Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing

Journal Article · Tue Sep 22 04:00:00 EDT 2009 · Proceedings of the National Academy of Sciences of the United States of America, 106(38):16151-16156

DOI:https://doi.org/10.1073/pnas.0905848106· OSTI ID:973985

Le Crom, Stphane; Schackwitz, Wendy; Pennacchiod, Len; Magnuson, Jon K; Culley, David E; Collett, James R; Martin, Joel X; Druzhinina, Irina S; Mathis, Hugues; Monot, Frdric; Seiboth, Bernhard; Cherry, Barbara; Rey, Michael; Berka, Randy; Kubicek, Christian P; Baker, Scott E; Margeot, Antoine

Trichoderma reesei (teleomorph Hypocrea jecorina) is the main industrial source of cellulases and hemicellulases harnessed for the hydrolysis of biomass to simple sugars, which can then be converted to biofuels, such as ethanol, and other chemicals. The highly productive strains in use today were generated by classical mutagenesis. To learn how cellulase production was improved by these techniques, we performed massively parallel sequencing to identify mutations in the genomes of two hyperproducing strains (NG14, and its direct improved descendant, RUT C30). We detected a surprisingly high number of mutagenic events: 223 single nucleotides variants, 15 small deletions or insertions and 18 larger deletions leading to the loss of more than 100 kb of genomic DNA. From these events we report previously undocumented non-synonymous mutations in 43 genes that are mainly involved in nuclear transport, mRNA stability, transcription, secretion/vacuolar targeting, and metabolism. This homogeneity of functional categories suggests that multiple changes are necessary to improve cellulase production and not simply a few clear-cut mutagenic events. Phenotype microarrays show that some of these mutations result in strong changes in the carbon assimilation pattern of the two mutants with respect to the wild type strain QM6a. Our analysis provides the first genome-wide insights into the changes induced by classical mutagenesis in a filamentous fungus, and suggests new areas for the generation of enhanced T. reesei strains for industrial applications such as biofuel production.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 973985
• Report Number(s): PNNL-SA-67636; BM0102070
• Journal Information: Proceedings of the National Academy of Sciences of the United States of America, 106(38):16151-16156, Journal Name: Proceedings of the National Academy of Sciences of the United States of America, 106(38):16151-16156 Journal Issue: 38 Vol. 106; ISSN 0027-8424; ISSN PNASA6
• Country of Publication: United States
• Language: English

Related Subjects

09 BIOMASS FUELS
BIOFUELS
BIOMASS
CARBON
CELLULASE
DNA
DNA SEQUENCING
ETHANOL
FUNCTIONALS
GENES
HYDROLYSIS
METABOLISM
MUTAGENESIS
MUTANTS
MUTATIONS
NUCLEOTIDES
PHENOTYPE
SACCHARIDES
STRAINS
TRANSCRIPTION
TRICHODERMA VIRIDE
Trichoderma
cellulase
fungi
genomics