The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of D-galacturonic acid from pectin
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus niger
PROVIDER: GSE80227 | GEO | 2017/02/10
SECONDARY ACCESSION(S): PRJNA318352
REPOSITORIES: GEO
Similar Datasets
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:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value ≤ 0.0001 and |log2 of the ratio of the RPM values| ≥ 2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control.
2015-11-22 | GSE55086 | GEO
Project description:Aim: Analyse inhibitory effects of galacturonic acid, an important constituent of plant biomass hydrolysates, on growing and starving cultures of Saccharomyces cerevisiae CEN.PK113-7D. Method & Results: Biomass yields in aerobic and anaerobic glucose-limited chemostat cultures (pH 3.5) were reduced by 25 and 10%, respectively, upon addition of 10 g∙l-1 galacturonic acid. Genes previously reported to show a transcriptional response to other organic acids were overrepresented in a set of galacturonic-acid responsive genes identified by microarray analysis. These results suggested that galacturonic acid causes weak-acid uncoupling of the yeast plasma membrane pH gradient. Consistent with this hypothesis, galacturonate-accelerated loss of viability in starving cell suspensions was strongly pH dependent. Loss of viability was much slower in a strain in which all HXT (hexose transporter) genes were deleted. Moreover, deletion of HXT genes alleviated growth inhibition on ethanol observed at galacturonic acid concentrations of 10 g∙l-1 and above. Conclusions: At low pH, galacturonic acid negatively affects the physiology of S. cerevisiae. Reduced sensitivity of hexose-transporter mutants indicated that one or more HXT transporters are involved in transport of galacturonic acid. Significance and Impact: This study shows that galacturonic acid toxicity should be taken into account in process development for yeast-based fermentative conversion of pectin-rich feedstocks such as sugar beet pulp and citrus peel. Involvement of hexose transporters in galacturonic acid toxicity provides leads for improving tolerance. To investigate the impact of galacturonic acid on S. cerevisiae, a DNA microarray-based transcriptome analysis was performed on aerobic, glucose-limited chemostat cultures grown in the presence and absence of 10 g∙l-1 galacturonic acid at pH3.5.
2015-04-14 | E-GEOD-43474 | biostudies-arrayexpress
Project description:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value ⤠0.0001 and |log2 of the ratio of the RPM values| ⥠2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control. After incubation at 45 â, 145rpm for 20 hours with sucrose as the carbon source, mycelia were induced for 16 hours using xylan, cellulose and rice straw, respectively. Transcriptome induced by sucrose was used as the control when comparing the differences between other three transcriptomes (induced by xylan, cellulose and rice straw, respectively).
2015-11-22 | E-GEOD-55086 | biostudies-arrayexpress
Project description:Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide.
2015-10-28 | GSE74379 | GEO
Project description:Aim: Analyse inhibitory effects of galacturonic acid, an important constituent of plant biomass hydrolysates, on growing and starving cultures of Saccharomyces cerevisiae CEN.PK113-7D. Method & Results: Biomass yields in aerobic and anaerobic glucose-limited chemostat cultures (pH 3.5) were reduced by 25 and 10%, respectively, upon addition of 10 g∙l-1 galacturonic acid. Genes previously reported to show a transcriptional response to other organic acids were overrepresented in a set of galacturonic-acid responsive genes identified by microarray analysis. These results suggested that galacturonic acid causes weak-acid uncoupling of the yeast plasma membrane pH gradient. Consistent with this hypothesis, galacturonate-accelerated loss of viability in starving cell suspensions was strongly pH dependent. Loss of viability was much slower in a strain in which all HXT (hexose transporter) genes were deleted. Moreover, deletion of HXT genes alleviated growth inhibition on ethanol observed at galacturonic acid concentrations of 10 g∙l-1 and above. Conclusions: At low pH, galacturonic acid negatively affects the physiology of S. cerevisiae. Reduced sensitivity of hexose-transporter mutants indicated that one or more HXT transporters are involved in transport of galacturonic acid. Significance and Impact: This study shows that galacturonic acid toxicity should be taken into account in process development for yeast-based fermentative conversion of pectin-rich feedstocks such as sugar beet pulp and citrus peel. Involvement of hexose transporters in galacturonic acid toxicity provides leads for improving tolerance.
2015-04-14 | GSE43474 | GEO
Project description:Enzymatic degradation of plant biomass requires the coordinated action of various enzymes. In this study, the production of reducing sugars from pectic substrates and sugar beet pulp (SBP) was investigated and compared using commercial enzyme preparations, including M2, pectinase (E1) from Aspergillus niger, Viscozyme® L (V-L) and L-40. V-L, a cellulolytic enzyme mix produced by Aspergillus sp. was further evaluated as the most robust enzyme cocktail with the strongest SBP degradation ability in terms of dynamic release of monosaccharides, methanol, and acetate from substrate SBP. Glucose, the building block of cellulose, was the first product to reach its maximum concentration within 2.5 hours. In contrast, the major monosaccharides in pectin, including arabinose and galacturonic acid, were continuously released from the residue until reaching a peak of 2,092 mg L-1 and 7,069 mg L-1 after 19 hours of fermentation. Label-free proteomics analysis (MS/MS) of V-L revealed 151 individual proteins. Of these, 137 proteins were annotated as containing a carbohydrate-active enzymes (CAZyme) module. Notably, of the 50 most abundant proteins, which accounted for over 90% of the protein amount in V-L, ca. 40% were predicted to be involved in pectin degradation (belonging mainly to CAZyme families GH28, CE8, CE16, PL1 and PL3). To reveal the role of individual putative key enzymes of pectic substrate decomposition, two galacturonases (PglA and PglB), which are core of pectin-degrading enzymes of the GH28 family, were heterologously expressed in Pichia pastoris strain GB10 and further characterized. PglA and PglB demonstrated maximum activity at 57 °C and 67 °C, respectively. Both enzymes exhibited endo-cleavage patterns towards polygalacturonic acid (PGA) and released oligosaccharides with different degrees of polymerization (DP). In conclusion, our study identified two pectin-cleaving enzymes present in major amounts in a highly efficient SBP-saccharifying enzyme mix and characterized some of their properties. Further studies along this line may facilitate the understanding of SBP degradation and may help to design improved artificial enzyme mixtures with a lower complexity than V-L for future application in biotechnology.
2024-04-09 | PXD045553 | Pride
Project description:Csac growth on monosaccharides found in lignocellulose
| PRJNA123621 | ENA
Project description:Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide. Simple two-way comparisons between pectin or xylan sources (treatment) and glucose or xylose (control), collected during mid- and late-log phase. Three replicates per condition.
2015-10-28 | E-GEOD-74379 | biostudies-arrayexpress
Project description: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. In this study, we applied the genetic resources of the filamentous ascomycete species Neurospora crassa to screen for transcription factors that play a major role in pectinase induction. Results: The pectin degradation regulator-1 (PDR-1) was identified through a transcription factor mutant screen in N. crassa. The Δpdr-1 mutant exhibited a severe growth defect on pectin and all tested pectin-related poly- and monosaccharides. Biochemical as well as transcriptional analyses of WT and the Δpdr-1 mutant revealed that while PDR-1-mediated gene induction was dependent on the presence of L-rhamnose, it also strongly affected the degradation of the homogalacturonan backbone. The expression of the endo-polygalacturonase gh28-1 was greatly reduced in the Δpdr-1 mutant, while the expression levels of all pectate lyase genes increased. Moreover, a pdr-1 overexpression strain displayed substantially increased pectinase production. Promoter analysis of the PDR-1 regulon allowed refinement of the putative PDR-1 DNA binding motif. Conclusions: PDR-1 is highly conserved in filamentous ascomycete fungi and is present in many pathogenic and industrially important fungi. Our data demonstrate that the function of PDR-1 in N. crassa combines features of two recently described transcription factors in Aspergillus niger (RhaR) and Botrytis cinerea (GaaR). The results presented in this study contribute to a broader understanding of how pectin degradation is orchestrated in filamentous fungi and how it could be manipulated for optimized pectinase production. The data here are associated with the following BioProjects: PRJNA256749, PRJNA349646, PRJNA349647, PRJNA349695, PRJNA349696, PRJNA349697, PRJNA349547, PRJNA349548, PRJNA349549, PRJNA349698, PRJNA349699, PRJNA349700 See the links on GSM entries for access to raw data at SRA.
2017-05-19 | GSE88985 | GEO