Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 reveals vib1 to be essential for cellulase induction
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ABSTRACT:
ORGANISM(S): Trichoderma reesei
PROVIDER: GSE89199 | GEO | 2017/09/15
SECONDARY ACCESSION(S): PRJNA350625
REPOSITORIES: GEO
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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: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: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: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: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:Light represents an important environmental cue, which exerts considerable influence on the metabolism of fungi. Studies with the biotechnological fungal workhorse Trichoderma reesei (Hypocrea jecorina) have revealed an interconnection between transcriptional regulation of cellulolytic enyzmes and the light response. The filamentous fungus, Neurospora crassa, has been used as a model organism to study light and circadian rhythm biology. We therefore investigated whether light also regulates transcriptional regulation of cellulolytic enzymes in N. crassa. We show that the N. crassa photoreceptor genes wc-1, wc-2 and vvd are involved in regulation of cellulase gene expression, indicating that this phenomenon is conserved among filamentous fungi. Genome wide analysis of photoreceptor mutants and evaluation of results by analysis of mutant strains identified several candidate genes likely to play a role in light modulated cellulase gene expression. Three deletion strains (delta-wc-1 (FGSC 11712), delta-wc-2 (FGSC 11124) and delta-vvd (FGSC 11556)) and the wild type strain (FGSC 2489) at two different timepoints (28h or 40h) were analyzed. Cy3 and Cy5 dye swaps were performed.
2011-10-11 | E-GEOD-32871 | biostudies-arrayexpress
Project description:Light represents an important environmental cue, which exerts considerable influence on the metabolism of fungi. Studies with the biotechnological fungal workhorse Trichoderma reesei (Hypocrea jecorina) have revealed an interconnection between transcriptional regulation of cellulolytic enyzmes and the light response. The filamentous fungus, Neurospora crassa, has been used as a model organism to study light and circadian rhythm biology. We therefore investigated whether light also regulates transcriptional regulation of cellulolytic enzymes in N. crassa. We show that the N. crassa photoreceptor genes wc-1, wc-2 and vvd are involved in regulation of cellulase gene expression, indicating that this phenomenon is conserved among filamentous fungi. Genome wide analysis of photoreceptor mutants and evaluation of results by analysis of mutant strains identified several candidate genes likely to play a role in light modulated cellulase gene expression.
2011-10-12 | GSE32871 | 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 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: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