The gene expression difference in strain AT01, a mutant of Trichoderma reesei, with high ability of copper accumulation
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ABSTRACT:
ORGANISM(S): Trichoderma reesei QM6a
PROVIDER: GSE37518 | GEO | 2012/04/27
SECONDARY ACCESSION(S): PRJNA160977
REPOSITORIES: GEO
Similar Datasets
Project description:The gene expression profile of AT01 was compared with a wild-type T. reesei strain in medium containing 0.7 mM Cu2+. A total of 627 genes were up-regulated and 305 genes were down-regulated under copper stress. The expression analysis showed that amino acid transport- and metabolism-related genes are up-regulated, which is associated with adenine metabolism. Furthermore, inorganic ion transport- and metabolism-associated genes, such as superoxide dismutase and copper transporters, were also up-regulated. Strain AT01 and wild-type strain were inoculated into YPD medium containing 1 mM CuSO4, and cultured at 25 M-BM-0C for 5 d. Each sample was carried out with two repetitions.
2012-04-26 | E-GEOD-37518 | biostudies-arrayexpress
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
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 One control and three sample points, checked by a marker enzyme for sporulation and by microscopy, were done in two biologicvao replicas
2011-12-08 | E-GEOD-27471 | biostudies-arrayexpress
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
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: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).
2011-03-02 | GSE27581 | GEO
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
Project description:The induction of genes in response to exposure of T. reesei to wheat straw was explored using genome-wide RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to the lignocellulose. After 24 h of exposure to straw, transcript levels of known and predicted lignocellulose-degrading enzymes increased to around 8% of total cellular mRNA in T. reesei, which was much less when compared to A. niger. The bulk of enzymes used to deconstruct wheat straw is similar in both fungi. Other, non-plant cell wall-degrading enzymes which may aid in lignocellulose degradation were also uncovered in T. reesei and similar to those described in A. niger. Antisense transcripts were also shown to be present in T. reesei and their expession can be regulated by the respective growth condition.
2013-04-01 | GSE44648 | GEO
Project description:We perform a self hybridisation comprative genomic hybridization (CGH) in order to validate the probe tiling design we done on Trichoderma reesei. This hybridization was done using QM6a wild type strain.
2010-03-16 | GSE17752 | 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