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Protein abundance changes and ubiquitylation targets identified upon inhibition of the proteasome with Syringolin A

ABSTRACT: The numerous roles of the ubiquitin proteasome system (UPS) in cellular control have triggered interest in the identification of these ubiquitylation targets and their sites of ubiquitylation. For the identification of ubiquitylated proteins we employed affinity enrichment using an ubiquitin binding domains (UBAs). A change in the experimental set-up allowed for the identification of proteins that so far have been refractory to identification. We also investigated the changes in protein abundance upon interfering with the UPS by inhibition of the proteasome with the specific inhibitor Syringolin A and using a mutant overexpressing ubiquitin that cannot form K48-linked polyubiquitin chains.

INSTRUMENT(S): LTQ Orbitrap XL

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Root

SUBMITTER: Katja Baerenfaller

LAB HEAD: Katja Baerenfaller

PROVIDER: PXD000565 | Pride | 2014-04-15

REPOSITORIES: Pride

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Protein abundance changes and ubiquitylation targets identified after inhibition of the proteasome with syringolin A.

Svozil Julia J Hirsch-Hoffmann Matthias M Dudler Robert R Gruissem Wilhelm W Baerenfaller Katja K

Molecular & cellular proteomics : MCP 20140413 6

As proteins are the main effectors inside cells, their levels need to be tightly regulated. This is partly achieved by specific protein degradation via the Ubiquitin-26S proteasome system (UPS). In plants, an exceptionally high number of proteins are involved in Ubiquitin-26S proteasome system-mediated protein degradation and it is known to regulate most, if not all, important cellular processes. Here, we investigated the response to the inhibition of the proteasome at the protein level treating ...[more]

PMID: 24732913

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Protein abundance changes and ubiquitylation targets identified upon inhibition of the proteasome with Syringolin A

Project description:The numerous roles of the ubiquitin proteasome system (UPS) in cellular control have triggered interest in the identification of these ubiquitylation targets and their sites of ubiquitylation. For the identification of ubiquitylated proteins we employed affinity enrichment using an ubiquitin binding domains (UBAs). A change in the experimental set-up allowed for the identification of proteins that so far have been refractory to identification. We also investigated the changes in protein abundance upon interfering with the UPS by inhibition of the proteasome with the specific inhibitor Syringolin A and using a mutant overexpressing ubiquitin that cannot form K48-linked polyubiquitin chains.

2014-04-15 | PXD000521 | Pride

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2014-05-19 | PXD000568 | Pride

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Differences in proteasome targeting in Arabidopsis leaf mesophyll, epidermal and vascular cells

Project description:For the detailed and sensitive detection of the responses to a specific treatment it is important to perform tissue or cell type specific analyses, but this is not easily achievable for the different leaf tissues. Here we developed a method termed MeSelect to effectively separate leaf epidermis, vascular and mesophyll cells basically without contamination from other tissues. The high yield of the MeSelect method allowed for tissue specific high-throughput proteome analyses after inhibition of the proteasome with Syringolin A and the affinity enrichment of polyubiquitylated proteins in epidermis, mesophyll and vasculature.

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Differences in proteasome targeting in Arabidopsis leaf mesophyll, epidermal and vascular cells

2015-05-14 | PXD000941 | Pride

Expression data from human HeLa cells exposed to interferon gamma for 2, 4, and 6 hours

Project description:The ubiquitin proteasome system (UPS) is known to possess important regulatory functions in the immune response. To gain a better and first comprehensive insight into the mechanisms of remodelling of UPS related gene expression inresponse to interferon-gamma, we undertook a comparative gene expression profiling during interferon-gamma stimulation at very early time points. Keywords: time course Human HeLa cells were harvested at 3 different periods of time following stimulation with interferon-gamma for RNA extraction and hybridization on Affymetrix microarrays.

2010-05-28 | E-GEOD-21760 | biostudies-arrayexpress

Transcription profiling of human monocyte-derived dendritic cells stimulated with LPS, Poly(I:C), CD40L or a combination of IL-1-b, IL-6, TNF-a and PGE2

Project description:The ubiquitin proteasome system (UPS) is known to possess important regulatory functions in the immune response. To gain a better and first comprehensive insight into the mechanisms underlying the conversion of immature to mature DC in terms of the expression of UPS related genes, we undertook a comparative gene expression profiling during DC maturation in response to four different prototypic maturation stimuli. Experiment Overall Design: Monocyte-derived DC were harvested at 3 different periods of time following stimulation for RNA extraction and hybridization on Affymetrix microarrays.

2009-02-09 | E-GEOD-10316 | biostudies-arrayexpress

Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation

Project description:Ubiquitin-proteasome system (UPS) protein degradation regulates protein abundance and eliminates misfolded and damaged proteins from eukaryotic cells. Variation in UPS activity influences numerous cellular and organismal phenotypes. However, to what extent such variation results from individual genetic differences is almost entirely unknown. Here, we developed a statistically powerful mapping approach to characterize the genetic basis of variation in UPS activity. Using the yeast Saccharomyces cerevisiae, we systematically mapped genetic influences on the N-end rule, a UPS pathway that recognizes N-degrons, degradation-promoting signals in protein N-termini. We identified 149 genomic loci that influence UPS activity across the complete set of N-degrons. Resolving four loci to individual causal nucleotides identified regulatory and missense variants in ubiquitin system genes whose products process (NTA1), recognize (UBR1 and DOA10), and ubiquitinate (UBC6) cellular proteins. Each of these genes contained multiple causal variants and several individual variants had substrate-specific effects on UPS activity. A cis-acting promoter variant that modulates UPS activity by altering UBR1 expression also alters the abundance of 36 proteins without affecting levels of the corresponding mRNAs. Our results demonstrate that natural genetic variation shapes the full sequence of molecular events in protein ubiquitination and implicate genetic influences on the UPS as a prominent source of post-translational variation in gene expression.

2022-10-26 | GSE213689 | GEO

Expression data from embryonic stem cells following siRNA transfection of UPS members [self_renewal]

Project description:While transcriptional regulation of stem cell self-renewal and differentiation has been extensively studied, only a small number of studies have addressed the roles for post-translational modifications in these processes. A key mechanism of post-translational modification is ubiquitination by the ubiquitin-proteasome system (UPS). Using UPS-targeted RNAi screens, we identify novel regulators of pluripotency and differentiation. We focus on two of these proteins, the deubiquitinating enzyme, Psmd14, and the E3 ligase, Fbxw7, and characterize their importance in ES cell pluripotency and cellular reprogramming. Embryonic stem cells were reverse transfected with siRNA, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays

2012-07-31 | E-GEOD-39771 | biostudies-arrayexpress

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