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Effects of lipid diets on the metaproteome of the mice colon submucosa

ABSTRACT: Eight mice colon (submucosa) samples were submitted for iTRAQ labeling, high pH reversed phase fractionation and LC-MS/MS analysis.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Firmicutes Mn01-01 Bacteroidetes Mus Musculus (mouse)

TISSUE(S): Colon

SUBMITTER: Nijiati Abulizi

LAB HEAD: Deanna Gibson

PROVIDER: PXD008165 | Pride | 2019-02-20

REPOSITORIES: pride

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			Action	DRS
	20151223_REC-1555_Fr_01.raw	Raw
	20151223_REC-1555_Fr_02.raw	Raw
	20151223_REC-1555_Fr_03.raw	Raw
	20151223_REC-1555_Fr_04.raw	Raw
	20151223_REC-1555_Fr_05.raw	Raw

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Publications

Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids.

Abulizi Nijiati N Quin Candice C Brown Kirsty K Chan Yee Kwan YK Gill Sandeep K SK Gibson Deanna L DL

Nutrients 20190216 2

The dynamics of the tripartite relationship between the host, gut bacteria and diet in the gut is relatively unknown. An imbalance between harmful and protective gut bacteria, termed dysbiosis, has been linked to many diseases and has most often been attributed to high-fat dietary intake. However, we recently clarified that the type of fat, not calories, were important in the development of murine colitis. To further understand the host-microbe dynamic in response to dietary lipids, we fed mice ...[more]

PMID: 30781503

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Effects of lipid diets on the metaproteome of mouse colon mucosa

Project description:Eight mice colon samples were submitted for iTRAQ labeling, high pH reversed phase fractionation and LC-MS/MS analysis.

2019-02-20 | PXD008152 | Pride

Profiling of the human Fallopian tube matrisome

Project description:Characterization of the protein composition of the extracellular matrix (ECM) of normal human Fallopian tube samples.

2021-11-02 | PXD023707 | Pride

Spirocyclic dimer (SpiD7) activates unfolded protein response (UPR) to selectively inhibit growth and induce apoptosis of cancer cells

Project description:Protein homeostasis is maintained by a combination of tightly controlled processes which include synthesis, folding, trafficking and degradation. Transient accumulation of unfolded / misfolded proteins in the endoplasmic reticulum (ER) due to cell intrinsic and / or extrinsic signals results in the activation of unfolded protein response (UPR), an adaptation mechanism. Failure to resolve the transient accumulation results in UPR mediated programmed cell death. Loss of tumor suppressor gene or oncogene addiction in cancer cells result in a sustained higher basal UPR levels. This higher basal UPR levels in cancer cells when compared to normal cells provides a therapeutic window that can be exploited by UPR activators. Here we explored covalent modification of surface exposed cysteine (SEC) residues to simulate unfolded / misfolded proteins and induce UPR activation. A proteome-wide click-pulldown-MS study using an alkyne tagged isatin-derived spirocyclic -methylene--butyrolactone analog identified > 330 protein targets that were covalently modified. Evaluation for UPR activation with a set of analogs that can covalently modify SECs identified a spirocyclic -methylene--butyrolactone dimer (SpiD7) as a UPR activator. SpiD7 induced XBP1 splicing protected normal cells from caspase-mediated apoptosis, no such induction was observed in cancer cells, which resulted in caspase-mediated apoptosis in cancer cells. SpiD7 inhibits growth of high-grade serous carcinoma (HGSC) cell lines ~3-15 fold more potently than immortalized fallopian tube epithelial (normal) cells and reduced clonogenic growth of HGSC cell lines. Our results suggest that induction of UPR by covalent modification of SEC residues is a cancer cell vulnerability and can be exploited to discover novel therapeutics.

2022-05-20 | PXD029783 | Pride

Analysis of fulvestrant-treated breast cancer cells by LC-MS/MS

Project description:Identification of a novel variant of estrogen receptor alpha in breast cancer cells

2022-08-30 | PXD027087 | Pride

Analysis of ERalpha PPI in breast cancer cells by LC-MS/MS

Project description:Identification of protein-protein interaction (PPI) of a novel variant of estrogen receptor alpha in breast cancer cells

2022-08-30 | PXD027088 | Pride

The endoplasmic reticulum-associated mRNA-binding protein ERBP1 from Trypanosoma brucei

Project description:Kinetoplastids rely heavily on post-transcriptional mechanisms for control of gene expression, and on RNA-binding proteins that regulate mRNA splicing, translation and decay. Trypanosoma brucei ERBP1 (Tb927.10.14150) and ERBP2 (Tb927.9.9550) were previously identified as mRNA binding proteins that lack canonical RNA-binding domains. We here show that ERBP1 is associated with the endoplasmic reticulum, like ERBP2, and that the two proteins interact in vivo. Loss of ERBP1 from bloodstream-form T. brucei initially resulted in a growth defect but proliferation was restored after more prolonged cultivation. Results from a pull-down of tagged ERBP1 suggest that it preferentially binds to ribosomal protein mRNAs. The ERBP1 sequence resembles that of Saccharomyces cerevisiae Bfr1, which also localises to the endoplasmic reticulum and binds to ribosomal protein mRNAs. However, unlike Bfr1, ERBP1 does not bind to mRNAs encoding secreted proteins, and it is also not recruited to stress granules after starvation.

2020-05-27 | PXD016136 | Pride

Proteomic analysis of mitochondria isolated from the frontal cortex and hippocampus of apolipoprotein E knockout mice treated with Alda-1, an activator of mitochondrial aldehyde dehydrogenase (ALDH2)

Project description:Recently, it has been shown that mitochondrial dysfunction and oxidative stress play important roles in the pathogenesis of neurodegeneration. Mitochondrial aldehyde dehydrogenase (ALDH2), an enzyme responsible for the detoxification of reactive aldehydes – the end products of lipid peroxidation, is considered to exert protective function in mitochondria. The aim of our study was to use the methods of differential proteomics in concert with molecular and morphological techniques to elucidate the changes in the frontal cortex and hippocampus of apolipoprotein E knockout (apoE-/-) mice (an animal model of the early stages of Alzheimer’s disease) upon treatment with Alda-1 – a small molecular weight activator of ALDH2.

2017-02-23 | PXD004022 | Pride

Identification of ELC interacting proteins in zebrafish heart

Project description:The essential myosin light chain (ELC) is part of the cardiac myosin motor regulating the contractility of the heart. Recently, we have demonstrated ELC phosphorylation to be responsible not only for basal maintenance of cardiac contractility, but also for the adaptation of sarcomere function to increased demands in adult zebrafish (Scheid et al. Cardiovascular Research, 2016). However, the direct interacting kinases, phosphatases as well as the signaling pathway mediating the ELC phosphorylation are mostly unknown. Here, we aim to identify ELC interacting proteins in zebrafish heart tissue using an ELC-specific precipitation assay followed by mass spectrometry. In brief, ELC specific co-immunoprecipitation was performed by using the Dynabeads Co-immunoprecipitation Kit (Invitrogen, #14321D). Custom-specific polyclonal ELC antibodies (Eurogentec, peptide for immunization: NH2-CAPVPETPKEPEVDLK-CONH2) against zebrafish ELC were covalently coupled to DynabeadsTM M-270 Epoxy (Invitrogen, #14302D) and whole zebrafish heart protein was used as input. All steps were carried out according to the manufacturer's instructions.

2022-07-24 | PXD016357 | Pride

15-141 The endoplasmic reticulum-associated mRNA-binding protein ERBP1

2020-01-16 | PXD016106 | Pride

Analysis of myosin light chain migration pattern in 2D gels of human left ventricular proteins - proximity labeling

Project description:NIMA-related kinase 9 (NEK9) was identified to interact with the essential myosin light chain (ELC). To validate these findings ascorbate peroxidase (APEX) catalyzed proximity labeling (Hung et al. Nat Protoc. 2016) was performed. To do so, human ELC fused to APEX was overexpressed in HEK293 cells. Empty pcDNA3-APEX2-NES vector serves as negative control. Half of each sample was treated with H2O2, which catalyzes protein labeling in close proximity of ELC. After streptavidin pull down of labeled proteins, the samples were analyzed by mass spectrometry.

2022-07-24 | PXD034115 | Pride

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