GEO DataSets

(Submitter supplied) We have studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA-sequencing we showed that, 24 hours after exposure to straw, gene expression of known plant cell wall degrading enzymes represents a huge investment for the cells (about 20 % of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal degradative arsenal. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14910

9 Samples

Download data: TXT

(Submitter supplied) Background: Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16343

6 Samples

Download data: TXT

(Submitter supplied) Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16343

8 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Trichoderma reesei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16719

8 Samples

Download data: TXT

(Submitter supplied) Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. more...

Organism:

Aspergillus niger; Penicillium chrysogenum; Trichoderma reesei

Type:

Expression profiling by high throughput sequencing

7 related Platforms

30 Samples

Download data: FASTA, TXT

(Submitter supplied) The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

59 Samples

Download data: CEL

(Submitter supplied) Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening starvation conditions, carbon from extra- and intracellular resources becomes mobilized to fuel fungal self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal starvation responses in a temporal and spatial resolution. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

6 Samples

Download data: CEL

(Submitter supplied) Filamentous fungi are ubiquitous organisms and major plant biomass degraders. As a single colony, some fungal species can colonize large areas as up to five soccer stadia. During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of Aspergillus niger. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 5-day-old sugar beet pulp grown colonies. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

10 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24128

20 Samples

Download data: TXT

(Submitter supplied) Expression of genes encoding plant biomass degrading enzymes in ascomycetes is controlled by transcriptional activators that respond to the presence of monomeric components of plant polymers. It can be expected that a similar system exists in basidiomycetes, but no homologs of the ascomycete regulators could be identified in basidiomycetes.

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24128

6 Samples

Download data: GFF3, TXT

(Submitter supplied) Expression of genes encoding plant biomass degrading enzymes in ascomycetes is controlled by transcriptional activators that respond to the presence of monomeric components of plant polymers. It can be expected that a similar system exists in basidiomycetes, but no homologs of the ascomycete regulators could be identified in basidiomycetes.

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24128

14 Samples

Download data: TXT

(Submitter supplied) Aspergillus niger is a filamentous ascomycete fungus that is commonly found in most biotopes around the globe. In nature, A. niger degrades the plant biomass polysaccharides to monomeric sugars, transports them into the cells, and uses a variety of catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived monomeric sugars (and maltose) in a highly sequential manner, rather than simultaneously. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

8 Samples

Download data: CEL

(Submitter supplied) Plant biomass is the most abundant and renewable carbon source for many fungal species. The composition of biomass consists of about 40-45% cellulose, 20-30% hemicellulose, and 15-25% lignin and varies among plant species. In the bio-based industry, Aspergillus species and other fungi are used for the production of lignocellulolytic enzymes to pretreat agricultural waste biomass (e.g. wheat bran). In this study, we aimed to evaluate if it would be possible to create an Aspergillus strain that releases but does not metabolize hexoses from plant biomass. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19470

8 Samples

Download data: XLS

(Submitter supplied) Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. This gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. more...

Organism:

Coprinopsis cinerea AmutBmut pab1-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32332

7 Samples

Download data: GTF, TSV

(Submitter supplied) Hemicellulose, the second most abundant plant biomass fraction after cellulose, is widely viewed as a potential feedstock for the production of liquid fuels and other value-added materials. Degradation of hemicellulose by filamentous fungi requires production of many different enzymes, which are induced by biopolymers or its derivatives and regulated mainly at the transcriptional level through transcription factors (TFs). more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL14949

23 Samples

Download data: GPR, TXT

(Submitter supplied) In this study, we compared the gene expression pattern of A. niger grown in liquid sugar beet pulp (SBP) at different time points, a by-product of the sugar industry that consists mainly of cellulose, xyloglucan, and pectin. Finally, we compared A. niger genetic response to liquid SBP to that of the same fungus when grown on solid SBP plates and polygalacturonic acid (PGA).

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL6758

8 Samples

Download data: CEL, 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) White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. In order to improve our understanding on the enzymatic mechanisms leading to lignocellulose breakdown, we analysed the early response of the white-rot fungus Pycnoporus coccineus CIRM-BRFM310 to various lignocellulosic substrates at two time points; Day 3 and Day 7.

Organism:

Trametes coccinea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23066

22 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to better understand the contribution of the transcriptional activators GaaR, RhaR and AraR in regulation of pectin degradation in A. niger.

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21721

32 Samples

Download data: TXT

(Submitter supplied) Here comparative transcriptomic analyses of Penicillium oxalicum grown on wheat bran (WB), WB plus rice straw (WR) and WB plus Avicel (WA) as the sole carbon source under solid-state fermentation (SSF) revealed that most of differentially expressed genes (DEGs) were involved in metabolism specifically carbohydrate metabolism.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26664

15 Samples

Download data: FA, TXT