engineered xyr1 allele containing the truncating point mutation into the moderate producer T. reesei QM9414 rendered this strain also cellulase-negative. The correspondingly truncated XYR1 protein was still able to enter the nucleus, but failed to be expressed over the basal constitutive level. In conclusion, the missing 140 C-terminal amino acids of XYR1 are therefore responsible for its previously observed auto-regulation which is essential for cellulases to be expressed. Our data present a working example of the use of genome sequencing leading to a functional explanation of the QM9136 cellulase-negative phenotype.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Genomics Division; Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE Office of Science (SC). Joint Genome Institute; Austrian Science Fund (FWF); USDOE
• Grant/Contract Number: AC02-05CH11231 P-23202; I-1249; P24219; AC02-05CH11231; AC05-76RL01830
• OSTI ID: 1242698
• Alternate ID(s): OSTI ID: 1185053; OSTI ID: 1208746
• Report Number(s): LBNL-177776; PNNL-SA-110701; ir:177776
• Journal Information: BMC Genomics, Vol. 16, Issue 1; Related Information: The Erratum to this article has been published in BMC Genomics 2015 16:725; ISSN 1471-2164
• Publisher: Springer
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
single nucleotide polymorphism
SNP
indel
comparative genomics
classical mutant
XYR1
transcription
factor shuttling
cellulases
Trichoderma reesei
QM9136
Trichoderma reesei
transcription factor shuttling