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

ABSTRACT: 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.

ORGANISM(S): Trichoderma reesei

PROVIDER: GSE66915 | GEO | 2017/02/11

SECONDARY ACCESSION(S): PRJNA278361

REPOSITORIES: GEO

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Genome-wide RNA-seq analysis during carbon catabolite repression inÂ Trichoderma reeseiÂ 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 Îcre1 with its parental, QM9414. T. reesei (QM9414 and Îcre1) was grown in Mandels-Andreotti medium, supplemented with 1% of cellulose or 2% of glucose. The cultures were incubated on an orbital shaker (200 rpm) at 28Â°C for 24, 48 and 72 hours using cellulose as carbon source and for 24 and 48 hours with glucose as the carbon source. All experiments were performed in three biological replicates. The resultant mycelia were collected by filtration, frozen and stored at -80Â°C until RNA extraction. After growth, total RNA was isolated from the mycelia using TRIzolÂ® reagent. RNA-seq experiments were performed by LGC Genomics GmbH (Berlin/Germany) using the platform Illumina/HiSeq2000. The samples from the parental strain QM9114 were previously submitted in GSE53629.

2017-05-01 | E-GEOD-57374 | biostudies-arrayexpress

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

2017-05-01 | GSE57374 | GEO

The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation

Project description:The identification and characterization of the transcriptional regulatory networks governing the physiological behaviour and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. This system has been investigated in bacteria, yeast and filamentous fungi. In the latter, the C2H2 zinc finger protein has been shown to act as the central transcriptional repressor in this process. Here, we deciphered the CRE1 regulon by profiling transcription in a wild-type and delta-cre1 mutant strains on glucose in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) at constant growth rates known to per se repress and derepress CCR-affected genes.

2011-06-01 | GSE21072 | GEO

The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation

2011-06-01 | E-GEOD-21072 | biostudies-arrayexpress

Identification of microRNA-like RNAs in the filamentous fungus Trichoderma reesei by Solexa sequencing

Project description:MicroRNAs (miRNAs) are small non-coding RNAs capable of negatively regulating gene expression. Trichoderma reesei is an industrial filamentous fungus that can secrete abundant hydrolases for cellulosic biofuels. Recently, microRNA-like RNAs (milRNAs) were discovered in several filamentous fungi rather than T. reesei. The purpose of this study was to explore the presence of milRNA in T. reesei, to characterize the differential expression of T. reesei milRNA under cellulose induction, and to reveal the target genes of milRNA involved in cellulase production. Two small RNA libraries of cellulose induction (IN) or non-induction (CON) were generated and sequenced using Solexa sequencing technology. A total of 664,463 and 529,545 unique sequences, representing 1,271 and 1,021 unique small RNAs, were obtained from the IN and CON samples, respectively. Thirteen milRNAs were finally identified in T. reesei using the hairpin structure analysis. The milRNAs profiles obtained in deep sequencing were validated by RT-qPCR assay. The miRanda program predicts a number of potential targets for T. reesei milRNAs, including several hydrolases and carbon catabolite repressor Cre1.The presence and differential expression of T. reesei milRNAs, along with their predicted targets indicate that milRNAs might play a regulatory role in cellulase induction. This work lays foundation for further functional study of fungal milRNAs and their industrial application.

2014-12-31 | GSE46679 | 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. T. reesei (QM9414) was grown in Mandels-Andreotti medium, supplemented with 1% of cellulose, 2% of glucose or 1mM of sophorose. The cultures were incubated on an orbital shaker (200 rpm) at 28M-BM-0C for 24, 48 and 72 hours using cellulose as carbon source; for 24 and 48 hours with glucose as the carbon; and 2, 4 and 6 hours with sophorose as the carbon source. In the latter, the mycelium was previously grown on glycerol for 24 hours and then transferred to 20 mL of Mandels-Andreotti medium without peptone. All experiments were performed in three biological replicates. The resultant mycelia were collected by filtration, frozen and stored at -80M-BM-0C until RNA extraction. After growth, total RNA was isolated from the mycelia using TRIzolM-BM-. reagent. RNA-seq experiments were performed by LGC Genomics GmbH (Berlin/Germany) using the platform Illumina/HiSeq2000.

2014-04-01 | E-GEOD-53629 | biostudies-arrayexpress

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

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

2017-02-09 | GSE66982 | GEO

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

2014-04-01 | GSE53629 | GEO

Inducer Free Cellulase Secretion in Neurospora Crassa and comparitive analysis of cellulase induction in Aspergillus nidulans

Project description:Purpose: To explore conservation of gene regulation by the transcription factor clr-2/clrB in Neurospora crassa and Aspergillus nidulans Methods: mRNA from wild type and clr-2/clrB mutants were collected after a culture shift from sucrose/glucose to Avicel (crystaline cellulose) or no carbon media Results: We show that N. crassa and A. nidulans have similair global transcriptional responses to Avicel, with several hundred genes showing specific induction, though the induced genes are more specifically targeted at cellulose for N. crassa and more targeted at hemicellulose and pectin for A. nidulans. clr-2/clrB has a conserved fundamental function in cellulose induction, though the mechanism has diverged. Misexpression of clr-2 is sufficeint for inducer free cellulase secretion in N. crassa, but neither clrB or heterologous clr-2 is sufficient for inducer free cellulase secretion in A. nidulans. Conclusions: Our study demonstrates a conserved and essential role in cellulose utilization for the transcription factor clr-2 in filamentous ascomycetes and demonstrates that manipulation of clr-2 expression can be used to control cellulase expression in some species.

2013-09-01 | GSE44100 | GEO

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