Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Transfer of the high-quality sugar metabolic model of Aspergillus niger is reliable within the same fungal phylum, but limited for fungi of other phyla

ABSTRACT: Validation of metabolic models, extrapolated from the reference sugar catabolism genetic network of Aspergillus niger by using an orthology-based approach, of evolutionarily diverse fungi.

INSTRUMENT(S): Agilent 7890A GC with 5975C inert XL MSD

ORGANISM(S): Trichoderma Reesei (ncbitaxon:51453) Penicillium Subrubescens (ncbitaxon:1316194) Aspergillus Niger (ncbitaxon:5061) Phanerochaete Chrysosporium Rp-78 (ncbitaxon:273507) Aspergillus Nidulans (ncbitaxon:162425)

SUBMITTER: Ronald de Vries

PROVIDER: MSV000090441 | GNPS |

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum.

Li Jiajia J Chroumpi Tania T Garrigues Sandra S Kun Roland S RS Meng Jiali J Salazar-Cerezo Sonia S Aguilar-Pontes Maria Victoria MV Zhang Yu Y Tejomurthula Sravanthi S Lipzen Anna A Ng Vivian V Clendinen Chaevien S CS Tolić Nikola N Grigoriev Igor V IV Tsang Adrian A Mäkelä Miia R MR Snel Berend B Peng Mao M de Vries Ronald P RP

Journal of fungi (Basel, Switzerland) 20221217 12

Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as carbon and energy sources. We mapped the well-established sugar metabolic network of Aspergillus niger to five taxonomically distant species (Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium and Dichomitus squalens) using an orthology-based approach. The diversity of sugar metabol ...[more]

PMID: 36547648

Similar Datasets

Transfer of the high-quality sugar metabolic model of Aspergillus niger is reliable within the same fungal phylum, but limited for fungi of other phyla

Project description:Validation of metabolic models, extrapolated from the reference sugar catabolism genetic network of Aspergillus niger by using an orthology-based approach, of evolutionarily diverse fungi.

| MSV000090441 | MassIVE

The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA

Project description: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. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA, which has been shown to mediate the use of preferential carbon sources over non-preferential carbon sources. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate physiological processes in A. niger.

2018-04-23 | GSE98434 | GEO

Experimental validation of a central carbon metabolic model in Aspergillus niger to enable metabolic engineering of a fungal cell factory

Project description:The influence of selected pentose catabolic pathway (PCP) deletion strains on growth of plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of the fungus Aspergillus niger in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains grown on wheat bran (WB) and sugar beet pulp (SBP) were evaluated. Proteomics samples were digested with trypsin then analyzed by LC-MS/MS with fractionation. Metabolomics samples were derivitized using a modified Fiehn protocol and analyzed by GC-MS with FAME added for retention alignment. Proteomics data was searched with MS-GF+ using PNNL's DMS Processing pipeline.

2020-12-17 | MSV000086614 | MassIVE

Comparative study of gene expression in Aspergillus niger solid and submerged growth during sugar beet pulp utilization

Project description: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).

2021-08-04 | GSE175954 | GEO

Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates

Project description: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. In this study, the influence of selected pentose catabolic pathway (PCP) deletion strains on growth on plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of this fungus in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains, ΔlarAΔxyrAΔxyrB, ΔladAΔxdhAΔsdhA and ΔxkiA, grown on wheat bran (WB) and sugar beet pulp (SBP), was evaluated. Our results showed that despite the absolute impact of these PCP mutations on pure pentose sugars, they are not as critical for growth of A. niger on more complex biomass substrates, such as WB and SBP. However, significant phenotypic variation was observed between the two biomass substrates, but also between the different PCP mutants. This shows that the high sugar heterogeneity of these substrates in combination with the high complexity and adaptability of the fungal sugar metabolism allow for activation of alternative strategies to support growth.

2021-03-08 | GSE162901 | GEO

High-quality co-expression networks for accurate gene function predictions in the fungal cell factory Aspergillus niger and beyond

Project description:Co-expression networks have recently emerged as a useful approach for updating and improving gene annotation at a near-genome level. This is based on the hypothesis that function can be inferred by delineating transcriptional networks in which a gene of interest is embedded. In this study, we generated a co-expression network for the filamentous cell factory Aspergillus niger from 128 RNA-seq experiments. We confirm that over 70% of the >14,000 A. niger genes are represented in this network and show that gene functions can be accurately predicted as evidenced by analysis of various control sub-networks. Our analyses further indicate that this RNA-seq co-expression network has a higher predictive power compared to the microarray co-expression network that we published in 2019. To demonstrate the potential of the new co-expression network to unveil complex and non-intuitive predictions for gene regulation phenomena, we provide here new insights into the temporal, spatial and metabolic expression profile that connects a secreted antifungal peptide with mycelial growth, asexual development, secondary metabolism and pectin degradation in A. niger. To empower biologists to generate or apply co-expression networks in the fungal kingdom and beyond, we also demonstrate that (i) high quality networks can be generated from only 32 transcriptional experiments; (ii) such low numbers of experiments can be safely compensated for by using higher thresholds for defining co-expression pairs; and (iii) a ’safety in numbers’ rule applies, whereby experimental conditions have minimal impact on network content provided a certain number of experiments are included.

2024-10-01 | GSE241846 | GEO

Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization

Project description:Degradation of plant biomass to fermentable sugars is of critical importance for the use of plant materials for biofuels. Filamentous fungi are ubiquitous organisms and major plant biomass degraders. Single colonies of some fungal species can colonize massive areas as large as five soccer stadia.During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a major determinant of spatial gene expression in colonies of Aspergillus niger. We analyzed whole-genome gene expression in five concentric zones of 5-day-old colonies utilizing sugar beet pulp as a complex carbon source. Growth, protein production and secretion occurred throughout the colony. Genes involved in carbon catabolism and nitrate utilization were expressed uniformly from the centre to the periphery whereas genes encoding plant biomass degrading enzymes were expressed differentially across the colony. A combined adaptive response of carbon-catabolism and enzyme production to locally available monosaccharides was observed. Finally, our results demonstrate a fine-tuning of the different enzymatic tools available in A. niger and reveal how this fungus adapts as it colonizes complex environments.

2015-09-09 | PXD002130 | Pride

Aspergillus niger An76 LC-MS/MS analysis

Project description:Xylan constituted with β-1,4-D-xylose linked backbone and diverse substituted side-chains is the most abundant hemicellulose component of biomass, which can be completely and rapidly degraded into fermentable sugars by Aspergillus niger. This is of great value for obtaining renewable biofuels and biochemicals. To clarify the underlying mechanisms associated with highly efficient xylan degradation, assimilation, and metabolism by A. niger, we utilized functional proteomics to analyze the secreted proteins, sugar transporters and intracellular proteins of A. niger An76 grown on xylan-based substrates.

2018-02-06 | PXD008879 |

Transfer of the high-quality sugar metabolic model of Aspergillus niger is reliable within the same fungal phylum, but limited for fungi of other phyla

Project description:Proteomic data from fungi; intracellular-proteome of five of the studied fungi (A. niger, A. nidulans, P. subrubescens, T. reesei and P. chrysosporium) grown on nine different monosaccharide conditions (L-arabinose, D-fructose, D-galacturonicAcid, D-galactose, D-glucuronicAcid, D-glucose, D-mannose, L-rhamnose, D-xylose) was analyzed to reveal the fungal response to each specific sugar at the proteome level ; 3 biological replicates. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline against FASTA files obtained from Mycocosm.

2022-10-05 | MSV000090477 | MassIVE

The galactose regulator GalX regulates the D-galactose oxido-reductive pathway in Aspergillus niger.

Project description:Galactose catabolism in Aspergillus nidulans is regulated by at least two regulators, GalR and GalX. In Aspergillus niger only GalX is present, and its role in D-galactose catabolism in this fungus was investigated. Phenotypic and gene expression analysis of a wild type and a galX disruptant revealed that GalX does not substitute for the absence of GalR in A. niger, it regulates the D-galactose oxido-reductive pathway, but not the Leloir pathway. Four genes, including the recently characterized ladB (galactitol dehydrogenase) were found to have differencial expressions that are highly relevant to GalX , indicating a novel oxido-reductive pathway in A.niger .

2012-09-20 | GSE40219 | GEO