GEO DataSets

(Submitter supplied) The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after D-glucose, being major constituents of xylan, pectin and xyloglucan. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21818

90 Samples

Download data: TXT

(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) 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) Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae, are naturally unable to convert many component plant cell wall polysaccharides, the identification of organisms with broad catabolism capabilities represents an opportunity to expand the range of substrates used in fermentation biorefinery approaches. more...

Organism:

Rhodotorula toruloides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26239

9 Samples

Download data: TAB

(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) 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) D-glucose, D-xylose and L-arabinose are three major monosaccharides in the plant cell wall. Complete utilization of all three sugars is still a bottleneck for second-generation cellulolytic bioethanol production, especially for L-arabinose. However, little is known about the gene expression profiles during L-arabinose utilization in fungi at genome-wide level and a comparison of the genome-wide fungal response to these three major monosaccharides has not yet been reported. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

5 Samples

Download data: TXT

(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) The aim of this study is to investigate the role of the transcription factor Xyr1 in the regulation of cellulolytic and xylanolytic genes of the filamantous fungus Myceliophthora thermophila

Organism:

Thermothelomyces thermophilus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27455

20 Samples

Download data: XLS

(Submitter supplied) Saprotrophic fungi, such as Aspergillus niger, grow as mycelial colonies that are often considered uniform entities. To test this uniformity, we analyzed pie-slice sections of a colony grown on spatially separated substrates (glucose, wheat bran, sugar beet pulp) using transcriptomics, proteomics and metabolomics. The colony tuned its response to the local carbon source composition. Plant biomass degrading CAZymes and intracellular carbon catabolic enzymes were more abundant in parts of the colony containing the corresponding sugars. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25482

27 Samples

Download data: 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) 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) Background: Pectin is an abundant component in many fruit and vegetable wastes and could therefore be an excellent resource for biorefinery, but is currently underutilized. Fungal pectinases already play a crucial role for industrial purposes, such as for foodstuff processing. However, the regulation of pectinase gene expression is still poorly understood. For an optimal utilization of plant biomass for biorefinery and biofuel production, a detailed analysis of the underlying regulatory mechanisms is warranted. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

20 Samples

Download data: CSV, TXT

(Submitter supplied) Rumen bacterial species belonging to the genera Butyrivibrio are important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four distinct species are recognized which have very similar substrate utilization profiles, but little is known about how these microorganisms are able to co-exist in the rumen. To investigate this question, Butyrivibrio hungatei MB2003 and Butyrivibrio proteoclasticus B316T were grown alone or in co-culture on the insoluble substrates, xylan or pectin, and their growth, release of sugars, fermentation end products and transcriptomes were examined. more...

Organism:

Butyrivibrio hungatei; Butyrivibrio proteoclasticus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25616 GPL25614 GPL25615

18 Samples

Download data: TXT