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An Aspergillus niger colony locally adapts its molecular responses to spatially separated substrates

ABSTRACT: A. niger colony sections grown on spatially separated substrates (glucose, wheat bran, sugar beet pulp) using transcriptomics, proteomics and metabolomics showed high diversity and plasticity within the colony.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Aspergillus Niger

TISSUE(S): Heterotroph

SUBMITTER: Matthew Monroe

LAB HEAD: Ronald de Vries

PROVIDER: PXD010431 | Pride | 2020-05-26

REPOSITORIES: Pride

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Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation.

Daly Paul P Peng Mao M Mitchell Hugh D HD Kim Young-Mo YM Ansong Charles C Brewer Heather H de Gijsel Peter P Lipton Mary S MS Markillie Lye Meng LM Nicora Carrie D CD Orr Galya G Wiebenga Ad A Hildén Kristiina S KS Kabel Mirjam A MA Baker Scott E SE Mäkelä Miia R MR de Vries Ronald P RP

Environmental microbiology 20200106 3

Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high l ...[more]

PMID: 31876091

Similar Datasets

An Aspergillus niger colony locally adapts its molecular responses to spatially separated substrates

Project description: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. For example a stronger pectinolytic response was observed in the part of the colony grown on the pectin-rich sugar beet pulp. Our results argue against a situation in which small molecules are transported efficiently through the colony and favour high diversity within the fungal colony in natural biotopes, where the substrate is typically heterogeneous. It also demonstrates the high level of plasticity of A. niger in reponse to the composition of the prevailing lignocellulose.

2019-08-23 | GSE118894 | 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

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

Project description: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. Growth, protein production and secretion were occurring throughout the whole colony. Carbon and nitrate utilization were constant from the centre to the periphery whereas genes encoding plant cell wall degrading enzymes were expressed with a different pattern across the colony. Finally our results demonstrate a fine-tuning of the different enzymatic tools available in A. niger and expand the knowledge on how this fungus adapts as it colonizes complex environments.

2016-03-04 | GSE66641 | GEO

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

An Aspergillus niger colony locally adapts its molecular responses to spatially separated substrates

Project description:An Aspergillus niger colony locally adapts its molecular responses to spatially separated substrates

| PRJNA487168 | ENA

Metabolic engineering reveals the relative importance of different sugar catabolic pathways during growth of Aspergillus niger on plant biomass

Project description:To evaluate the relative contribution of individual sugar catabolic pathways to the overall physiology of A. niger during growth on plant biomass, the A. niger sugar catabolic pathways involved in converting the most common monomers of plant biomass polysaccharides were blocked, and the phenotype as well as the transcriptomic response of these single-pathway deletion mutants was analysed on two distinct plant biomass substrates: wheat bran (WB) and sugar beet pulp (SBP). Deletion of all the above catabolic pathways were also combined in a single strain (?all), to evaluate whether other compounds of plant biomass could still support growth of A. niger when utilization of the major sugar components is blocked. On both WB and SBP, the strongest affected single-pathway deletion mutants were the PCP and glycolysis deficient mutants, delta-xkiA and delta-hxkA/delta-glkA, respectively. Especially on WB, which is a particularly rich substrate in pentose sugars, blocking PCP caused a significant effect in delta-xkiA with respect to both growth and transcriptomic response. However, delta-hxkA/delta-glkA was shown to be the most critically affected strain. On both substrates, combined deletion of hxkA and glkA resulted in the strongest growth reduction of all the single-pathway mutants, very similar to the multi-pathway deletion mutant delta-all. This result clearly pointed to glycolysis as the most essential and indispensable pathway for the survival of A. niger on these substrates. Since cellulose is not a preferred carbon source for A. niger, it seems that the double deletion of hxkA and glkA mostly affected the utilization of starch. (Note: A portion of this research was performed on a project award (10.46936/expl.proj.2019.51072/60006675) from the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830)

2022-08-31 | GSE196397 | 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

Genomic Survey of Aspergilli Proteases

Project description:We have performed a combined analysis of comparative genomics, proteomics and enzymology tests on seven Aspergillus species grown on wheat bran and sugar beet pulp to identify the various proteases and their productivities in Aspergilli.

2017-01-04 | PXD000982 | Pride

Blocking utilization of major plant biomass polysaccharides leads Aspergillus niger towards utilization of minor components.

Project description:Fungi produce a wide range of enzymes that allow them to grow on diverse plant biomass. Wheat bran is a low-cost substrate with high potential for biotechnological applications. It mainly contains cellulose and (arabino)xylan, with starch, proteins, lipids and lignin as minor components. In this study, we dissected the regulatory network governing wheat bran degradation in Aspergillus niger. Deletion of genes encoding transcription factors involved in (hemi-)cellulose utilization (XlnR, AraR, ClrA and ClrB) individually and in combination significantly reduced production of polysaccharide-degrading enzymes, but retained substantial growth on wheat bran. Proteomic analysis suggested the ability of A. niger to grow on minor carbon components, such as starch, which was confirmed by the additional deletion of the amylolytic regulator AmyR. Growth was further reduced but not impaired, indicating that other minor components provide sufficient energy for residual growth, displaying the flexibility of A. niger, and likely other fungi, in carbon utilization.

2021-06-28 | PXD023338 | Pride

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

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