Aspergillus niger
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ABSTRACT:
PROVIDER: PRJNA378383 | ENA |
REPOSITORIES: ENA
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Project description:In Aspergillus niger, the enzymes encoded by gaaA, gaaB, gaaC and gaaD catabolize D-galacturonic acid (GA) consecutively into L-galactonate, 2-keto-3-deoxy-L-galactonate, pyruvate and L-glyceraldehyde, and glycerol. We show here that deletion of gaaB or gaaC results in severely impaired growth on GA and accumulation of pathway intermediates L-galactonate and 2-keto-3-deoxy-L-galactonate, respectively. Expression levels of several GA-induced genes were specifically elevated in the ∆gaaC mutant on GA as compared to the reference strain or other GA catabolic pathway deletion mutants. The hyper-induction of GA-induced genes in ∆gaaC indicates that 2-keto-3-deoxy-L-galactonate is the inducer of genes required for GA utilization.
2017-08-15 | GSE95776 | GEO
Project description:Aspergillus niger is a filamentous fungus well known for its ability to produce a wide variety of pectinolytic enzymes, which have many applications in the industry. The transcriptional activator GaaR is induced by 2-keto-3-deoxy-L-galactonate, a compound derived from D-galacturonic acid, and plays a major role in the regulation of pectinolytic genes. The requirement for inducer molecules can be a limiting factor for the production of enzymes. Therefore, the generation of chimeric transcription factors able to activate the expression of pectinolytic genes by using underutilized agricultural residues would be highly valuable for industrial applications. In this study, we used the CRISPR/Cas9 system to generate three chimeric GaaR::XlnR transcription factors by swapping the N-terminal region of the xylanolytic regulator XlnR to that of the GaaR in A. niger. As a test case, we constructed a PpgaX:hph reporter strain to evaluate the alteration of transcription factor specificity in the chimeric mutants. Additionally, we generated a constitutively active GaaR::XlnR V756F version of the most efficient chimeric transcription factor to better assess its activity. Our results showed that the chimeric GaaR::XlnR transcription factor was no longer induced in the presence of D-galacturonic acid, but in the presence of D-xylose instead. Moreover, proteomics analysis and saccharification assays confirmed the production of enzymes involved in the release of L-arabinose from pectin, while the constitutive version of this chimeric transcription factor showed consistently improved D-galacturonic acid release from pectin in a gaaR deletion background.
2021-11-18 | PXD025383 | Pride
Project description:We identified the D-galacturonic acid (GA) responsive transcriptional activator GaaR of the saprotrophic fungus Aspergillus niger, which was found to be essential for growth on GA and polygalacturonic acid (PGA). Growth of the ΔgaaR strain was reduced on complex pectins. Genome-wide expression analysis showed that GaaR is required for the expression of genes necessary to release GA from PGA and more complex pectins, to transport GA into the cell and to induce the GA-catabolic pathway. Residual growth of ΔgaaR on complex pectins is likely due to expression of pectinases acting on rhamnogalacturonan and subsequent metabolism of the monosaccharides other than GA.
2017-02-10 | GSE80227 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE37758: Aspergillus niger : Control (fructose) vs. steam-exploded sugarcane induction (SEB) GSE37760: Aspergillus niger : Control (fructose) vs. xylose + arabinose (XA) Refer to individual Series
2012-05-06 | E-GEOD-37795 | biostudies-arrayexpress
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
Project description:Overexpression of GaaR, a D-galacturonic acid responsive transcription factor, enables inducer-independent production of pectinases in Aspergillus niger
| PRJNA396925 | ENA
Project description:The aim of this study was to investigate the regulatory role of Aspergillus niger AmyR and InuR during growth on inulin and sucrose
2023-05-03 | GSE204768 | GEO
Project description:The genes of the non-phosphorylative L-rhamnose catabolic pathway have been identified for several yeast species. In Pichia stipitis, all L-rhamnose pathway genes are organized in a cluster, which is conserved in Aspergillus niger, except for the lra-4 ortholog (lraD). The A. niger cluster also contains the gene encoding the L-rhamnose responsive transcription factor (RhaR) that has been shown to control the expression of genes involved in L-rhamnose release and catabolism. In this paper, we confirmed the function of the first three putative L-rhamnose utilisation genes from A. niger through gene deletion. We explored the identity of the inducer of the pathway regulator (RhaR) through expression analysis of the deletion mutants grown in transfer experiments to L-rhamnose and L-rhamnonate. Reduced expression of L-rhamnose-induced genes on L-rhamnose in lraA and lraB deletion strains, but not on L-rhamnonate (the product of LraB), demonstrate that the inducer of the pathway is of L-rhamnonate or a compound downstream of it. Reduced expression of these genes in the lraC deletion strain on L-rhamnonate show that it is in fact a downstream product of L-rhamnonate. This work showed that the inducer of RhaR is beyond L-rhamnonate dehydratase (LraC) and is likely to be the 2-keto-3-L-deoxyrhamnonate.
2017-09-14 | GSE99865 | GEO
Project description:We report the genes regulated during citrate fermentation. Examination of 5 different time points during fermentation in Aspergillus niger H915-1.
2016-06-30 | E-GEOD-74544 | biostudies-arrayexpress
Project description:The full genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger and Aspergillus oryzae has opened the possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are presenting an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose-and xylose media has been performed, and used to validate the performance of the micro array. By doing gene comparisons of all three species, and cross-analysing this with the expression data, 23 genes, including the xylose transcriptional activator XlnR, have been identified to be a conserved response across the Aspergillus sp. Promoter analysis of the upregulated genes in all three species suggest the XlnR-binding site to be 5’-GGNTAAA-3’. We are thus presenting a validated tool for transcription analysis of three Aspergillus species and a methodology for comparative transcriptomics. Keywords: Physiological response
2008-02-15 | GSE9276 | GEO