Trichoderma reesei
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PROVIDER: PRJNA259795 | ENA |
REPOSITORIES: ENA
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Project description:The filamentous fungus Trichoderma reesei is the main industrial cellulytic enzymes producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome sequencing, transcriptome) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG14 and RUT C30. In this follow-up work, we examined how these mutations affect phenotype at the level of the transcriptome and cultivation behavior. We performed kinetic transcriptome analysis of the NG14 and RUT C30 strains of early cellulase production induced by lactose using bioreactor cultivations close to industrial conditions. RUT C30 exhibited both earlier onset of cellulase production and higher steady-state productivity. A rather low number of genes were regulated, most of them being specific to the NG14 strains. Clustering of these genes highlighted similar behavior for some functional categories, and allowed to distinguish between induction-related genes and productivity-related genes. The lower number of genes regulated in RUT C30 could not formally be linked to the relief in catabolic repression that is characteristic of this strain. Cross-comparison of our transcriptome data with mutations previously identified revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting these clusters contain genes playing a role in strain performance. This is the first kinetic transcriptome study carried out in industry-relevant conditions with two related strains of T. reesei showing distinctive performances. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggest that the induction mechanism is essentially intact and that there is room for further improvement of T. reesei. We also provide some potential target for further genetic improvement of these strains.
2014-12-10 | GSE60908 | GEO
Project description:The filamentous fungus Trichoderma reesei is the main industrial cellulytic enzymes producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome sequencing, transcriptome) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG14 and RUTM-BM- C30. In this follow-up work, we examined how these mutations affect phenotype at the level of the transcriptome and cultivation behavior.M-BM- We performed kinetic transcriptome analysis of the NG14 and RUTM-BM- C30 strains of early cellulase production induced by lactose using bioreactor cultivations close to industrial conditions. RUTM-BM- C30 exhibited both earlier onset of cellulase production and higher steady-state productivity. A rather lowM-BM- number of genes were regulated, most of them being specific to the NG14 strains. Clustering of these genes highlighted similar behavior for some functional categories, and allowed to distinguish between induction-related genes and productivity-related genes. The lower number of genes regulated in RUTM-BM- C30 could not formally be linked to the relief in catabolic repression that is characteristic of this strain. Cross-comparison of our transcriptome data with mutations previously identified revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting these clusters contain genes playing a role in strain performance. This is the first kinetic transcriptome study carried out in industry-relevant conditions with two related strains of T. reesei showing distinctive performances. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggest that the induction mechanism is essentially intact and that there is room for further improvement of T. reesei. We also provide some potential target for further genetic improvement of these strains. 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.
2014-12-10 | E-GEOD-60908 | biostudies-arrayexpress
Project description:The ascomycete Trichoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes and also serves as a model for investigations on these enzymes and their genes. The strain QM9978 has a cellulase negative phenotype and therefore presents a valuable tool for understanding the mechanisms underlying cellulase regulation. A transcriptomic analyses of the cellulase negative strain QM9978 and the original strain QM6a have been performed to identify the genetic differences between QM6a and QM9978 leading to the cellulase-negative phenotype
2017-09-15 | GSE89199 | GEO
Project description:Lactose (1,4-0-M-CM-^_-d-galactopyranosyl-d-glucose), a by-product from cheese manufacture or whey processing industries, is known to induce the formation of plant biomass hydrolyzing enzymes needed for the biorefinery industry in the fungus Trichoderma reesei, but the reason for this induction and the underlying mechanism are not fully understood. Here, we used systems analysis of the Trichoderma reesei transcriptome during utilization of lactose. We found that the respective CAZome encoded glycosyl hydrolases specifically tailored for the attack of monocotyledon xyloglucan. In addition, genes for a high number of putative transporters of the major facilitator superfamily were also induced. Systematic knock out of them identified a gene whose knock-out completely impaired lactose utilization and cellulase induction in Trichoderma reesei. These data shed new light on the mechanism by which Trichoderma reesei metabolizes lactose and illuminate the key role of M-CM-^_-D-galactosides in habitat specificity of this fungus. We used two biological replicas of Trichoderma reesei growing on lactose, glucose and glycerol
2013-06-30 | E-GEOD-39276 | biostudies-arrayexpress
Project description:The ascomycete Trichoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes and also serves as a model for investigations on these enzymes and their genes. Most of them are obligatorily dependent on the Zn(II)Cys(VI) transcriptional activator XYR1. XYR1 is constitutively expressed at a low basal, but induced in the presence of cellulase- and hemicellulose inducers, and transported into the nucleus. The factors mediating its import and export across the nuclear pore complexes (karyopherins) are therefore expected to play a key role in its function. We identified 14 karyopherins in T. reesei, of which 8 were predicted to be involved nuclear protein import. Their systematic knock-out and testing for cellulase formation identified KAP8 (an orthologue of A. nidulans KapI, and Saccharomyces cerevisiae Kap121/Pse1p) to be essential for cellulase gene expression, and for the appearance of GFP-XYR1 in the nucleus. Transcriptomic analysis of Δkap8 and a retransformant under cellulase-inducing conditions revealed the downregulation of 64 Cazymes in the Δkap8 strain under inducing conditions, including all cellulases and hemicellulases known to be under XYR1 control, and of 12 transcription factors of which 2 were known to be associated with cellulase regulation (ACE3, CLR2). Together, these new observations underscore the role of nuclear transport of XYR1 in the regulation of cellulase and hemicellulose gene expression in T. reesei, and identify KAP8 as the major karyopherin involved in this process. Two strains were used: T. reesei ku70 (pyr4-), in which the kap8 (=kapI/Pse1/Kap121) reading frame has been replaced by the T. reesei pyr4 gene; and a kap8-retransformant of the same strain and two time points for each strain T0h and T3h. All samples are in tricplicate.
2015-03-03 | E-GEOD-59600 | biostudies-arrayexpress
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.
2010-11-26 | GSE19606 | GEO
Project description:Lactose (1,4-0-ß-d-galactopyranosyl-d-glucose), a by-product from cheese manufacture or whey processing industries, is known to induce the formation of plant biomass hydrolyzing enzymes needed for the biorefinery industry in the fungus Trichoderma reesei, but the reason for this induction and the underlying mechanism are not fully understood. Here, we used systems analysis of the Trichoderma reesei transcriptome during utilization of lactose. We found that the respective CAZome encoded glycosyl hydrolases specifically tailored for the attack of monocotyledon xyloglucan. In addition, genes for a high number of putative transporters of the major facilitator superfamily were also induced. Systematic knock out of them identified a gene whose knock-out completely impaired lactose utilization and cellulase induction in Trichoderma reesei. These data shed new light on the mechanism by which Trichoderma reesei metabolizes lactose and illuminate the key role of ß-D-galactosides in habitat specificity of this fungus.
2013-06-30 | GSE39276 | GEO
Project description:The disruption of vacuolar protein sorting related genes vps13 and vps21 in filamentou fungi Trichoderma reesei resulted in a dramtic increase in cellulase transcription especially in the late Avicel induction phase, relieving the RESS (REpression under Secretion Stress) effect. Great interest arisen concered about the reason and underlying mechanism of vps13 and vps21 disruption for increased cellulase transcription. Thus, transcriptome analysis through RNA-Seq could give a deep insight of the potential pathways involved in enhanced cellulase transcription in late Avicel induction.
2021-11-10 | GSE187573 | GEO
Project description:The ascomycete Trichoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes and also serves as a model for investigations on these enzymes and their genes. Most of them are obligatorily dependent on the Zn(II)Cys(VI) transcriptional activator XYR1. XYR1 is constitutively expressed at a low basal, but induced in the presence of cellulase- and hemicellulose inducers, and transported into the nucleus. The factors mediating its import and export across the nuclear pore complexes (karyopherins) are therefore expected to play a key role in its function. We identified 14 karyopherins in T. reesei, of which 8 were predicted to be involved nuclear protein import. Their systematic knock-out and testing for cellulase formation identified KAP8 (an orthologue of A. nidulans KapI, and Saccharomyces cerevisiae Kap121/Pse1p) to be essential for cellulase gene expression, and for the appearance of GFP-XYR1 in the nucleus. Transcriptomic analysis of Δkap8 and a retransformant under cellulase-inducing conditions revealed the downregulation of 64 Cazymes in the Δkap8 strain under inducing conditions, including all cellulases and hemicellulases known to be under XYR1 control, and of 12 transcription factors of which 2 were known to be associated with cellulase regulation (ACE3, CLR2). Together, these new observations underscore the role of nuclear transport of XYR1 in the regulation of cellulase and hemicellulose gene expression in T. reesei, and identify KAP8 as the major karyopherin involved in this process.
2015-03-03 | GSE59600 | GEO
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