Dataset Information

Unraveling the Gene Regulatory Networks of the Global Regulators VeA and LaeA in Aspergillus nidulans [ChIP-seq]

ABSTRACT: In the filamentous fungus Aspergillus nidulans, the velvet family protein VeA and the global regulator of secondary metabolism LaeA govern fungal development and secondary metabolism mostly by acting as the VelB/VeA/LaeA heterotrimeric complex. While functions of these highly conserved controllers have been well studied, the genome-wide regulatory networks governing cellular and chemical development remain to be uncovered. Here, by integrating transcriptomic analyses, protein-DNA interactions, and the known A. nidulans gene/protein interaction data, we have unraveled the gene regulatory networks governed by VeA and LaeA. Within the networks, VeA and LaeA directly control the expression of numerous genes involved in asexual/sexual development and primary/secondary metabolism in A. nidulans. Totals of 3,190 and 1,834 potential direct target genes of VeA and LaeA were identified, respectively, including several important developmental and metabolic regulators such as flbA·B·C, velB·C, areA, mpkB, and hogA. Moreover, by analyzing over 8,800 ChIP-seq peaks, we have revealed the predicted common consensus sequences 5’-TGATTGGCTG-3’ and 5’-TCACGTGAC-3’ that VeA and LaeA might bind to interchangeably. These findings further expand the biochemical and genomic studies of the VelB/VeA/LaeA complex functionality in gene regulation. In summary, this study unveils genes that are under the regulation of VeA and LaeA, proposes the VeA- and LaeA-mediated gene regulatory networks, and demonstrates their genome-wide developmental and metabolic regulations in A. nidulans. This entry is for the ChIP-seq data.

ORGANISM(S): Aspergillus nidulans

PROVIDER: GSE217819 | GEO | 2023/02/08

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Neurospora crassa is a reference organism to study carotene biosynthesis and light regulation for decades. However, there is no evidence of its capacity to produce secondary metabolites, a characteristic of many filamentous fungi. In this work, we report the role of the fungal specific velvet regulator complex in development and secondary metabolism in N. crassa. Four velvet genes were found in the genome. Deletion of ve-1 or ve-2 affects asexual and sexual development, secondary metabolism and light-dependent carotene biosynthesis. Deletion of vos-1 did not show significant differences in comparison to wild type. Deletion of lae-1 resulted in reduced protoperithecia formation and affected secondary metabolism. VE-1, VE-2, LAE-1 and VOS-1 showed nucleo-cytoplasmic localization, which was independent of light input. Two distinct velvet complexes were found in vivo: a heterotrimeric VE-1/VE-2/LAE-1 and a heterodimeric VE-2/VOS-1 complex, respectively. The heterotrimer-complex positively regulated sexual development and repressed asexual spore formation. Moreover, it repressed siderophore coprogen production under iron starvation conditions. The VE-1/VE-2 heterodimer controlled the production of carotene pigments. VE-1 regulated the expression of more than 15% of the whole genome, which corresponded mainly to regulatory, developmental and redox proteins. We also studied intergenera functions of the velvet complex through complementation of A. nidulans veA, velB, laeA, vosA mutants with their Neurospora crassa orthologues ve-1, ve-2, lae-1 and vos-1, respectively. Expression of VE-1 and VE-2 in A. nidulans successfully substituted the developmental and secondary metabolite functions of VeA and VelB by forming two functional chimeric velvet complexes in vivo, VelB/VE-1/LaeA and VE-2/VeA/LaeA, respectively. The N. crassa lae-1 and vos-1 genes did not complement respective A. nidulans mutants and failed to form corresponding complexes. Reciprocally, expression of veA restored the phenotypes of the N. crassa ve-1 mutant. All N. crassa velvet proteins heterologously expressed in A. nidulans were predominantly localized to nuclear fraction independent of light signal. These data highlight the conservation of the complex formation potential in N. crassa and A. nidulans. However, they also underline the similarities and differences of the velvet roles across genera according to the different life styles, niches and ontogenetic processes.

Project description:Aspergillus flavus is a common saprophyte and opportunistic pathogen producing aflatoxin (AF) and many other secondary metabolites. 5-Azacytidine (5-AC), a derivative of nucleoside cytidine, is widely used for studies in epigenetics and cancer biology as an inactivator of DNA methyltransferase and is also used for studying secondary metabolism in fungi. Our previous studies showed that 5-AC affects development and inhibits AF production in A. flavus, and that A. flavus lacks DNA methylation. How this common DNA methyltransferase inhibitor affects development and AF production is not clear. In this study, we applied an RNA-Seq approach to elucidate the mechanism of 5-ACM-bM-^@M-^Ys effect on A. flavus. In our current study, we identified 240 significantly differently expressed (Q-value<0.05) genes after 5-AC treatment, including two backbone genes in secondary metabolite clusters #27 and #35, which are involved in development or survival of sclerotia. With 5-AC treatment, about three quarters of the genes in the AF biosynthetic gene cluster in A. flavus were down-regulated to a certain degree. Strikingly, at least two genes aflI and aflLa, were completely inhibited. Interestingly, several genes involved in fungal development were down-regulated, especially veA, which is a gene that encodes protein bridges VelB and LaeA. This result supports the hypothesis that 5-AC affects development and AF production through weakening or even interrupting the connection between VelB and LaeA and then causing dysregulation of the expression pattern of genes involved in development and secondary metabolism. Our results improved the A. flavus genome annotation, provided a comprehensive view of the transcriptome of A. flavus responding to 5-AC and confirmed that fungal development and secondary metabolism are co-regulated. In additon, the RNA-Seq data of another sample treated with gallic acid was used to improve A. flavus genome annotation. mRNA of Aspergillus flavus cultured in three different culture media PDB, PDB+5-AC(5-Azacytidine),and PDB+GA(gallic acid) was subjected to sequence independently.

Project description:Genetic and molecular evidence to support the hypothesis that fungal secondary metabolites play a significant role in protecting the fungi against fungivory is scarce. We investigated the impact of fungal secondary metabolites on transcript regulation of stress related expressed sequence tags (ESTs) of the Collembola Folsomia candida feeding on mixed vs. single diets. Aspergillus nidulans wildtype (WT; Ascomycota) able to produce secondary metabolites including sterigmatocystin (ST) and a knockout mutant with reduced secondary metabolism (A. nidulans ?LaeA) were combined with the high quality fungus Cladosporium cladosporioides as mixed diets or offered as single diets. We hypothesized that (i) A. nidulans WT triggers more genes associated with stress responses compared to the A. nidulans ?laeA strain with suppressed secondary metabolism, (ii) C. cladosporioides causes significantly different transcript regulation than the A. nidulans strains ?laeA and WT, and (iii) mixed diets will cause significantly different transcript expression levels than single diets. All three hypotheses are generally supported despite the fact that many functions of the affected ESTs are unknown. The results bring molecular evidence for the existence of a link between fungal secondary metabolites and responses in springtails supporting the hypothesis that fungal secondary metabolites act as a shield against fungivory. Twenty-three day old Folsomia candida were fed ad libitum for five days to fungal cuts respectively Cladosporium cladosporoides, Aspergillus nidulans WT, Aspergillus nidulans ?LaeA and two mixed diets of C.cladosporoides/A. nidulans WT (mix 1) and C. cladosporoides/A. nudlans ?LaeA (mix2) respectively. Four biological replicates were used for every treatment and a dye swap was used with the Cy3/Cy5 labels. This resulted in 20 samples which were analysed in 10 hybridisations executed in an interwoven loop design. The C. cladosporoides diet was used as the reference in the data analysis.

Dataset Information

Unraveling the Gene Regulatory Networks of the Global Regulators VeA and LaeA in Aspergillus nidulans [ChIP-seq]

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets