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Profiling HeLa cell ubiquitylome with OtUBD and FK2

ABSTRACT: This project compares the novel ubiquitin affinity reagent OtUBD with a monoclonal ubiquitin antibody FK2 in their abilities to facilitae the profiling of the ubiquitylated proteome of HeLa cells. Enrichments were done side by side using a semi-denaturing condition.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Mengwen Zhang

LAB HEAD: Mark Hochstrasser

PROVIDER: PXD032675 | Pride | 2022-05-30

REPOSITORIES: Pride

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			Action	DRS
	F525644.mgf	Mgf
	F525644.xml	Xml
	F525645.mgf	Mgf
	F525645.xml	Xml
	F525646.mgf	Mgf

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Profiling yeast ubiquitylome with OtUBD pulldowns

Project description:This project includes two separate experiments where the ubiquitylated proteome of the budding yeast Saccharomyces cerevisiae was enriched from whole cell lysate by affinity purification using a novel OtUBD affinity resin. In the first experiment, two distinct experimental conditions (native, denaturing) were used to compare the proteins enriched by OtUBD affinity resin and the negative control resin. In the second experiment, the ubiquitylation profile of proteins were compared among wildtype yeast cells and yeasts lacking certain E3 ligase enzymes.

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FOXK2 targeting by the SCF-E3 ligase subunit FBXO24 for ubiquitin mediated degradation modulates mitochondrial respiration

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BAG5 functionally interacts with the autophagy adaptor protein p62

Project description:Molecular chaperones are critical to maintaining intracellular proteostasis and have been shown to have a protective role against alpha-synuclein mediated toxicity. Co-chaperone proteins regulate the activity of molecular chaperones and connect the chaperone network to protein degradation and cell death pathways. Bcl-2 associated athanogene 5 (BAG5) is a co-chaperone that modulates proteostasis by inhibiting the activity of Hsp70 and several E3 ubiquitin ligases, resulting in enhanced neurodegeneration in models of Parkinson’s disease (PD). Here we identify a novel interaction between BAG5 and p62/sequestosome-1 (SQSTM1), suggesting that BAG5 may bridge the chaperone network to autophagy-mediated protein degradation. The interaction was discovered using affinity purifaction followed by mass spectrometry to identify BAG5 interacting proteins and was validated by subsequent in vitro immunoprecipitation studies.

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chicken deubiquitinases in Salmonella infection

Project description:We infected HD11 macrophages with Salmonella Typhimurium, followed by chemical proteomic analysis of deubiquitinases by using ubiquitin-specific active-site probe.

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Effect of Cln3-deficiency on protein secretion in Dictyostelium

Project description:This project investigated the effect of Cln3-deficiency on protein secretion in the social amoeba Dictyostelium discoideum by performing LC-MS/MS on conditioned media harvested from starved WT and cln3- cells.

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Proteomic analysis of NK3.3-derived extracellular vesicles

Project description:Our study investigates the features and anti-tumor function of extracellular vesicles (EVs) isolated from our well described NK cell line - NK3.3 - the only published clonal, normal human cell line to date. Natural killer (NK) cells, critical for proper immune function, destroy tumor cells primarily through the release of granules containing potent cytolytic molecules. NK cells also release these molecules within membrane-bound exosomes and microvesicles collectively known as EVs. We show that NK3.3 EVs contain the cytolytic molecules perforin, granzymes A and B, and granulysin, and an array of common EV proteins. We previously showed that the E3 ubiquitin ligase identified by our laboratory, natural killer lytic-associated molecule (NKLAM/RNF19b), is localized to NK granules and is essential for maximal NK killing; our current study shows NKLAM situated within the NK3.3 EV membrane. Analysis of NK3.3 EV contents also identified multiple RNA species including miRNAs associated with anti-tumor activity. We demonstrate that treatment of an array of hematopoietic and non-hematopoietic tumor cell lines with NK3.3 EVs inhibits proliferation and induces apoptosis and cell death while leaving normal cells unaffected. Taken together, our study suggests that NK3.3 EVs have the potential to be effective immunotherapeutic agents.

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The proteasome acts as a hub for local and systemic plant immunity in Arabidopsis thaliana and constitutes a virulence target of Pseudomonas syringae type-III effector proteins

Project description:Recent evidence suggests that the ubiquitin-proteasome system (UPS) is involved in several aspects of plant immunity and a range of plant pathogens subvert the UPS to enhance their virulence. Here we show that proteasome activity is strongly induced during basal defense in Arabidopsis. Mutant lines of the proteasome subunits RPT2a and RPN12a support increased bacterial growth of virulent Pseudomonas syringae pv. tomato DC3000 (Pst) and Pseudomonas syringae pv. maculicola ES4326. Both proteasome subunits are required for Pathogen-associated molecular patterns (PAMP)-triggered immunity (PTI) responses. Analysis of bacterial growth after a secondary infection of systemic leaves revealed that the establishment of systemic-acquired resistance (SAR) is impaired in proteasome mutants, suggesting that the proteasome also plays an important role in defense priming and SAR. In addition, we show that Pst inhibits proteasome activity in a type-III secretion dependent manner. A screen for type-III effector proteins from Pst for their ability to interfere with proteasome activity revealed HopM1, HopAO1, HopA1 and HopG1 as putative proteasome inhibitors. Biochemical characterization of HopM1 by mass-spectrometry indicates that HopM1 interacts with several E3 ubiquitin ligases and proteasome subunits. This supports the hypothesis that HopM1 associates with the proteasome leading to its inhibition. Thus, the proteasome is an essential component of PTI and SAR, which is targeted by multiple bacterial effectors.

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