Trichoderma reesei
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA126739 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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. Two biological pool by condition in dye switch. For the two biological replicates on each four experiments we apply on the pretreated results the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes from the limma R package (Smyth 2004). We select the list of statistically regulated genes using a 5% significance threshold.
2011-06-01 | E-GEOD-21072 | biostudies-arrayexpress
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
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
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
Project description:Genome-wide RNA-seq analysis during CRE1-mediated carbon catabolite repression in Trichoderma reesei grown in sophorose
| PRJNA278361 | ENA
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 28°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 -80°C until RNA extraction. After growth, total RNA was isolated from the mycelia using TRIzol® 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
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
Project description:Trichoderma reesei is known for its ability to produce large amounts of extracellular proteins and is one of the most important industrially used filamentous fungus. Xylanase regulator 1 (XYR1) as the master regulator is responsible for the activation of cellulase and hemicellulase gene expression, normally under inducing conditions. It has been reported that strains with point mutations in certain areas of xyr1 bypass the carbon catabolite repression, allowing cellulase and hemicellulase production even in the presence of glucose. These mutations also change the profile of produced proteins, shifting it more towards xylanase production, and increase the overall protein production in inducing conditions. However, how these mutations alter the metabolism and other cellular processes to cause these changes remains unclear. In the present study, our aim was to explore changes caused by a point mutation in xyr1 on transcriptomic and metabolic level to better understand the reasons behind the increased protein production in both repressing glucose and inducing lactose conditions. We observed that the xyr1 mutant strain built more biomass and produced more extracellular proteins during growth on lactose compared to the wild type xyr1 strain. Genes involved in oxidoreductive D-galactose catabolism pathway were upregulated in the xyr1 mutant strain, potentially contributing to the more efficient utilization of lactose. The shift from utilizing lactose to using glucose as carbon source seemed faster in the xyr1 mutant strain. Clustering and enrichment analysis showed over-representation of mitochondria-related Gene Ontology terms in clusters where gene expression was higher in the xyr1 mutant, indicating that mitochondria play a role in the altered metabolic state associated with the xyr1 mutation. Metabolomics revealed that free tyrosine was more abundant in the xyr1 mutant strain in all measured timepoints, whereas multiple fatty acids were less abundant in the mutant strain on glucose. The results contribute to more in-depth knowledge on T. reesei physiology and aid in finding new targets for improved protein production.
2024-07-19 | GSE260567 | GEO
Project description:The filamentous fungus Trichoderma reesei is a saprophyte involved with polysaccharides cell wall depolymerization, being the most important industrial source of cellulases, which have been used for bioethanol production. The regulation of cellulase expression is controlled at the transcriptional level and in a carbon source-dependent manner. However, the signaling pathways and mechanisms involved in regulating the expression of these enzymes in T. reesei are still poorly understood. In this study, we demonstrate through transcriptional analysis by RNA-Seq the main changes in gene expression that occur in functional mutants for two genes of the MAPK, tmk1 and tmk2. The results obtained allowed us to identify that these proteins in T. reesei regulate independent processes, but sometimes might regulate the same process through different mechanisms of action, being responsible for modulating gene expression in this organism. Regarding to Δtmk2 strain, it was demonstrated that growth in sugarcane bagasse and glucose modulates the expression of genes involved with chromatin remodeling, metabolism of carbohydrates and cell signaling genes such as GPCR, calcium signaling and phospholipases. On the other hand, deletion of MAPK TMK1 promotes more discrete changes in the transcriptional profile and the main changes are related to the decrease in the expression of the major genes for cellulases and xylanases, repressing the expression of transporters belonging to the MFS family, transporters of amino acids and ions such as Ca2+ and Mg2+. Our results revealed that the MAPK signaling pathway in T. reesei regulates many important processes that allow the fungus to promote the recognition, transport and metabolism of different carbon sources during the process of cell wall degradation. Therefore, the clustering of these data will contribute to the construction of a global model for the events that occur during the degradation of lignocellulose in T. reesei, which will lead to the development of more efficient strains in the plant biomass degradation.
2018-10-08 | GSE100602 | GEO