GEO DataSets

(Submitter supplied) 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. more...

Organism:

Trichoderma reesei

Type:

Expression profiling by array

Platforms:

GPL9076 GPL19095

32 Samples

Download data: GPR, TXT

(Submitter supplied) 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

Organism:

Trichoderma reesei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18110

12 Samples

Download data: TXT

(Submitter supplied) The fungus Trichoderma reesei is one of the most used industrial cellulase producers due to its high capacity of protein secretion. The strain was shown to possess an expanded endoplasmic reticulum, but the genetic factors responsible for this phenotype remain still unidentified. Recently, three new transcription factors were described in Neurospora crassa which were demonstrated to be involved in protein secretion. more...

Organism:

Trichoderma reesei RUT C-30

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33444

16 Samples

Download data: GFF, TSV

(Submitter supplied) Study of the impact of the carbon source (various mixture of glucose and lactose) on the cellulase production.

Organism:

Trichoderma reesei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18977

36 Samples

Download data: TSV

(Submitter supplied) 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. more...

Organism:

Trichoderma reesei

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9821

14 Samples

Download data: PAIR

(Submitter supplied) The aim of this study was to evaluate changes in the transcriptome in the mentioned strains upon growth on cellulose

Organism:

Trichoderma reesei

Type:

Expression profiling by array

Platforms:

GPL10642 GPL16051

10 Samples

Download data: PAIR, TXT

(Submitter supplied) 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. more...

Organism:

Trichoderma reesei

Type:

Expression profiling by array

Platform:

GPL10642

6 Samples

Download data: PAIR, TXT

(Submitter supplied) 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. more...

Organism:

Trichoderma reesei

Type:

Expression profiling by array

Platform:

GPL10642

8 Samples

Download data: CALLS, PAIR, TXT

(Submitter supplied) 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. more...

Organism:

Trichoderma reesei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30923

24 Samples

Download data: TXT

(Submitter supplied) We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions. Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30 % of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair and iron homeostatis. more...

Organism:

Trichoderma reesei; Trichoderma reesei QM9414

Type:

Expression profiling by array

Platform:

GPL10642

3 Samples

Download data: PAIR, TXT

(Submitter supplied) The aim of this study was to evaluate changes in the transcriptome in the mentioned strains during mating conditions

Organism:

Trichoderma reesei

Type:

Expression profiling by array

Platforms:

GPL16051 GPL10642

10 Samples

Download data: PAIR, TXT

(Submitter supplied) Comparison of T. reesei grown on lactose fed chemostat cultivations in different growth rates and cell densities The analysis is further described in paper Correlation of gene expression and protein production rate - a system wide study. Mikko Arvas, Tiina Pakula, Bart Smit, Jari Rautio, Heini Koivistoinen, Paula Jouhten, Erno Lindfors, Marilyn Wiebe, Merja Penttilä and Markku Saloheimo, Submitted. Abstract: Background:Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on Saccharomyces cerevisiae chemostat cultivations provided the first analysis on genome wide effects of growth rate. In this work we study the filamentous fungus Trichoderma reesei (Hypocrea jecorina) that is an industrial protein production host known for its exceptional protein secretion capability. Interestingly, it exhibits a low growth rate protein production phenotype. Results: We have used transcriptomics and proteomics to study the effect of growth rate and cell density on protein production in chemostat cultivations of T. reesei. Use of chemostat allowed control of growth rate and exact estimation of the extracellular specific protein production rate (SPPR). We find that major biosynthetic activities are all negatively correlated with SPPR. We also find that expression of many genes of secreted proteins and secondary metabolism, as well as various lineage specific, mostly unknown genes are positively correlated with SPPR. Finally, we enumerate possible regulators and regulatory mechanisms, arising from the data, for this response. Conclusions: Based on these results it appears that in low growth rate protein production energy is very efficiently used primarly for protein production. Also, we propose that flux through early glycolysis or the TCA cycle is a more fundamental determining factor than growth rate for low growth rate protein production and we propose a novel eukaryotic response to this i.e. the lineage specific response (LSR).

Organism:

Trichoderma reesei

Type:

Expression profiling by array

Platform:

GPL13828

9 Samples

Download data: PAIR, TXT

(Submitter supplied) Trichoderma reesei (Hypocrea jecorina) NimbleGen design name 2005-09-27_Treesei_25mers Nimblegen design id 2604. Array contains 11 25-mer probes for each open reading frame. The design includes random GC and other control probes. The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf and .ngd files are linked below as supplementary files. more...

Organism:

Trichoderma reesei

1 Series

9 Samples

Download data: NDF, NGD