GEO DataSets

(Submitter supplied) Neurospora crassa recently has become a novel system to investigate cellulase induction. Here, we discovered a novel membrane protein, CLP1 (NCU05853), a putative cellodextrin transporter-like protein, that is a critical component of the cellulase induction pathway in N. crassa. Although CLP1 protein cannot transport cellodextrin, the suppression of cellulase induction by this protein was discovered on both cellobiose and Avicel. more...

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15146

3 Samples

Download data: TXT

(Submitter supplied) The mechanism of cellulase induction in the filamentous fungi is still not completely understood, and the components of this pathway are not well characterized. In this study, the mechanism of how the non-anchored cell wall protein NCW-1 (NCU05137) affect the cellulases induction was investigated. Transcriptome analysis of this quadruple deletion strain △3βG△ncw-1 showed that the expression of major cellulase, cellodextrin transporters and cellulase regulators were significantly increased. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

2 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling with next-generation sequencing methods demonstrated that a Neurospora crassa mutant with the three most highly expressed beta-glucosidase genes deleted had a transcriptional response to cellobiose similair to that of wild type N. crassa exposed to cellulose.

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15147 GPL15146

13 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling with next-generation sequencing methods refined our understanding of the N. crassa transcriptional response to cellulose and demonstrated that the newly characterized transcription factors clr-1 and clr-2 were required for the bulk of that response including induction all major cellulase and some major hemicellulase genes.

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15146 GPL15147

26 Samples

Download data: TXT

(Submitter supplied) Filamentous fungi are one of the primary degraders of plant biomass because of their ability to produce enzymes that break down complex polysaccharides. The production of cellulolytic enzymes in fungi is dependent on transcription factors. In this article, we identified a N. crassa Zn2Cys6 transcription factor Clr5 that regulates the expression of cellulase on cellulose. N. crassa Δclr5 exhibited a significant decrease in secreted proteins (~46%), endo-glucanase (~55%), xylanase (~33%), β-glucosidase (~38%), and exocellulase (~40%) compared with the WT, while transcriptomic analysis revealed that clr5 was essential in cellulase expression. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

12 Samples

Download data: XLSX

(Submitter supplied) 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. more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL13956

20 Samples

Download data: GPR

(Submitter supplied) Purpose: To explore conservation of gene regulation by the transcription factor clr-2/clrB in Neurospora crassa and Aspergillus nidulans Methods: mRNA from wild type and clr-2/clrB mutants were collected after a culture shift from sucrose/glucose to Avicel (crystaline cellulose) or no carbon media Results: We show that N. crassa and A. nidulans have similair global transcriptional responses to Avicel, with several hundred genes showing specific induction, though the induced genes are more specifically targeted at cellulose for N. more...

Organism:

Neurospora crassa OR74A; Aspergillus nidulans FGSC A4

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15146 GPL16600 GPL15147

22 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) In filamentous ascomycete fungi, the utilization of alternate carbon sources is influenced by the zinc finger transcription factor CreA/CRE-1, which encodes a carbon catabolite repressor protein homologous to Mig1 from Saccharomyces cerevisiae. In Neurospora crassa, deletion of cre-1 results in increased secretion of amylase and β-galactosidase. Here, we determined the CRE-1 regulon by investigating the transcriptome of a Δcre-1 strain compared to wild type when grown on Avicel versus minimal medium (MM). more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL13956

8 Samples

Download data: GPR, TXT

(Submitter supplied) Purpose: To explore the function of VIB1 in regulating cellulase production in Neurospora crassa. Method: mRNA from vib-1 mutants were collected after a culture shift from sucrose to Avicel (crystaline cellulose) or carbon-free media. Expression profiles of vib-1 mutants were compared with published profiles of wild type created under the same conditions. Results: We found that many genes that specifically upregulated in wild type upon exposure to Avicel were expressed at low levels in ∆vib-1 and many other genes involved in metabolism and energy were expressed at high levels compared to wild type. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17918 GPL16164

9 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Identifying nutrients available in the environment and utilizing them in the most efficient manner is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of carbohydrates, from simple sugars to the complex carbohydrates found in plant cell walls. The zinc binuclear cluster transcription factor CLR-1 is necessary for utilization of cellulose, a major, recalcitrant component of the plant cell wall; however, expression of clr-1 in the absence of an inducer is not sufficient to induce cellulase gene expression. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23150 GPL16164

42 Samples

Download data: TXT

(Submitter supplied) Purpose: Evaluate and analyze the transcriptional response of N. crassa germinating conidia and determined the main gene functions related with the exposure to chitosan. Identification of main chitosan gene tragets in N. crassa. Methods: From samples in contact with chitosan for 4, 8 and 16h total RNA was isolated from material using TRIzol reagent. Total RNA was washed and then resuspended. For first strand cDNA synthesis, the fragmented poly (A+) RNA was incubated with random hexamers. more...

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15146

6 Samples

Download data: XLS

(Submitter supplied) Staurosporine induces programmed cell death in a series of organisms. Here, we analyse gene expression of the filamentous fungus Neurospora crassa following exposure to staurosporine for different time periods.

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL13956

30 Samples

Download data: GPR, TXT

(Submitter supplied) Transcriptional profiling of Neurospora crassa ∆mak-2 strain grown under phosphate-shortage were compared the transcription profile of the control strain grown in both low- and high-Pi cultures. The filamentous fungus Neurospora crassa provides an excellent model system for the study of molecular responses to ambient signaling in eukaryotic microorganisms. Inorganic phosphate is an essential growth-limiting nutrient in nature and is crucial in genetic information. more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL14949

16 Samples

Download data: TXT

(Submitter supplied) Plant biomass holds tremendous potential as a renewable feedstock in the production of biofuels and biochemicals. The effective co-utilization of the main components cellulose and hemicellulose in plant lignocellulose is critical to the economic viability of lignocellulosic biorefineries. Here, we found that the thermophilic cellulolytic fungi Myceliophthora thermophila can utilize cellulose and hemicellulose synchronously. more...

Organism:

Thermothelomyces thermophilus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27455

14 Samples

Download data: XLSX

(Submitter supplied) Purpose: To explore the pathway cross-talk of endoplasmic reticulum (ER) stress response and cellulases synthesis in Neurospora crassa. Methods: To identify ER stress response targets(ESRTs), conidial suspensions of WT were obtained and 1 x 10^6 cells/ml incubated in cellulases induction medium (1x vogel’s salts , 1% w/v crystalline cellulose (Avicel PH-101; Sigma-Aldrich), 0.2% w/v NH4NO3 ,pH 7.0 )for 36 hours (25ºC, 200 rpm, constant light) followed by the addition of dithiothreitol (DTT, final concentration of 0.1mM for mild stress level while 5mM for acute stress level) or tunicamycin (TM, final concentration of 5ug/mL for mild stress level while 40ug/mL for acute stress level) and growth for 1 more hour.To identify which ESRTs regulated by IRE-1/Hac-1 mediated UPR pathway,conidial suspensions of the Ire-1 and Hac-1 KO mutants as well as their parental strains (FGSC#2489 and FGSC#9720, respectively) were obtained and 1 x 10^6 cells/ml incubated in minimal medium containing 2% sucrose for 16 hours, then young hyphae was harvested and transferred into cellulases induction medium as mentioned above culture for 4 hours followed by the addition of DTT (final concentration of 5mM)(or H2O as mock)and growth for 1 more hour.For Hac-1 KO mutant and FGSC#9720,cultures were plus with final concentration of 100ug/ml L-histidine.To explore the function of transcription factors RES-1, RES-2 and RRG-2 in response to ER stress and cellulases synthesis, each conidial suspension of the three strains was obtained and 1 x 10^6 cells/ml incubated in cellulases induction medium for 36 hours followed by the addition of dithiothreitol (DTT, final concentration of 5mM ) (or H2O as mock)and growth for 1 more hour.Cells were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

21 Samples

Download data: TXT

(Submitter supplied) Schizosaccharomyces pombe Clp1 is a Cdc14-family phosphatase that reverses mitotic Cdk1 phosphorylation. Despite evolutionary conservation, Clp1’s mammalian orthologs do not share this function. Rather, higher eukaryotic Cdc14 enzymes act in DNA repair, ciliogenesis, and gene regulation. To examine if Clp1 regulates gene expression, we compared the transcriptional profiles of cells lacking Clp1 function to that of wildtype. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL34165

8 Samples

Download data: TXT