Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Correlating citric acid formation and manganese limitation in Aspergillus niger using transcriptome and proteome analysis

ABSTRACT: Aspergillus niger is well known for its capability to produce citrate in high amounts but the detailed metabolic response causing citrate production has not been fully elucidated. Manganese is known to have an important effect as its limitation is a requirement to obtain high-level citrate formation. To identify the translational regulation causing citric acid overflow metabolism, transcriptome and proteome data from cultivations in manganese limitation and manganese excess conditions were analyzed. In addition to four already described main responses, two novel events were identified. The first metabolic response was down regulation of phosphoenolpyruvate carboxykinase (PEPCK) during manganese limited conditions, which was confirmed by in vivo experiments. Down regulation of the first step in the gluconeogenesis, while maintaining a high activity through glycolysis, promoted secretion of citrate into the medium as an alternative regulatory mechanism for adjusting the intracellular concentrations of TCA intermediates. The other novel observation was down regulation of two cation transporters at manganese limited conditions. It was hypothesized that lowered cation transport across the mitochondrial membrane reduced the ability of the cell to maintain homeostasis thereby favoring citric acid secretion. Finally, upregulation of an ABC transporter was measured, which was assumed to be a citrate permease.

ORGANISM(S): Aspergillus niger Aspergillus nidulans Aspergillus oryzae

PROVIDER: GSE61985 | GEO | 2014/10/03

SECONDARY ACCESSION(S): PRJNA262895

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Correlating citric acid formation and manganese limitation in Aspergillus niger using transcriptome and proteome analysis

Project description:Aspergillus niger is well known for its capability to produce citrate in high amounts but the detailed metabolic response causing citrate production has not been fully elucidated. Manganese is known to have an important effect as its limitation is a requirement to obtain high-level citrate formation. To identify the translational regulation causing citric acid overflow metabolism, transcriptome and proteome data from cultivations in manganese limitation and manganese excess conditions were analyzed. In addition to four already described main responses, two novel events were identified. The first metabolic response was down regulation of phosphoenolpyruvate carboxykinase (PEPCK) during manganese limited conditions, which was confirmed by in vivo experiments. Down regulation of the first step in the gluconeogenesis, while maintaining a high activity through glycolysis, promoted secretion of citrate into the medium as an alternative regulatory mechanism for adjusting the intracellular concentrations of TCA intermediates. The other novel observation was down regulation of two cation transporters at manganese limited conditions. It was hypothesized that lowered cation transport across the mitochondrial membrane reduced the ability of the cell to maintain homeostasis thereby favoring citric acid secretion. Finally, upregulation of an ABC transporter was measured, which was assumed to be a citrate permease. 9 samples in total. Three conditions in triplicates

2014-10-03 | E-GEOD-61985 | biostudies-arrayexpress

Medium pH influences citric acid and lipid production in oleaginous yeast Yarrowia lipolytica

Project description:The goal of this study is to find out how Yarrowia lipolytica W29’s transcriptome changes in response to different pHs in certain medium, where the production of citric acid and lipid vary significantly at different pHs. The changes in transcriptome will give us insight about the mechanism of citric acid and/or lipid production are regulated. We harvested Y. lipolytica cells from bioreactor cultures from three different pHs: 2.0, 4.0 and 6.0 in triplicates. We sequenced the mRNA by Illumina HiSeq 2500 and generated an average of 20 million reads for each sample. We did not find distinct gene expression changes for the enzymes right downstream the intersection where citrate is cleaved into acetyl-CoA. Instead, from gene ontology enrichment analysis, we observed proteins with transport activities were overrepresented in gene groups that were up-regulated higher pH conditions, where citric acid secretion is favored.

2019-04-26 | GSE80717 | GEO

FaDu treated with citric buffer vs. rCTGF

Project description:FaDu treated with citric buffer vs. rCTGF FaDu treated with citric buffer for 24 hours FaDu treated with rCTGF 100 ng/mL for 24 hours

2013-01-01 | E-GEOD-30423 | biostudies-arrayexpress

FaDu treated with citric buffer vs. rCTGF

Project description:FaDu treated with citric buffer vs. rCTGF

2013-01-01 | GSE30423 | GEO

Cap analysis gene expression (CAGE) of Aspergillus luchuensis mut. kawachii control and laeA disruptant strains

Project description:LaeA, a putative methyltransferase, is a global regulator for metabolic and development process in filamentous fungi. We characterized the laeA homologous genes in the white koji fungus, Aspergillus luchuensis mut. kawachii (A. kawachii) to examine their role in citric acid production. The ΔlaeA strain showed a significant reduction in the citric acid productivity. The cap-analysis gene expression (CAGE) revealed the laeA is required for the gene expression of a putative citrate exporter encoding cexA, which has a critical role for the citric acid production. The deficient citric acid productivity of the ΔlaeA strain was remedied by overexpression of cexA to a comparative level to that of the cexA overexpressing ΔcexA strain. In addition, chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) analysis indicated that LaeA regulates gene expression of the citrate exporter encoding cexA gene via histone H3K4 and histone H3K9 methylation levels. These results indicate that LaeA is involved in the citric acid production through epigenetic regulation of cexA in A. kawachii.

2019-08-15 | GSE135849 | GEO

Substrate and oxygen dependent citric acid production by Yarrowia lipolytica: Insights through transcriptome and fluxome analysis

Project description:The goal of the study is to use Next generation sequencing (RNA-seq) and 13C based flux analysis to study the underlying regulation of citric acid metabolism in mixed culture fermentation (glucose and glycerl) of Yarrowia lipolytica. We sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) under oxygen excess and limited conditions with 2 replicates each . Transcriptional profiles showed that under oxygen limited conditions, due to deficient mitochondrial activity, citric acid is being consumed back after glycerol exhaustion eventhough glucose is present in excess. Transcriptome and fluxome profiles showed that glucose is mainly directed towards the Pentose phosphate pathway in the dual substrate fermentations.

2017-05-08 | GSE83109 | GEO

Aspergillus niger

Project description:Correlating citric acid formation and manganese limitation in Aspergillus niger using transcriptome and proteome analysis

| PRJNA262895 | ENA

The hierarchy of transition metal homeostasis: Iron controls manganese accumulation in a unicellular cyanobacterium.

Project description:Iron and manganese are part of a small group of transition metals required for photosynthetic electron transport. Here, we present evidence for a functional link between iron and manganese homeostasis. In the unicellular cyanobacterium, Synechocystis sp. PCC 6803 Fe and Mn deprivation resulted in distinct modifications of the function of the photosynthetic apparatus. For example, iron limitation modifies the rate of QA re-oxidation in photosystem II, a complex that contains more Mn than Fe. The intracellular elemental quotas of Fe and Mn are also linked. Fe limitation reduces the intracellular Mn quota. Mn limitation did not exert a reciprocal effect on Fe quotas. Microarray analysis comparing Mn and Fe limitation revealed a stark difference in the extent of the transcriptional response to the two limiting conditions, reflective of the physiological data. The effects of Fe limitation on the transcriptional network are widespread while the effects on Mn limitation are highly specific. Our analysis also revealed an overlap in the transcriptional response of specific Fe and Mn transporters. This overlap provides a framework for explaining Fe limitation induced changes in Mn quotas. Fe transporters can serve as a low affinity Mn transport system. Under iron limitation the specificity of the Fe transport system changes, making it a less efficient Mn transport system. We monitored the gene expression of Synechocystis PCC6083 at standard conditions and after 2 days of iron limitation (0Fe), manganese limitation (0Mn) and combined iron and manganese limitation (0Fe0Mn). Each timepoint and condition was sampled in triplicates. Due to strong deviations in one of the three repeats for the 0Mn and 0Fe0Mn conditions, the corresponding replicates were excluded from further analysis.

2013-06-29 | E-GEOD-48416 | biostudies-arrayexpress

Effect of Escherichia coli B2 on gene expression before and after citric acid-induced antibiotic tolerance

Project description:In order to explore the differentially expressed genes of E. coli B2 after citric acid induced antibiotic tolerance, we artificially induced the antibiotic tolerance of E. coli O157: H7 and verified its phenotype.

2023-02-26 | GSE225782 | GEO

Pseudomonas aerugiosa tctED deletion strain compared to wildtype

Project description:Purpose of study was to investigate whole genome expression changes of a strain with deletion of the two-component system TctD-TctE and determine genes dysregulate relative to the parental wildtype to gain insight into possible regulatory targets of TctD-TctE. TctD-TctE is a two-component system in Pseudomonas aeruginosa that responds to and regulates uptake of tricarboxylic acids such as citric acid. It accomplishes this through derepression of the porin encoding the gene opdH, thereby regulating influx of citrate metabolites from the surrounding environment. Deletion of the tctED operon (ΔtctED) resulted in a reduced growth phenotype when citric acid is present in media. In the ΔtctED strain the presence of citric acid was found to have an inhibitory effect on growth. When the alternative carbon source arginine was present, wildtype levels of growth could not be restored. Static cultures of ΔtctED had low cell density in the presence of citric acid but maintained the same levels of biofilm formation compared to conditions when no citric acid was present. This suggests a dysregulation of biofilm formation in the presence of citric acid. In the ΔtctED strain there was also greater accumulation of tobramycin within the biofilm compared to the PA14 wildtype strain. Additionally, analysis of whole-genome expression found that multiple metabolic genes were dysregulated in ΔtctED. Here it is concluded that TctD-TctE is involved in biofilm tolerance to tobramycin in the presence of citrate metabolites.

2018-05-15 | GSE114431 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data