Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional memory drives accelerated re-activation of secondary metabolite production in Aspergillus nidulans [RNA-seq]

ABSTRACT: Transcriptional memory drives accelerated re-activation of secondary metabolite production in Aspergillus nidulans [RNA-seq]

PROVIDER: PRJNA1151726 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30358200_1.fastq.gz	Fastqsanger.gz
	SRR30358200_2.fastq.gz	Fastqsanger.gz
	SRR30358169_1.fastq.gz	Fastqsanger.gz
	SRR30358169_2.fastq.gz	Fastqsanger.gz
	SRR30358170_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 64

Similar Datasets

Transcriptional memory drives accelerated re-activation of secondary metabolite production in Aspergillus nidulans [ChIP-seq]

Project description:Transcriptional memory drives accelerated re-activation of secondary metabolite production in Aspergillus nidulans [ChIP-seq]

| PRJNA1151725 | ENA

Transcriptional memory drives accelerated re-activation of secondary metabolite production in Aspergillus nidulans [RNA-seq]

Project description:Organisms are repeatedly exposed to fluctuating environmental and nutritional conditions. Transcriptional memory has been shown to be a mechanism to cope with these fluctuations because it increases the speed and the magnitude of the cellular response to a certain re-occurring condition and therefore optimizes adaptation and fitness in a given environment. We found that genes coding for sterigmatocystin (ST) production in Aspergillus nidulans are activated stronger when cells are repeatedly exposed to nutrient starvation, compared to cells that experience this condition for the first time. We studied possible underlying mechanisms and found that persistence of the transcription factor AflR as well as a chromatin-based mechanism through histone H3 lysine 4 dimethylation (H3K4me2) are mediating the memory process. Our data indicate that AflR can undergo activation-inactivation cycles. On the other hand, an unknown mechanism mediated by a so far non-identified signal that originates from culture supernatants that were already starved once, specifically enhances the activation of starvation-dependent BGCs, including ST cluster activation. Finally, our ChIP-Seq data show that the ST cluster harbors i) three loci of constitutive and two of inducible H3K4me2 near the aflR locus, the latter two building up H3K4me3 after sufficient time, ii) bindings sites of histone demethylase KdmB near these H3K4me2 marks. Overall, using the ST cluster as model we provide insights on transcriptional memory and BGC activation dynamics in A. nidulans.

2024-09-30 | GSE275592 | GEO

Transcriptional memory drives accelerated re-activation of secondary metabolite production in Aspergillus nidulans [ChIP-seq]

2024-09-30 | GSE275591 | GEO

Expression analysis of Aspergillus nidulans AN1599 (PbcR) overexpression mutant

2012-04-16 | GSE32954 | GEO

Metabolic regulation of filamentous fungi is tailored for secondary secondary metabolite production

Project description:We investigated the metabolism of six secondary metabolite producing fungi of the Penicillium genus, during nutrient depletion in the stationary phase of batch fermentations and assessed conserved metabolic responses across species using genome-wide transcriptional profiling. Coexpression analysis revealed that expression of secondary metabolite biosynthetic genes correlates with expression of genes associated with pathways responsible for generation of precursor metabolites for secondary metabolism. Our results highlight the main metabolic routes for precursor supply of the secondary metabolism during nutrient depletion, and suggests that regulation of fungal metabolism is tailored to meet the demands for secondary metabolite production. These findings can aid in identifying wild type species, which are optimized for production of specific secondary metabolites, and therefore can be utilized as high yielding cell factories.

2017-11-17 | GSE106983 | GEO

Deletion of the celA gene in Aspergillus nidulans triggers overexpression of secondary metabolite biosynthetic genes

Project description:The cell wall is a structure involved in important stages of fungal growth and morphogenesis. Several studies in the literature have shown how perturbations at the cell wall-level trigger dramatic effects on growth (e.g. Horiuchi, 2009). Despite the importance of fungal cell walls and despite the great advances made in the field, there are still missing pieces in our understanding of cell wall dynamics in filamentous fungi. Some cell wall biosynthetic genes, for example, are still uncharacterized (for a detailed inventory of Aspergillus nidulans cell wall-related genes, see de Groot et al., 2009). The chief polysaccharides in the cell wall of the model organism A. nidulans are β-glucans (β-1,3-, β-(1,3;1,4)- and β-1,6-glucans), chitin and α-1,3-glucans. While much is known about the chitin and α-1,3-glucan biosynthetic genes in A. nidulans (Horiuchi et al., 1999; Fujiwara et al., 2000; Ichinomiya et al., 2002 and 2005; Takeshita et al., 2006; Yoshimi et al., 2013), no characterization is yet available for the celA gene (ANIA_08444) encoding a putative mixed-linkage glucan synthase (de Groot et al., 2009). Recently, a study on A. fumigatus has characterized Tft1, an enzyme shown to be responsible for the production of β-(1,3;1,4)-glucans in this organism (Samar et al., 2015). Deletion of Tft1 causes no obvious phenotype in A. fumigatus and a modest increase in virulence. To characterize the role of β-(1,3;1,4)-glucans in the growth and development of filamentous fungi, we here sought to provide transcriptomics data of an A. nidulans strain showing reduced expression of the gene encoding the putative mixed linkage glucan synthase celA.

2017-07-26 | GSE94110 | GEO

Expression analysis of Aspergillus nidulans AN1599 (PbcR) overexpression mutant

Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans AN1599 (PbcR) overexpression mutant, compared to the FGSC A4 wild-type strain. Overexpression of the Zn(II)2Cys6 M-bM-^@M-^Stype transcription factor, AN1599.4 (PbcR, pimaradiene biosynthetic cluster regulator), activates a secondary metabolite gene cluster in Aspergillus nidulans. Activation of the pathway in Aspergillus nidulans lead to a production of ent-pimara-8(14),15-diene. 12x135K array of two separate cultures of FGSC A4 and two separate cultures of oe:AN1599(PbcR) with three separate RNA extractions from each culture. Each 135K array measures expression level of 10,546 genes with 6 probes/transcript. In addition, the array format contains tiling probes for 36 longer transcripts. All probes are in duplicates, giving the total number of 137,562 probes per array.

2012-04-15 | E-GEOD-32954 | biostudies-arrayexpress

RNA-seq experiment of Drosophila melanogaster larvae reared on Aspergillus nidulans infested breeding substrate

Project description:Drosophila melanogaster larvae and filamentous fungi both utilise organic material. Here they compete for resources. Filamentous fungi can defend themselves and their substrate from predation respectively competition by the production and excretion of secondary metabolites, including substances with antibiotic and insecticidal properties. To analyse the traits that enables D. melanogaster larvae to reduce the harmful effects of fungal secondary metabolites and to develop on fungal infested substrate we confronted larvae with a toxin-producing wild type of Aspergillus nidulans, with a toxin-production-impaired mutant strain of A. nidulans, and with sterigmatocystin, a highly toxic metabolite of A. nidulans. Early first instar larvae were transferred to breeding substrate inhabited by fungal colonies respectively inoculated with the purified mycotoxin or controls. After 3, 6, 12, and 24 hours of confrontation larvae were collected and samples prepared for whole transcriptome shotgun sequencing.

2017-12-01 | E-MTAB-5344 | biostudies-arrayexpress

Influence of International Space Station Conditions on Fungal ‘Omics’ in Aspergillus nidulans

Project description:This study presents the first global genomic, proteomic, and secondary metabolomic characterization of the filamentous fungus, Aspergillus nidulans, following growth on the International Space Station (ISS). The investigation included the A. nidulans wild-type and 3 mutant strains, two of which were genetically engineered to enhance secondary metabolite (SM) production. Whole genome sequencing (WGS) revealed that ISS conditions altered the A. nidulans genome in specific regions. In strain CW12001, which features overexpression of the SM global regulator laeA, ISS conditions induced a point mutation that resulted in the loss of the laeA stop codon. Differential expression of proteins involved in stress response, carbohydrate metabolic processes, and SM biosynthesis was observed. ISS conditions significantly decreased prenyl xanthone production in the wild-type strain and increased asperthecin production in LO1362 and CW12001, which are deficient in a major DNA repair mechanism. Together, these data provide valuable insights into the genetic and molecular adaptation mechanism of A. nidulans to the spacecraft environment and present many economic benefits.

2022-05-19 | PXD010778 | Pride

The Rim15p homolog RimO mediates starvation response and is required for secondary metabolite production in Aspergillus nidulans

Project description:The Rim15p homolog RimO mediates starvation response and is required for secondary metabolite production in Aspergillus nidulans

| PRJNA765369 | ENA

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