Gene expression changes in the absence of the carbon catabolite repressor, CreA.
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ABSTRACT:
ORGANISM(S): Aspergillus fumigatus
PROVIDER: GSE97539 | GEO | 2017/04/19
SECONDARY ACCESSION(S): PRJNA382191
REPOSITORIES: GEO
Similar Datasets
Project description:Saprobic microorganisms, such as filamentous fungi of the genus Aspergillus, are of particular interest for biotechnological applications due to their natural capacity to secrete plant cell wall-degrading enzymes that are known as carbohydrate-active enzymes (CAZy). The presence of easily metabolizable sugars such as glucose, whose concentrations increase during plant biomass hydrolysis, results in the repression of CAZy-encoding genes, in a process known as carbon catabolite repression (CCR), which is undesired for the purpose of large-scale enzyme production. To date, the C2H2 transcription factor CreA has been described as the major CC-repressor in Aspergillus spp. Although CreA-mediated CCR has been extensively studied, less is known about the regulation of CreA itself and the role of post-translational modifications in this process. In this work, phosphorylation sites were identified by mass spectrometry on A. nidulans CreA and subsequently four sites, S262, S268, T308 and S319, were chosen to be mutated to non-phosphorylatable residues before their effects on CCR in both CC-repressing and de-repressing conditions were studied. Sites S262, S268 and T308 are important for CreA protein accumulation and cellular localization and repression of enzyme activities. In contrast, site S319 is key for CreA degradation and induction of enzyme activities. All sites were shown to be important for glycogen and trehalose metabolism. This study highlights the importance of CreA phosphorylation sites for the regulation of CCR. Furthermore, these sites are interesting targets for biotechnological strain engineering without the need to delete essential genes which can result in undesired side effects.
2021-02-18 | PXD018967 | Pride
Project description:Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources. Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger.
2011-01-31 | GSE19952 | GEO
Project description:Carbon catabolite repression (CCR) is a process that selects the energetically most favorable carbon source in an environment. CCR represses the use of less favorable carbon sources when a better source is available. Glucose is the preferential carbon source for most microorganisms because it is rapidly metabolized, generating quick energy for growth. In the filamentous fungus Aspergillus nidulans, CCR is mediated by the transcription factor CreA, a C2H2 finger domain DNA-binding protein. The aim of this work was to investigate the regulation of CreA and characterize its functionally distinct protein domains. CreA depends in part on de novo protein synthesis and is regulated in part by ubiquitination. CreC, the scaffold protein in the CreB-CreC deubiquitination (DUB) complex, is essential for CreA function and stability. Deletion of select protein domains in CreA resulted in persistent nuclear localization and target gene repression. A region in CreA conserved between Aspergillus spp. and Trichoderma reesei was identified as essential for growth on various carbon, nitrogen, and lipid sources. In addition, a role of CreA in amino acid transport and nitrogen assimilation was observed. Taken together, these results indicate previously unidentified functions of this important transcription factor. These novel functions serve as a basis for additional research in fungal carbon metabolism with the potential aim to improve fungal industrial applications.
| S-EPMC4858783 | biostudies-literature
Project description:Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources. Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger. Triplicate batch fermentations of each of the four Aspergillus niger strains used, the wild type A. niger strain ATCC 1015 and three gene deletion mutants, were carried out using glucose or glycerol as carbon source, and transcriptome analysis was performed. Biomass from each batch cultivation was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.
2011-01-31 | E-GEOD-19952 | biostudies-arrayexpress
Project description:Aspergillus niger is a filamentous ascomycete fungus that is commonly found in most biotopes around the globe. In nature, A. niger degrades the plant biomass polysaccharides to monomeric sugars, transports them into the cells, and uses a variety of catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived monomeric sugars (and maltose) in a highly sequential manner, rather than simultaneously. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA, which has been shown to mediate the use of preferential carbon sources over non-preferential carbon sources. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate physiological processes in A. niger.
2018-04-23 | GSE98434 | GEO
Project description:Acremonium cellulolyticus is one of several fungi that offer promise as an alternative to Trichoderma reesei for use in industrial cellulase production. However, the mechanism of cellulase production has not been studied at the molecular level because adequate genetic engineering tools for use in A. cellulolyticus are lacking. In the present study, we developed a gene disruption method for A. cellulolyticus, which needs a longer homologous region length. We cloned a putative A. cellulolyticus creA gene that is highly similar to the creA genes derived from other filamentous fungi, and isolated a creA disruptant strain by using the disruption method. Growth of the creA disruptant on agar plates was slower than that of the control strain. In the wild-type strain, the CreA protein was localized in the nucleus, suggesting that the cloned gene encodes the CreA transcription factor. Cellulase and xylanase production by the creA disruptant were higher than that of the control strain at the enzyme and transcription levels. Furthermore, the creA disruptant produced cellulase and xylanase in the presence of glucose. These data suggest both that the CreA protein functions as a catabolite repressor protein, and that disruption of creA is effective for enhancing enzyme production by A. cellulolyticus.
| S-EPMC3917621 | biostudies-literature
Project description:In nature, the fungus Aspergillus niger degrades plant biomass polysaccharides to monomeric sugars, transports them into its cells, and uses catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived sugars in a largely sequential manner. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate processes in A. niger.
| S-EPMC5923239 | biostudies-literature
Project description:A transcriptomic assessment of a kinase deletion mutant (ΔpkaA) and a control strain revealed many cellular activities this kinase is impacting. Studies were conducted in the model filamentous fungi, Aspergillus nidulans¸ under rich growth conditions. PkaA is a known kinase that mediates a wide range of processes including: nutrient sensing, stress responses, regulation of metabolism, as well as development and pathogenicity. Here, fungi were grown in rich media containing glucose. The comparison between the control strain and the deletion mutant transcript levels revealed previously unknown targets, such as the transcription factor CreA, the main repressor responsible for carbon catabolite repression (CCR).
2018-07-04 | GSE116579 | GEO
Project description:ObjectiveWith the aim to decipher the mechanisms involved in the transcriptional regulation of feruloyl esterase encoded by faeB, a genetic screen was performed to isolate A. niger mutants displaying inducer-independent expression from the faeB promoter.ResultPfaeB-amdS and PfaeB-lux dual reporter strains were constructed and used to isolate trans-acting mutants in which the expression of both reporters was increased, based on the ability to grow on acetamide plates and higher luciferase activity, respectively. The genetic screen on the non-inducing carbon source D-fructose yielded in total 111 trans-acting mutants. The genome of one of the mutants was sequenced and revealed several SNPs, including a point mutation in the creA gene encoding a transcription factor known to be involved in carbon catabolite repression. Subsequently, all mutants were analyzed for defects in carbon catabolite repression by determining sensitivity towards allyl alcohol. All except four of the 111 mutants were sensitive to allyl alcohol, indicating that the vast majority of the mutants are defective in carbon catabolite repression. The creA gene of 32 allyl alcohol sensitive mutants was sequenced and 27 of them indeed contained a mutation in the creA gene. Targeted deletion of creA in the reporter strain confirmed that the loss of CreA results in constitutive expression from the faeB promoter.ConclusionLoss of function of CreA leads to low but inducer-independent expression from the faeB promoter in A. niger.
| S-EPMC8197723 | biostudies-literature
Project description:Filamentous fungi of the genus Aspergillus are of particular interest for biotechnological applications due to their natural capacity to secrete carbohydrate-active enzymes (CAZy) that target plant biomass. The presence of easily metabolizable sugars such as glucose, whose concentrations increase during plant biomass hydrolysis, results in the repression of CAZy-encoding genes in a process known as carbon catabolite repression (CCR), which is undesired for the purpose of large-scale enzyme production. To date, the C2H2 transcription factor CreA has been described as the major CC repressor in Aspergillus spp., although little is known about the role of posttranslational modifications in this process. In this work, phosphorylation sites were identified by mass spectrometry on Aspergillus nidulans CreA, and subsequently, the previously identified but uncharacterized site S262, the characterized site S319, and the newly identified sites S268 and T308 were chosen to be mutated to nonphosphorylatable residues before their effect on CCR was investigated. Sites S262, S268, and T308 are important for CreA protein accumulation and cellular localization, DNA binding, and repression of enzyme activities. In agreement with a previous study, site S319 was not important for several here-tested phenotypes but is key for CreA degradation and induction of enzyme activities. All sites were shown to be important for glycogen and trehalose metabolism. This study highlights the importance of CreA phosphorylation sites for the regulation of CCR. These sites are interesting targets for biotechnological strain engineering without the need to delete essential genes, which could result in undesired side effects.IMPORTANCE In filamentous fungi, the transcription factor CreA controls carbohydrate metabolism through the regulation of genes encoding enzymes required for the use of alternative carbon sources. In this work, phosphorylation sites were identified on Aspergillus nidulans CreA, and subsequently, the two newly identified sites S268 and T308, the previously identified but uncharacterized site S262, and the previously characterized site S319 were chosen to be mutated to nonphosphorylatable residues before their effect on CCR was characterized. Sites S262, S268, and T308 are important for CreA protein accumulation and cellular localization, DNA binding, and repression of enzyme activities. In agreement with a previous study, site S319 is not important for several here-tested phenotypes but is key for CreA degradation and induction of enzyme activities. This work characterized novel CreA phosphorylation sites under carbon catabolite-repressing conditions and showed that they are crucial for CreA protein turnover, control of carbohydrate utilization, and biotechnologically relevant enzyme production.
| S-EPMC8545104 | biostudies-literature