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Nuclear functions of KaeA, the subunit of KEOPS complex in Aspergillus nidulans

ABSTRACT: The aim of this project is to confirm that KaeA, the subunit of highly conserved KEOPS/EKC complex, participates in the transcription regulation in Aspergillus nidulans.The ChIP-seq experiment was performed to identify chromatin regions directly or indirectly bound by KaeA.

ORGANISM(S): Aspergillus nidulans

PROVIDER: GSE206874 | GEO | 2022/10/28

REPOSITORIES: GEO

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Nuclear functions of KaeA, the subunit of KEOPS complex in Aspergillus nidulans.

Project description:The aim of this project is to confirm that KaeA a subunit of highly conserved KEOPS/EKC complex, participates in the transcription regulation in Aspergillus nidulans. To identify genes directly or indirectly regulated by KaeA, the RNA-seq experiments were performed using kaeA mutants and the wild type kaeA+ strain.

2022-10-28 | GSE206830 | GEO

Nuclear Functions of KaeA, a Subunit of the KEOPS Complex in <i>Aspergillus nidulans</i>.

Project description:Kae1 is a subunit of the highly evolutionarily conserved KEOPS/EKC complex, which is involved in universal (t6A37) tRNA modification. Several reports have discussed the participation of this complex in transcription regulation in yeast and human cells, including our previous observations of KaeA, an Aspergillus nidulans homologue of Kae1p. The aim of this project was to confirm the role of KaeA in transcription, employing high-throughput transcriptomic (RNA-Seq and ChIP-Seq) and proteomic (LC-MS) analysis. We confirmed that KaeA is a subunit of the KEOPS complex in A. nidulans. An analysis of kaeA19 and kaeA25 mutants showed that, although the (t6A37) tRNA modification is unaffected in both mutants, they reveal significantly altered transcriptomes compared to the wild type. The finding that KaeA is localized in chromatin and identifying its protein partners allows us to postulate an additional nuclear function for the protein. Our data shed light on the universal bi-functional role of this factor and proves that the activity of this protein is not limited to tRNA modification in cytoplasm, but also affects the transcriptional activity of a number of nuclear genes. Data are available via the NCBI's GEO database under identifiers GSE206830 (RNA-Seq) and GSE206874 (ChIP-Seq), and via ProteomeXchange with identifier PXD034554 (proteomic).

| S-EPMC9570407 | biostudies-literature

Nuclear functions of KaeA, the subunit of KEOPS complex in Aspergillus nidulans.

Project description:Nuclear functions of KaeA, the subunit of KEOPS complex in Aspergillus nidulans.

| PRJNA852273 | ENA

Nuclear functions of KaeA, the subunit of KEOPS complex in Aspergillus nidulans

Project description:Nuclear functions of KaeA, the subunit of KEOPS complex in Aspergillus nidulans

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Identification of proteins interacting with KaeA, the subunit of KEOPS complex in Aspergillus nidulans in vivo.

Project description:The Kae1/KaeA protein is a subunit of the highly evolutionarily conserved KEOPS complex (Kinase, Endopeptidase and Other Proteins of Small size). The Kae1/KaeA gene has been identified in all previously sequenced genomes of Archea, Bacteria and Eucaryota, except for the most reduced genomes. The KEOPS complex participates in the universal modification of the tRNA converting adenosine A37 to N6-threonylcarbamoyl adenosine (t6A37). This modification of A37, immediately 3’ of anticodons decoding ANN codons, is one of the few tRNA modifications present in all organisms and plays an extremely important role in the accuracy of the translation process. We characterized two mutations in kaeA of filamentous fungus Aspergillus nidulans that result in the derepression of arginine catabolic enzymes and also showed that kaeA is involved in the regulation of several other genes that control various domains of cellular metabolism. This suggests that kaeA has additional function apart from t6A37 modification. To support this hypothesis we looked for proteins interacting with KaeA.

2023-03-11 | PXD034554 | Pride

A tri-species Aspergillus array (nidulans arrays)

Project description:The full genome sequencing of the ﬁlamentous fungi Aspergillus nidulans, Aspergillus niger and Aspergillus oryzae has opened the possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are presenting an Aﬀymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose-and xylose media has been performed, and used to validate the performance of the micro array. By doing gene comparisons of all three species, and cross-analysing this with the expression data, 23 genes, including the xylose transcriptional activator XlnR, have been identiﬁed to be a conserved response across the Aspergillus sp. Promoter analysis of the upregulated genes in all three species suggest the XlnR-binding site to be 5’-GGNTAAA-3’. We are thus presenting a validated tool for transcription analysis of three Aspergillus species and a methodology for comparative transcriptomics. Keywords: Physiological response

2008-02-15 | GSE9275 | GEO

Expression analysis of Aspergillus nidulans OE::rsmA

Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans OE::rsmA compared to wild-type RDIT9.32 (veA). A twelve array study using total RNA recovered from six separate cultures of Aspergillus nidulans wild-type RDIT9.32 (veA) and six separate cultures of Aspergillus nidulans overexpressing rsmA (restorer of secondary metabolism A), using custom-designed, four-plex arrays. The experiment was divided into two runs. In the first run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans carrying a plasmid overexpressing rsmA under the control of the gpdA promoter were assayed. In the second run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans overexpressing rsmA at the native locus under the control of the gpdA promoter were assayed.

2012-01-17 | E-GEOD-34220 | biostudies-arrayexpress

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 –type 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.

2012-04-16 | GSE32954 | GEO

Expression analysis of Aspergillus nidulans OE::rsmA

Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans OE::rsmA compared to wild-type RDIT9.32 (veA).

2012-01-17 | GSE34220 | GEO

Suberin degradation by Aspergillus nidulans

Project description:The study aims essentially at the characterisation of suberin degradation mechanisms by Aspergillus nidulans, at a fundamental level. Suberin is an important protective barrier in plant, thus the study of its biodegradation significantly impacts on phytopatology. In addition, fungal suberin degrading enzymes might provide important insights to develop new waste management, bioremediation and biodeterioration prevention strategies.

2014-07-31 | GSE54427 | GEO

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