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Activity-Guided Proteomic Profiling of Proteasomes - Whole proteome studies

ABSTRACT: A composition of proteasome complexes in WT yeast, and the changes these complexes undergo upon the deletion of Pre9 (Δα3) or of Sem1 (ΔSem1) based on whole-cell proteomic analysis and to activity-guided proteasome profiling of indicates that the amounts of proteasomal proteins and proteasome interacting proteins in the assembled active proteasomes differ significantly from their total amounts in the cell as a whole. This data set is of the whole-cell LFQ analysis.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Oded Kleifeld

LAB HEAD: Oded Kleifeld

PROVIDER: PXD045047 | Pride | 2024-02-15

REPOSITORIES: Pride

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	Seq63496_HF.raw	Raw
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Publications

Activity-Guided Proteomic Profiling of Proteasomes Uncovers a Variety of Active (and Inactive) Proteasome Species.

Sahoo Manisha Priyadarsini MP Lavy Tali T Cohen Noam N Sahu Indrajit I Kleifeld Oded O

Molecular & cellular proteomics : MCP 20240129 3

Proteasomes are multisubunit, multicatalytic protein complexes present in eukaryotic cells that degrade misfolded, damaged, or unstructured proteins. In this study, we used an activity-guided proteomic methodology based on a fluorogenic peptide substrate to characterize the composition of proteasome complexes in WT yeast and the changes these complexes undergo upon the deletion of Pre9 (Δα3) or of Sem1 (ΔSem1). A comparison of whole-cell proteomic analysis to activity-guided proteasome profiling ...[more]

PMID: 38296025

Similar Datasets

Activity-Guided Proteomic Profiling of Proteasomes

Project description:A composition of proteasome complexes in WT yeast, and the changes these complexes undergo upon the deletion of Pre9 (Δα3) or of Sem1 (ΔSem1) based on whole-cell proteomic analysis and to activity-guided proteasome profiling of indicates that the amounts of proteasomal proteins and proteasome interacting proteins in the assembled active proteasomes differ significantly from their total amounts in the cell as a whole. This data set is of the activity-guided profiling of the proteasome LFQ analysis.

2024-02-15 | PXD045051 | Pride

Activity guided profiling of yeast proteasome - protein extraction test

Project description:This experiment compared the impact of protein extraction conditions on the identification and quantification of proteasome subunits in WT yeast. It involved comparing proteins extracted from identical WT yeast samples under two different conditions: native and denaturing (in the presence of SDS and TCA).

2024-02-15 | PXD048380 | Pride

The 19S proteasome subunit Rpt3 regulates distribution of CENP-A by associating with centromeric chromatin

Project description:CENP-A, a variant of histone H3, is incorporated into centromeric chromatin and plays a role during kinetochore establishment. In fission yeast, the localization of CENP-A is limited to a region spanning 10 to 20 kb of the core domain of the centromere. Here, we report a mutant (rpt3-1) in which this region is expanded to 40 to 70 kb. Likely due to abnormal distribution of CENP-A, this mutant exhibits chromosome instability and enhanced gene silencing. Interestingly, the rpt3+ gene encodes a subunit of the 19S proteasome, which localizes to the nuclear membrane. While Rpt3 associates with centromeric chromatin, the mutant protein has lost this localization. A loss of the cut8+ gene encoding an anchor of the proteasome to the nuclear membrane causes similar phenotypes as observed in the rpt3-1 mutant. Thus, we propose that the proteasome (or its subcomplex) associates with centromeric chromatin and regulates distribution of CENP-A. Chromosomal distributions of differentially expressed centromere protein A in wild-type and a proteasome mutant.

2014-04-07 | E-GEOD-44594 | biostudies-arrayexpress

Gene Expression Kinetics

Project description:We have taken five different time points of a Yeast culture in exponential grow in rich medium, each one elapsed ten minutes from de previous one (from OD600 0.36 to 0.47). Then, for each time point we have measured the transcription rates (TR) and mRNA amounts (RA) for all the genes using the Genomic run-on (GRO) technique . For each time point we have measured the transcription rates (GRO) with 3 replicates (except for the t2 that only has 2 replicates due to technical problems) and mRNA amounts (cDNA RP) with 3 replicates for all the genes. The data were normalized using a gDNA hybridization for each filter.

2010-03-05 | E-GEOD-11521 | biostudies-arrayexpress

Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF)

Project description:Data independent acquisition modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions in each window are sampled. Making use of the correlation of molecular weight and ion mobility in a trapped ion mobility device (timsTOF Pro), we here devise a novel scan mode that samples up to 100% of the peptide precursor ion current in m/z and mobility windows. We extend an established targeted data extraction workflow by including the ion mobility dimension for both signal extraction and scoring, thereby increasing the specificity for precursor identification. Data acquired from whole proteome digests and mixed organism samples demonstrate deep proteome coverage and a very high degree of reproducibility as well as quantitative accuracy, even from 10 ng sample amounts.

2020-12-17 | PXD017703 | Pride

Lung Adenocarcinoma (A549) Immunopeptidomics

Project description:Alterations in cellular antigen processing and presenting machinery has gained increased interest as a hallmark of cancer-related inflammation. Growing evidence suggest that proteasome composition and immunoproteasome expression can influence antigen processing. By performing immunopeptidomics on A549 lung adenocarcinoma cell line following depletion of proteasome regulator PSME4 we identified alterations in the antigenic landscape resulting from changes in proteasome processing.

2023-03-30 | PXD037365 | Pride

Lung Adenocarcinoma (A549) Immunopeptidomics

2023-03-30 | PXD028364 | Pride

Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [Rec12]

Project description:Occupancy profiling of Rec12 during fission yeast meiosis. Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation. Whole cell extract DNA and DNA recovered by Rec12 ChIP from fission yeast undergoing synchronous meiosis were random-prime PCR amplified and labeled with Cy3 (whole cell extract) or Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.

2016-06-09 | E-GEOD-78821 | biostudies-arrayexpress

Gene Expression Analysis of Fat Body of Drosophila melanogaster Subjected to Sir2 Overexpression or Dietary Restriction

Project description:Sir2 is the most intensively discussed longevity gene in current aging research. Although the gene encoding for a NAD+-dependent histone deacetylase initially was found to extend lifespan of various organisms ranging from yeast to mammals, serious doubts regarding its role in longevity have been expressed recently. In this study, we tested whether tissue-specific overexpression of Sir2 in the adult fat body can extend lifespan when compared to genetically identical controls. We also wanted to elucidate the mechanisms by which fat body Sir2 promotes longevity by studying the phenotypic and transcriptional changes in the fat body. We found that moderate (3-fold) Sir2 overexpression in the fat body during adulthood only can promote longevity in both sexes by roughly 13 %. In addition, we obtained transcriptional profiles elicited by this overexpression and propose a role for Sir2 in lipid droplet biology especially under conditions of starvation. Furthermore, our data do not support the idea of Sir2 mediating the response to dietary restriction (DR) because transcriptional profiles of fat bodies after DR or Sir2 overexpression do not match. This study provides additional independent evidence for the concept of Sir2 as a longevity gene and as a promising pharmacological target to cure age-related diseases. 6 groups of sample types were included in the experiment: a) females overexpressing Sir2 in the fat body b) female controls c) males overexpressing Sir2 in the fat body d) male controls e) wildtype females subjected to DR f) wildtype females feeding on a normal diet. 3 biological replicates were included per group.

2013-05-01 | E-GEOD-45974 | biostudies-arrayexpress

Transcriptional regionalization of the fruit fly's airway epithelium

Project description:Although airway epithelia are primarily devoted to gas exchange, they have to fulfil a number of different tasks including organ maintenance and the epithelial immune response to fight airborne pathogens. These different tasks are at least partially accomplished by specialized cell types in the epithelium. In addition, a proximal to distal gradient mirroring the transition from airflow conduction to real gas exchange, is also operative. We analysed the airway system of larval Drosophila melanogaster with respect to region-specific expression in the proximal to distal axis. The larval airway system is made of epithelial cells only. Previously, it had been anticipated that these cells are very similar in their functional and transcript properties. We found differential expression between primary trunks of the airways and more distal ones comprising secondary and tertiary ones. Among these genes are especially those involved in signal transduction. A more detailed analysis was performed using DNA-microarray analyses to identify cohorts of genes that are either predominantly expressed in the primary or in the secondary/tertiary parts of the airways. Genes, including a putative mucin and the neuropeptide FMRFamide are predominantly found in primary branches, whereas the wnt- and the TGF-beta signalling pathways appear to be overrepresented in the secondary/tertiary ones. This differential expression is indicative for a proximal to distal transcriptional regionalization presumably reflecting functional differences in these parts of the flyM-bM-^@M-^Ys airway system. Trachea of wildtype L3 larvae were dissected and primary branches were processed seperately from secondary and tertiary branches. 3 biological replicates were included per group.

2014-04-01 | E-GEOD-53273 | biostudies-arrayexpress

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