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Effects of lipid diets on the metaproteome of mouse colon mucosa

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

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Firmicutes Bacterium Bacteroidetes Mus Musculus (mouse)

TISSUE(S): Colon

SUBMITTER: Nijiati Abulizi

LAB HEAD: Deanna Gibson

PROVIDER: PXD008152 | Pride | 2019-02-20

REPOSITORIES: pride

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			Action	DRS
	20160330_REC-1563_Fr_01.raw	Raw
	20160330_REC-1563_Fr_02.raw	Raw
	20160330_REC-1563_Fr_03.raw	Raw
	20160330_REC-1563_Fr_04.raw	Raw
	20160330_REC-1563_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 the mice colon submucosa

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

2019-02-20 | PXD008165 | Pride

Proteomic analysis reveals co-ordinated alterations in protein synthesis and degradation pathways in LRRK2 knockout mice

Project description:Mutations in leucine-rich repeat kinase 2 (LRRK2) segregate with familial Parkinson’s disease (PD) and genetic variation in LRRK2 contributes to risk of sporadic disease. Although knockout of LRRK2 or knock-in of pathogenic mutations into the mouse germline does not result in a PD phenotype, several defects have been reported in the kidneys of LRRK2 knockout mice. To understand LRRK2 function in vivo, we used an unbiased approach to determine which protein pathways are affected in LRRK2 knockout kidneys. We performed two iTRAQ screens on cytosol- and microsome-enriched fractions from 12-month old LRRK2-KO and G2019S knockin kidneys compared to wild type controls. We nominated changes in cytoskeletal-associated proteins, lysosomal proteases, proteins involved in vesicular trafficking and in control of protein translation in LRRK2-KO. Changes were not seen in mice expressing the pathogenic G2019S LRRK2 mutant.

2022-03-01 | PXD008531 | Pride

Early proteomic responses in shoot and root of FL478 under salinity stress

Project description:Climate change is affecting crop production due to soil salinization and water scarcity, and is predicted to worsen in the coming years. Rice is a major staple food and the most salt-sensitive cereal. High salinity in the soil triggers several adaptive responses in rice to cope with osmotic and ionic stress at the physiological, cellular and molecular levels. A major QTL for salinity tolerance, named Saltol, is present on chromosome 1 of Indian rice landrace varieties such as Pokkali and Nona Bokra. In this study, we characterized the physiological and early proteomic responses to salinity in FL478, an inbred rice line harboring the Saltol region. For this, plantlets were cultured in hydroponic cultures with 100 mM NaCl and evaluated at 6, 24 and 48h. At the physiological level, salinity significantly reduced shoot length after 48 h, whereas root length significantly increased. Moreover, the Na+/K+ ratio was maintained at lower levels in the shoots compared to the roots FL478 plantlets. On the other hand, roots showed a faster and more coordinated proteomic response than shoots, which was evident from only 6h of treatment. These responses were markedly related with transcription- and translation-related proteins. Moreover, roots exhibited a higher accumulation of stress-related proteins in response to salinity treatment, like peroxidase and SalT, which are both present in the Saltol QTL. Both, physiological and proteomic response, showed that roots respond in a highly adaptive manner to salinity stress compared to shoots, which suggests that this tissue is critical to the tolerance observed in varieties harbouring the Saltol region.

2020-12-21 | PXD014669 | Pride

Proteomic analysis of the liver isolated from the double (apolipoprotein E and endothelial nitric oxide synthase) knockout mice reveals decreased expression of major urinary proteins (MUPs)

Project description:Nitric oxide (NO) is a crucial gaseous signaling molecule engaged in a variety of physiological and pathological processes. It is produced by three isoenzymes called nitric oxide synthases (NOS): neuronal, inducible and endothelial NOS (eNOS). eNOS-derived NO plays an important role in endothelium-dependent vasodilation as well as in lipid and glucose homeostasis in the liver. In addition, it has been shown that NO exert a beneficial effect on mitochondrial biogenesis and respiration. Thus, the aim of our study was to used iTRAQ-based quantitative proteomics to investigate the changes in protein expression in the mitochondrial and cytosolic fractions isolated from the liver of the double (apolipoprotein E (apoE) and eNOS) knockout (apoE/eNOS-DKO) mice as compared to apoE-/- mice – an animal model of atherosclerosis and hepatic steatosis. Collectively, our proteomic approach revealed the increased expression of proteins related to gluconeogenesis, fatty acids and cholesterol biosynthesis as well as the decreased expression of proteins participated in triglyceride breakdown, cholesterol transport, protein transcription & translation and processing in endoplasmic reticulum (ER). Moreover, one of the most down-regulated proteins were major urinary proteins (MUPs), which are abundantly expressed in the liver and are involved in the regulation of lipid and glucose metabolism as well as mitochondrial function. However, the exact functional consequences of the revealed alterations require further investigation.

2018-03-05 | PXD006642 | 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

Diminazene aceturate (DIZE) stabilizes atherosclerotic plaques and attenuates hepatic steatosis in apolipoprotein E knockout mice by influencing macrophages polarization and taurine biosynthesis

Project description:Atherosclerosis and nonalcoholic fatty liver disease (NAFLD) are leading causes of morbidity and mortality in the Western countries. NAFLD is an important independent risk factor for the development of atherosclerosis. The renin-angiotensin system (RAS) with its two main opposing effectors: angiotensin II (Ang II) and Ang-(1-7) is widely recognized as a major regulator of cardiovascular function and body metabolic processes. Angiotensin-converting enzyme 2 (ACE2) by breaking-down Ang II forms Ang-(1-7) and thus favors Ang-(1-7) actions. Therefore, the aim of our study was to comprehensively evaluate the influence of prolonged treatment with ACE2 activator – diminazene aceturate (DIZE) on the development of atherosclerotic lesions and hepatic steatosis in apoE-/- mice fed a high-fat diet (HFD). We have shown that DIZE at a dose of 30 mg/kg/day given orally for 16 weeks was able to stabilize atherosclerotic lesions and attenuate hepatic steatosis in apoE-/- mice fed an HFD. Such effects were associated with decreased total macrophages content and increased α-smooth muscle actin levels in atherosclerotic plaques. Moreover, DIZE changed polarization of macrophages towards increased amount of anti-inflammatory M2 macrophages in atherosclerotic lesions. Interestingly, the anti-steatotic action of DIZE in the liver was related to the elevated HDL in the plasma, decreased triglycerides levels and increased biosynthesis and concentration of taurine in liver of apoE-/- mice. However, the exact molecular mechanisms of both the anti-atherosclerotic and anti-steatotic actions of DIZE require further investigations.

2021-09-09 | PXD022829 | Pride

Candidate proteins involved in the calyx abscission process of ‘Kuerlexiangli’ (Pyrus sinkiangensis Yu) identified by iTRAQ analysis

Project description:‘Kuerlexiangli’ (Pyrus sinkiangensis Yu) is an important market pear in China. The shape and quality of the fruit is negatively affected by the presence of a persistent calyx. Here, to explore the molecular mechanism of calyx abscission, we designed an experiment to compare protein expression at two critical stages of the calyx abscission process under three treatments: a calyx abscising treatment (6000 × Flusilazole + 300 × PBO), a calyx persisting treatment (50 mg L−1 GA3), and a water control. We investigated the collected protein fragments using isobaric tags for relative and absolute protein quantitation (iTRAQ) to identify candidate proteins and perform relative quantification. We identified 378,078 spectra and 3,873 proteins, of which there were 2,371 differentially abundant proteins (DAPs) having Gene Ontology terms and associating with 124 defined pathways from the Kyoto Encyclopedia of Genes and Genomes. The DAPs that were correlated with calyx abscission were mainly those known to be involved in photosynthesis, plant hormone signal transduction, cell-wall modification, and carbohydrate metabolism. Quantitative real-time PCR was used to confirm the results of the digital transcript abundance measurements. Among the isolated candidate proteins, polygalacturonase and chitinase appear to play key roles during the process of calyx abscission. We identified candidate proteins that exhibit highly dynamic expression changes during the calyx abscission progress. These proteins are potential targets for future functional identification and should be valuable to explore the mechanism of the calyx abscission, and finally for the development of a method for inducing calyx abscission in fruit production based on the use of small molecules.

2020-06-17 | PXD012499 | Pride

A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803

Project description:To improve ethanol production directly from CO2 in photosynthetic cyanobacterial systems, one key issue that needs to be addressed is the low ethanol tolerance of cyanobacterial cells. Our previous proteomic and transcriptomic analyses found that several regulatory proteins were up regulated by exogenous ethanol in Synechocystis sp. PCC 6803. In this study, through tolerance analysis of the gene disruption mutants of the up-regulated regulatory genes, we uncovered that one transcriptional regulator, Sll0794, was related directly to ethanol tolerance in Synechocystis. Using a quantitative iTRAQ-LC-MS/MS proteomics approach coupled with quantitative real-time reverse transcription-PCR (RT-qPCR), we further determined the possible regulatory network of Sll0794. The proteomic analysis showed that in the ∆sll0794 mutant grown under ethanol stress a total of 54 and 87 unique proteins were down- and up-regulated, respectively. In addition, electrophoretic mobility shift assays (EMSAs) demonstrated that the Sll0794 transcriptional regulator was able to bind directly to the upstream regions of sll1514, slr1512 and slr1838, which encode a 16.6 kDa small heat shock protein, a putative sodium-dependent bicarbonate transporter and a carbon dioxide concentrating mechanism protein CcmK, respectively. The study provided a proteomic description of the putative ethanol-tolerance network regulated by the sll0794 gene, and revealed new insights on the ethanol-tolerance regulatory mechanism in Synechocystis. As the first regulatory protein discovered related to ethanol tolerance, the gene may serve as a valuable target for transcription machinery engineering to further improve ethanol tolerance in Synechocystis.

2014-09-26 | PXD001266 | Pride

Insight into enzymatic degradation of corn, wheat, and soybean cell wall cellulose using quantitative secretome analysis of Aspergillus fumigatus

Project description:Aspergillus fumigatus, a saprophytic filamentous fungus, is known to harbor 263 glycoside hydrolase (GH) encoding genes, suggesting that A. fumigatus is an efficient lignocellulose degrader. Hence the present study uses corn, wheat or soybean as a sole carbon source to culture A. fumigatus under animal physiological condition as to understand how cellulolytic enzymes work together to achieve an efficient degradation of lignocellulose. Using isobaric tags for relative and absolute quantification (iTRAQ) approach, total of ~600 extracellular proteins were identified and quantified, in which ~50 proteins were involved in lignocellulolysis, including cellulases, hemicellulases, lignin-degrading enzymes and some hypothetical proteins.Functional classification of identified proteins showed 15% cellulases, 14 % hydrolases acting on glycosyl bond, and 22% hemicellulases。The approach of highly sensitive quantitative analysis of proteome and transcriptome respond to the probable enzyme combination required in agro industries and animal feeding purpose towards more efficient cellulose degradation and therefore better digestion of intracellular starch. Furthermore, number of important GH family protein, some CBM and polysaccharide lyase family proteins have been identified, which could attribute towards better degradation of lignocelluloses to release starch.

2016-09-29 | PXD004670 | Pride

Wheat spikelet LC-MSMS - iTRAQ-based quantitative proteome analysis reveals metabolic changes between a cleistogamous wheat mutant and its wild-type wheat counterpart

Project description:A novel wheat mutant, ZK001, characterized as cleistogamic and presumed to provide structural barriers for Fusarium head blight during the flowering stage, was created through static magnetic fields mutagenesis from YM18. The atrophied, thin and ineffective lodicules of ZK001 lost the ability to push the lemma and palea apart during the flowering stage. Compared to YM18, ZK001 exhibited lower Fusarium infection. comparative studies at the proteome level were employed between YM18 and ZK001. isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) were employed to characterize protein expression differences between YM18 and ZK001.

2019-05-14 | PXD010188 | Pride

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