Role of yeast Nup60 lysine 467 acetylation in regulation of transcription
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA821419 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18533232.fastq.gz | Fastqsanger.gz | |||
| SRR18533233.fastq.gz | Fastqsanger.gz | |||
| SRR18533234.fastq.gz | Fastqsanger.gz | |||
| SRR18533235.fastq.gz | Fastqsanger.gz | |||
| SRR18533236.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The experiment aimed to elucidate possible global effects of Nup60 K467 acetylation on transcription in S.cerevisiae. Result: Neither acetyl-mimic nor deacetyl-mimic mutations in Nup60K467 cause major shifts in expression profile.
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Project description:Lysine acetylation of proteins, a major post-translational modification, plays a critical regulatory role in almost every aspects in both eukaryotes and prokaryotes. Yarrowia lipolytica, an oleaginous yeast, is considered as a model for bio-oil production due to its ability to accumulate a large amount of lipids. However, the function of lysine acetylation in this organism is elusive. Here, we performed a global acetylproteome analysis of Y. lipolytica ACA-DC 50109. In total, 3163 lysine acetylation sites were identified in 1428 proteins, which account for 22.1% of the total proteins in the cell. Fifteen conserved acetylation motifs were detected. The acetylated proteins participate in a wide variety of biological processes. Notably, a total of 65 enzymes involved in lipid biosynthesis were found to be acetylated. The acetylation sites are distributed in almost every type of conserved domains in the multi-enzymatic complexes of fatty acid synthetases, suggesting an important regulatory role of lysine acetylation in lipid metabolism. Moreover, protein interaction network analysis reveals that diverse interactions are modulated by protein acetylation. The provided dataset probably illuminates the crucial role of reversible acetylation in oleaginous microorganisms, and serves as an important resource for exploring the physiological role of lysine acetylation in eukaryotes.
2018-11-22 | PXD006272 | Pride
Project description:Fungal pathogens cause deadly diseases in living organisms. Numerous studies suggest that lysine acetylation is a critical regulator in pathogenic fungi, but an in-depth and cross-species analysis of the acetylome in major pathogenic fungi is lacking, and our knowledge of the mechanism of acetylation in manipulating fungal pathogenicity is limited. Here, we show that lysine acetylation plays essential roles during cryptococcosis through modulating the gene expression of important virulence factors and the activity of key players in important pathways. We show that the Cryptococcus TOR pathway and translational elongation process are functionally regulated by acetylation via the HDAC and sirtuin families, respectively. Through comparative acetylome network analysis among pathogens and baker’s yeast, we demonstrate significant correlation between acetylation sites and virulence factors, indicating a unique selective pressure on lysine acetylation motifs in pathogenic fungi. These results provide a basis for understanding the regulation of fungal pathogenicity by posttranslational lysine acetylation.
2019-04-29 | PXD010354 | Pride
Project description:In this study, we set out to clarify the role of lysine acetylation on the major yeast Hsp40, Ydj1. We mutated a series of acetylation sites on Ydj1s J domain to either arginine to block acetylation or glutamine to mimic constitutive acetylation.
2024-04-14 | MSV000094536 | MassIVE
Project description:Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure directly regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification, occurring on the nucleosomal lateral surface. We show that H4K44ac is specific to yeast sporulation, rising during yeast meiosis and displaying genome-wide enrichment at recombination hotspots in meiosis. The H4K44 residue is required for normal meiotic recombination, for normal levels of double strand breaks during meiosis, and for optimal sporulation. Non-modifiable substitution H4K44R results in reduced MNase digestion and decreased binding of recombination-associated proteins at hotspots. Our results show that H4K44ac creates an accessible chromatin environment for key proteins to facilitate meiotic recombination. Two samples, one WT MNase-seq and one MNase-seq from yeast with a lysine->arginine mutation at H4K44, no replicates Two replicates each of MNase-seq in WT and H4K44->R mutant yeast grown in YPD or YPA.
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Project description:Sinorhizobium medicae 467 Resequencing
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Project description:Post-translational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S. cerevisiae contains several evolutionary conserved lysine acetyltransferases and deacetylases. However, only a few dozen acetylation sites in S. cerevisiae are known, presenting a major obstacle for further understanding the regulatory roles of acetylation in this organism. Here we use high resolution mass spectrometry to identify about 4000 lysine acetylation sites in S. cerevisiae. Acetylated proteins are implicated in the regulation of diverse cytoplasmic and nuclear processes including chromatin organization, mitochondrial metabolism, and protein synthesis. Bioinformatic analysis of yeast acetylation sites shows that acetylated lysines are significantly more conserved compared with nonacetylated lysines. A large fraction of the conserved acetylation sites are present on proteins involved in cellular metabolism, protein synthesis, and protein folding. Furthermore, quantification of the Rpd3-regulated acetylation sites identified several previously known, as well as new putative substrates of this deacetylase. Rpd3 deficiency increased acetylation of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex subunit Sgf73 on K33. This acetylation site is located within a critical regulatory domain in Sgf73 that interacts with Ubp8 and is involved in the activation of the Ubp8-containing histone H2B deubiquitylase complex. Our data provides the first global survey of acetylation in budding yeast, and suggests a wide-ranging regulatory scope of this modification. The provided dataset may serve as an important resource for the functional analysis of lysine acetylation in eukaryotes
2015-06-02 | PXD002287 | Pride
Project description:Cultured carcinoma cells were stimulated with growth factors and lysine acetylation and/or tyrosine phosphorylation dynamics were quantified.
2016-07-20 | MSV000079965 | MassIVE
Project description:Oxidative stress adaptation strategies are important to cell function and are linked to cardiac, neurodegenerative disease and cancer. Representatives of the domain Archaea are used as model organisms based on their extreme tolerance to oxidants and close evolutionary relationship with eukaryotes. Study of the halophilic archaeon Haloferax volcanii reveals lysine acetylation to be associated with oxidative stress responses. The strong oxidant hypochlorite: i) stimulates an increase in lysine acetyltransferase HvPat2 to HvPat1 abundance ratios and ii) selects for lysine deacetylase sir2 mutants. Here we report the dynamic occupancy of the lysine acetylome of glycerol-grown H. volcanii as it shifts in profile in response to hypochlorite. These findings are revealed by the: 1) quantitative multiplex LC-MS/MS analysis of the SILAC-compatible parent and Δsir2 mutant strains and 2) label free LC-MS/MS analysis of H26 ‘wild type’ cells. The results show that lysine acetylation is associated with key biological processes including DNA topology, central metabolism, cobalamin biosynthesis and translation. Lysine acetylation targets are found conserved across species. Moreover, lysine residues modified by acetylation and ubiquitin-like sampylation are identified suggesting post-translational modification (PTM) crosstalk. Overall, the results of this study expand the current knowledge of lysine acetylation in Archaea, with the long-term goal to provide a balanced evolutionary perspective of PTM systems in living organisms.
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