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Genomic Survey of Aspergilli Proteases

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Aspergillus Oryzae Var. Oryzae Aspergillus Terreus Aspergillus Fumigatus Af293 Aspergillus Niger Neosartorya Fischeri Emericella Nidulans (aspergillus Nidulans) Aspergillus Flavus

TISSUE(S): Cell Suspension Culture

SUBMITTER: Marcos Di Falco

LAB HEAD: Ronald de Vries

PROVIDER: PXD000982 | Pride | 2017-01-04

REPOSITORIES: Pride

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			Action	DRS
	DSMS12.dta.zip	Other
	DSMS12.mzXML	Mzxml
	DSMS12.pep.xml	Pepxml
	DSMS12.prot.xml	Xml
	DSMS22.dta.zip	Other

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Publications

A genomic survey of proteases in Aspergilli.

Budak Sebnem Ozturkoglu SO Zhou Miaomiao M Brouwer Carlo C Wiebenga Ad A Benoit Isabelle I Di Falco Marcos M Tsang Adrian A de Vries Ronald P RP

BMC genomics 20140625

<h4>Background</h4>Proteases can hydrolyze peptides in aqueous environments. This property has made proteases the most important industrial enzymes by taking up about 60% of the total enzyme market. Microorganisms are the main sources for industrial protease production due to their high yield and a wide range of biochemical properties. Several Aspergilli have the ability to produce a variety of proteases, but no comprehensive comparative study has been carried out on protease productivity in thi ...[more]

PMID: 24965873

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Comparative genomics reveals high biological diversity and specific adaptations in the fungal genus Aspergillus

Project description:The project compares the genomes of multiple Aspergillus species. In particular, the genes involved in the degradation of plant-derived biomass have been analyzed. As well, the extracellular proteins produced by the fungi during the utilization of sugar beet pulp and wheat bran were examined by LC-MS/MS. Results show that closely related species can deploy different enzyme mixtures in the hydrolysis of plant-derived biomass. These results imply that efficient hydrolysis of biomass can be achieved by combining enzyme mixtures from two or more fungi.

2018-10-26 | PXD005563 | Pride

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

Project description: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.

2020-05-26 | PXD010431 | Pride

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

Sexual crossing of thermophilic fungus Myceliophthora heterothallica improved enzymatic degradation of sugar beet pulp

Project description:Enzymatic degradation of plant biomass requires a complex mixture of many different enzymes. Like most fungi, thermophilic Myceliophthora species therefore have a large set of enzymes targeting different linkages in plant polysaccharides. The majority of these enzymes have not been functionally characterized and their role in plant biomass degradation is unknown. This study describes a strategy using sexual crossing and screening with the thermophilic fungus Myceliophthora heterothallica to identify specific enzymes associated with improved sugar beet pulp saccharification.Two genetically diverse M. heterothallica strains CBS 203.75 and CBS 663.74 were used to generate progenies with improved growth on sugar beet pulp. One progeny, named SBP.F1.2.11, had a different genetic pattern from the parental strains, and had improved saccharification activity after growth on 3% sugar beet pulp. Exo-proteome analysis of progeny and parental strains after 7 days growth on sugar beet pulp showed that only 17 of the 133 secreted CAZy enzymes were more abundant in progeny SBP.F1.2.11. Particularly one enzyme belonging to the carbohydrate esterase family 5 (CE5) was more present in SBP.F1.2.11. This CE5-CBM1 enzyme, named as Axe1, was phylogenetically related to acetyl xylan esterases.

2016-02-25 | PXD003130 | Pride

A genomic survey of proteases in Aspergilli.

Project description:BACKGROUND: Proteases can hydrolyze peptides in aqueous environments. This property has made proteases the most important industrial enzymes by taking up about 60% of the total enzyme market. Microorganisms are the main sources for industrial protease production due to their high yield and a wide range of biochemical properties. Several Aspergilli have the ability to produce a variety of proteases, but no comprehensive comparative study has been carried out on protease productivity in this genus so far. RESULTS: 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. Putative proteases were identified by homology search and Pfam domains. These genes were then clusters based on orthology and extracellular proteases were identified by protein subcellular localization prediction. Proteomics was used to identify the secreted enzymes in the cultures, while protease essays with and without inhibitors were performed to determine the overall protease activity per protease class. All this data was then integrated to compare the protease productivities in Aspergilli. CONCLUSIONS: Genomes of Aspergillus species contain a similar proportion of protease encoding genes. According to comparative genomics, proteomics and enzymatic experiments serine proteases make up the largest group in the protease spectrum across the species. In general wheat bran gives higher induction of proteases than sugar beet pulp. Interesting differences of protease activity, extracellular enzyme spectrum composition, protein occurrence and abundance were identified for species. By combining in silico and wet-lab experiments, we present the intriguing variety of protease productivity in Aspergilli.

| S-EPMC4102723 | biostudies-literature

Mixed colonies of Aspergillus niger and Aspergillus oryzae cooperatively degrading wheat bran

Project description:A. niger and A. oryzae are two filamentous fungi widely used in industry to produce various enzymes (e.g. pectinases, amylases) and metabolites (e.g. citric acid). Using proteomics, the co-cultivation of these two fungi in wheat bran showed an equal distribution of the two strains forming mixed colonies with a broad range of carbohydrate active enzymes produced. This stable mixed microbial system seems suitable for subsequent commercial processes such as enzyme production. XlnR knock-out strains for both aspergilli were used to study the influence of plant cell wall degrading enzyme production on the fitness of the mixed culture.

2017-02-27 | PXD005532 | Pride

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

Transcription profiling of Aspergillus niger grown in media containg different pectic substrates to study the pectinolytic system

Project description:To study the induction of the genes encoding known and putative enzymes from the pectinolytic system of A. niger, the transcriptional profiles of 58 selected known or putative pectinolytic genes were monitored by microarray experiments. For this purpose, A. niger was cultivated on the complex substrates, sugar beet pectin and polygalacturonic acid as primary carbon sources. Galacturonic acid, rhamnose and xylose were used to assess the effects on gene expression caused by simple well-defined carbon sources, representing the most abundant sugar residues present in the backbone of pectin. Fructose, as a strong repressor of the expression of genes that are under carbon catabolite regulation, and sorbitol, as a non-inducing sugar-like alcohol, which does not affect the carbon catabolite regulation mechanisms were selected as control substrates. Mycelia of A. niger were pregrown for 18 h on 2% fructose, transferred to medium containing the different pectic and control substrates, and sampled at four time points during 24 h of incubation.

2008-06-13 | E-MEXP-1626 | biostudies-arrayexpress

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

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