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MGA interactome in 293T cells using affinity purification and mass spectrometry

ABSTRACT: Tandem affinity purification of MGA-interacting proteins and mass spectrometry

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Yuzuru Shiio

LAB HEAD: Yuzuru Shiio

PROVIDER: PXD025930 | Pride | 2021-07-06

REPOSITORIES: pride

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			Action	DRS
	170918YS01_437.raw	Raw
	170918YS03_439.raw	Raw
	170918YS06_442.raw	Raw
	checksum.txt	Txt
	interact-fhis-mga-2153-2856_xtandem.prot.xml	Xml

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1 - 5 of 7

Publications

Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness.

Mathsyaraja Haritha H Catchpole Jonathen J Freie Brian B Eastwood Emily E Babaeva Ekaterina E Geuenich Michael M Cheng Pei Feng PF Ayers Jessica J Yu Ming M Wu Nan N Moorthi Sitapriya S Poudel Kumud R KR Koehne Amanda A Grady William W Houghton A McGarry AM Berger Alice H AH Shiio Yuzuru Y MacPherson David D Eisenman Robert N RN

eLife 20210708

MGA, a transcription factor and member of the MYC network, is mutated or deleted in a broad spectrum of malignancies. As a critical test of a tumor suppressive role, we inactivated <i>Mga</i> in two mouse models of non-small cell lung cancer using a CRISPR-based approach. MGA loss significantly accelerated tumor growth in both models and led to de-repression of non-canonical Polycomb ncPRC1.6 targets, including genes involved in metastasis and meiosis. Moreover, MGA deletion in human lung adenoc ...[more]

PMID: 34236315

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Clients of membrane-bound PDI family members

Project description:The client-specificity of TMX3, TMX4 and TMX5 in cellula, was assessed by expressing mutant forms of the enzymes, where the last cysteine residue of the TMX’s CXXC catalytic sites has been mutated to alanine, which stabilizes the mixed disulfide that oxidoreductases establish with clients. Clients remain disulfide-bonded to the oxidoreductase and are identified upon co-immunoprecipitation and mass spectrometry analyses.

2023-06-12 | PXD041156 | Pride

CDC14B interactome - The proteomic approach aimed at the identification of interaction partners for the human dual phosphatase and tumor suppressor CDC14B by Co-inmunoprecipitation (Co-IP) experiments. In this approach, CDC14B interactomes from unsynchronized and G2/M enriched cells were compared semi-quantitatively based on spectral counting. This approach yielded the deubiquitylase USP9X as a G2/M-specific CDC14B interactor which has been confirmed by Western-blot (WB).

Project description:The proteomic approach aimed at the identification of interaction partners for the human dual phosphatase and tumor suppressor CDC14B by Co-inmunoprecipitation (Co-IP) experiments. In this approach, CDC14B interactomes from unsynchronized and G2/M enriched cells were compared semi-quantitatively based on spectral counting. This approach yielded the deubiquitylase USP9X as a G2/M-specific CDC14B interactor which has been confirmed by Western-blot (WB).

2020-03-25 | PXD012732 | Pride

Endogenous interactors of the natural trapping mutant TMX5/TXNDC15

Project description:The endoplasmic reticulum (ER) is the organelle of nucleated cells that produces lipids, sugars and proteins. More than 20 ER-resident members of the Protein Disulfide Isomerase (PDI) family regulate formation, isomerization and disassembly of covalent bonds in newly synthesized polypeptides. The PDI family includes few membrane-bound members. Among these, TMX1, TMX2, TMX3, TMX4 and TMX5 belong to the thioredoxin-related transmembrane (TMX) protein family. TMX5 is the least known member of the family. Here, we establish that TMX5 covalently engages via its active site cysteine residue at position 220 a subset of secretory proteins, mainly single- and multi-pass Golgi-resident polypeptides. TMX5 also interacts non-covalently, and covalently, via non-catalytic cysteine residues, with the PDI family members PDI, ERp57 and ERp44. The association of TMX5 and ERp44 requires formation of a mixed disulfide between the catalytic cysteine residue 29 of ERp44 and the non-catalytic cysteine residues 114 and/or 124 of TMX5 and controls the ER retention of TMX5. Thus, TMX5 belongs to the family of proteins including Ero1, Ero1, Prx4, ERAP1, SUMF1 that do not display ER retention sequences and rely on ERp44 engagement for proper inter-compartmental distribution. The client-specificity of TMX5 in cellulo was assessed by expressing mutant forms of the enzymes, where the last cysteine residue of the TMX’s CXXC catalytic sites has been mutated to alanine, which stabilizes the mixed disulfide that oxidoreductases establish with clients. Clients remain disulfide-bonded to the oxidoreductase and are identified upon co-immunoprecipitation and mass spectrometry analyses.

2024-09-27 | PXD054716 | Pride

WELFARE OF RAINBOW TROUT AT SLAUGHTER: INTEGRATING BEHAVIOURAL, PHYSIOLOGICAL, PROTEOMIC AND QUALITY INDICATORS

Project description:This study compared the brain proteome response of fish submitted to cold shock by fast-chilling (FC) as a novel stunning method (with fish immersed in liquid water at -8ºC), asphyxia (ASP) (as the currently used method), electrical stunning (ES) and anaesthesia (AN) with MS-222, by integrating it with physiological, behavioural and quality welfare indicators. Fish trials were conducted in triplicate tanks and two fish per tank were randomly sampled for MS analysis. One of the objectives of this integrative work was to disclose most significant changes in the brain proteome of rainbow trout (O. mykiss) subjected to four types of stunning methods that could help to elucidate about welfare standards.

2024-01-10 | PXD044301 | Pride

Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits

Project description:The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed efficiency states, even when fed an identical diet. Here, we reveal that many microbial populations show divergent proteome production in function of the feed efficiency state. Thus, proteomic data serve as a strong indicator of host feed efficiency state phenotype, overpowering predictions based on genomic and taxonomic information. We highlight protein production of specific phylogenies associated with each of the feed efficiency states. We also find remarkable plasticity of the proteome both in the individual population and at the community level, driven by niche partitioning and competition. These mechanisms result in protein production patterns which exhibit functional redundancy and checkerboard distribution that are tightly linked to the host feed efficiency phenotype. By linking microbial protein production and the ecological mechanisms that act within the microbiome feed efficiency states, our present work reveals a layer of complexity that bears immense importance to the current global of food security and sustainability.

2022-08-25 | PXD033418 | Pride

Proteomics analysis of dorsal striatum reveals changes in synaptosomal proteins following ethamphetamine self-administration in rats

Project description:Methamphetamine is a widely abused, highly addictive drug. Regulation of synaptic proteins within the brain’s reward pathway modulates addiction behaviours, the progression of drug addiction and long-term changes in brain structure and function that result from drug use. Therefore, using large scale proteomics studies we aim to identify global protein expression changes within the dorsal striatum, a key brain region involved in the modulation of addiction. We performed LC-MS/MS analyses on rat striatal synaptosomes following 30 days of methamphetamine self-administration (2 hours/day) and 14 days abstinence. We identified a total of 84 differentially-expressed proteins with known roles in neuroprotection, neuroplasticity, cell cytoskeleton, energy regulation and synaptic vesicles. We identify significant expression changes in stress-induced phosphoprotein and protein Tppp, which have not previously been associated with addiction. In addition, we confirm the role of amphiphysin and phosphatidylethanolamine binding protein in addiction. This approach has provided new insight into the effects of methamphetamine self-administration on synaptic protein expression in a key brain region associated with addiction, showing a large set of differentially-expressed proteins that persist into abstinence.

2015-05-06 | PXD001443 | Pride

Shotgun proteomics of Sparus aurata hepatic stress response

Project description:This study characterizes the liver stress proteome of fish submitted to overcrowding (OC), repeated net-handling (NET) and hypoxia (HYP). Fish trials were conducted in triplicate tanks and two fish per tank were randomly sampled for MS analysis. This work aims to disclose most significant changes in signaling and metabolic pathways involved in the stress response. This data-driven knowledge may ultimately contribute for the improvement of species-specific welfare management protocols, towards a sustainable aquaculture.

2022-12-13 | PXD036392 | Pride

Discovery of stress biomarkers in the skin mucus of Sparus aurata by shotgun proteomics

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2023-04-20 | PXD038712 | Pride

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PD1 inhibits PKCθ-dependent phosphorylation of cytoskeleton-related proteins and immune synapse formation

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