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ArrayCGH of Trichoderma reesei strains QM9123, QM9414, NG14 and RutC-30

ABSTRACT: Trichoderma reesei is the main industrial producer of cellulases and hemicellulases used to depolymerize biomass in many biotechnical applications. Many production strains in use have been generated by classical mutagenesis. In this study we characterized genomic alterations in hyperproducing mutants of T. reesei by high-resolution comparative genomic hybridisation tiling array. We carried out aCGH analysis of four hyperproducing strains (QM9123, QM9414, NG14 and RutC-30) using QM6a genome as a reference. ArrayCGH analysis identified dozens of mutations in each strain analyzed.

ORGANISM(S): Trichoderma reesei

PROVIDER: GSE19606 | GEO | 2010/11/26

SECONDARY ACCESSION(S): PRJNA122443

REPOSITORIES: GEO

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ArrayCGH of Trichoderma reesei strains QM9123, QM9414, NG14 and RutC-30

Project description:Trichoderma reesei is the main industrial producer of cellulases and hemicellulases used to depolymerize biomass in many biotechnical applications. Many production strains in use have been generated by classical mutagenesis. In this study we characterized genomic alterations in hyperproducing mutants of T. reesei by high-resolution comparative genomic hybridisation tiling array. We carried out aCGH analysis of four hyperproducing strains (QM9123, QM9414, NG14 and RutC-30) using QM6a genome as a reference. ArrayCGH analysis identified dozens of mutations in each strain analyzed. 2.1 million oligonucleotide probe custom aCGH (HD2 format, RocheNimblegen) was designed according to T. reesei strain QM6a genome v2.0 (http://genome.jgi-psf.org/Trire2/Trire2.home.html). 14 samples are included in this set; 3 replicates of each strain (except two replicates of QM9123) were analyzed (four mutant strains and QM6a control strain for self-hybridization)

2010-11-26 | E-GEOD-19606 | biostudies-arrayexpress

Transcriptional landscape of XYR1 in Trichoderma reesei during the degradation of cellulosic material

Project description:Hypocrea jecorina (anamorph Trichoderma reesei) is one of the most well studied fungi used in biotechnology industry. This fungus is today a paradigm for the comercial scale production of different plant cell wall degrading enzymes, mainly cellulases and hemicellulases. The objective of this study was to analyze the transcriptional profiling of T. reesei (Δxyr1) grown in presence of cellulose, sophorose and glucose as the carbon source using RNA-seq approach.

2017-02-09 | GSE66982 | GEO

Trichoderma reesei

Project description:ArrayCGH of Trichoderma reesei strains QM9123, QM9414, NG14 and RutC-30

| PRJNA122443 | ENA

Expression analysis of Trichoderma reesei QM9414 and delta-phlp1, delta-gnb1 and delta-gng1 in light and darkness.

Project description:Investigation of whole genome gene expression level changes in response to different light conditions of the T. reesei QM9414 parental strain and the deletion strains delta-phlp1, delta-gnb1 and delta gng1, cultivated on 1 % microcrystalline cellulose. The mutants analyzed in this study are further described in Tisch et al. 2011: Carbohydrate degradation is significantly regulated by light and the phosducin like protein PhLP1 in Trichoderma reesei (Hypocrea jecorina). We used two biological replicates of four T. reesei strains (QM9414, delta-phlp1, delta-gnb1 and delta-gng1), cultivated in constant light (LL, 1800 lux) or constant darkness (DD) on microcrystalline cellulose.

2011-03-02 | E-GEOD-27581 | biostudies-arrayexpress

Expression analysis of Trichoderma reesei QM9414 and delta-phlp1, delta-gnb1 and delta-gng1 in light and darkness.

2011-03-02 | GSE27581 | GEO

Decoding the black box of cellulase formation in Hypocrea jecorina by RNA-Seq analysis

Project description:Hypocrea jecorina (anamorph Trichoderma reesei) is one of the most well studied fungi used in biotechnology industry. This fungus is today a paradigm for the comercial scale production of different plant cell wall degrading enzymes, mainly cellulases and hemicellulases. The objective of this study was to analyze the transcriptional profiling of T. reesei grown in presence of cellulose, sophorose and glucose as the carbon source using RNA-seq approach.

2014-04-01 | GSE53629 | GEO

Effect of LAE1 gene deletion on gene expression in Trichoderma

Project description:The mitosporic fungus Trichoderma reesei is an industrial producer of enzymes for degradation of lignocellulosic polysaccharides to soluble monomers that can be fermented to biofuels. The genes encoding these enzymes in T. reesei have recently been shown to be clustered in the genome. Here we will show that the expression of these genes is epigenetically controlled at the heterochromatin level by the protein methyltransferase LAE1. Deletion of lae1 led to a loss of expression of the major cellulase and hemicellulase encoding genes, and resulted in an inability to grow on cellulose. The cellulase null phenotype was also seen with known soluble inducers of enzymes active on cellulose. In contrast, introduction of a second copy of lae1 or its enhanced expression under a strong constitutive promoter resulted in increased levels of cellulases. Thus, our data provides an experiment-based explanation for the advantage for clustering of cellulases in the genome of T. reesei, and imply that the heterochromatin structure is a major determinant of cellulase gene expression and hence an attractive target for strain improvement. We used two biological replicas of four T. reesei strains growing on lactose, the parent strain (QM9414), a delta-lae1, and two overexpressing strains (tef1:lae1 mutant 1 and mutant 2).

2011-01-01 | E-GEOD-22687 | biostudies-arrayexpress

Genome-wide RNA-seq analysis during CRE1-mediated carbon catabolite repression in Trichoderma reesei grown in sophorose

Project description:The mechanism of carbon catabolite repression (CCR) mediated by CRE1 in Trichoderma reesei emerged as a way to adapt to the environment in which the fungus is found. In situations where there is the presence of readily available carbon sources such as glucose, the fungus activates this mechanism and inhibits the production of cellulolytic complex enzymes to avoid unnecessary energy expenditure. CCR has been well described for the growth of T. reesei in cellulose and glucose, however, little is known about this process when the carbon source available to the fungus is sophorose, one of the most potent inducer of cellulase production. Thus, we performed high-throughput RNA sequencing using the Illumina/HiSeq-2000 to contribute to the understanding of CCR during cellulase formation in the presence of sophorose, by comparing the mutant Δcre1 with its parental strain, QM9414. Of the 9129 genes present in the genome of T. reesei, 184 were up- and 344 down-regulated in the mutant strain Δcre1 compared to QM9414. Genes belonging to CAZy, transcription factors and transporters are among the gene classes that were repressed by CRE1 in the presence of sophorose, most of which was regulated by CRE1 in an indirect way. Overall, there was a similarity in the profile of repressed genes when compared with another inducing carbon source, cellulose. These results contribute to a better understanding of CRE1-meadiated CCR in T. reesei when glucose comes from a potent inducer as sophorose, which can be very useful in improving the production of cellulases by the biotechnology sector.

2017-02-11 | GSE66915 | GEO

Genome-wide RNA-seq analysis during carbon catabolite repression in Trichoderma reesei reveals a multilevel control of cellulase production and action

Project description:The ascomycete Trichoderma reesei is one of the most well studied cellulolytic fungi and widely used in the biotechnology industry, as in the production of second-generation bioethanol. Carbon catabolite repression (CCR) mechanism adopted by T. reesei is mediated by the transcription factor CRE1 and consists in the repression of genes related to the production of cellulase when a readily available carbon source is present in the medium. Using RNA sequencing this study aims to contribute to understanding of CCR during growth in cellulose and glucose, by comparing the mutant strain of T. reesei Δcre1 with its parental, QM9414.

2017-05-01 | GSE57374 | GEO

Transcriptome during shift of Trichoderma reesei from mycelial growth to asexual sporulation

Project description:The asexual spore or conidium plays a critical role in the life cycle of many filamentous fungi, being the primary means for dispersion in the environment. To investigate the transcriptional changes taking place during the sporulation phase in T. reesei, which culminates with the production of the conidiospores, microarray experiments were performed. Among the 1,994 distinct genes displaying >90 % confidence , a total of 900 were classified as differentially expressed, relative to time zero of sporulation, at at least one of the time points analyzed. The main functional categories (FunCat) overrepresented among upregulated genes were those involving solute transport, metabolism, transcriptional regulation, secondary metabolite synthesis, lipases, proteases and particularly cellulases and hemicellulases. Categories overrepresented among downregulated genes were especially those associated with ribosomal and mitochondrial functions. The upregulation of cellulase and hemicellulase genes was depending on the function of the positive transcriptional regulator XYR1, but the latter exerted no influence on sporulation itself. At least 20 % of the significantly regulated genes occured non-randomly distributed within the T. reesei genome suggesting an epigenetic component in the regulation of conidiation. The significant upregulation of cellulases and hemicellulases during conidiation, and thus cellulase and hemicelulase content in the spores of T. reesei lend to hypothesize that the ability to hydrolyse plant biomass is a major trait of this fungus to break dormancy and reinitiate vegetative growth after a period of facing unfavorable conditions

2011-12-08 | GSE27471 | GEO

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