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The host targets of SARS-CoV-2 protein NSP5

ABSTRACT: To identity the host targets of the SARS-CoV-2 protease NSP5, SILAC-based quantitative proteomics was performed in comparing the binding partners of wildtype or catalytically-inactive C145A mutant.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

DISEASE(S): Severe Acute Respiratory Syndrome

SUBMITTER: Yen-Yu Yang

LAB HEAD: Yinsheng Wang

PROVIDER: PXD023277 | Pride | 2021-10-27

REPOSITORIES: Pride

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The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation.

Meyers Jordan M JM Ramanathan Muthukumar M Shanderson Ronald L RL Donohue Laura L Ferguson Ian I Guo Margaret G MG Rao Deepti S DS Miao Weili W Reynolds David D Yang Xue X Zhao Yang Y Yang Yen-Yu YY Wang Yinsheng Y Khavari Paul A PA

bioRxiv : the preprint server for biology 20210223

Viral proteins localize within subcellular compartments to subvert host machinery and promote pathogenesis. To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 SARS-CoV-2 viral proteins using proximity proteomics. This identified viral proteins at specific intracellular locations, such as association of accessary proteins with intracellular membranes, and projected SARS-CoV-2 impacts on innate immune signaling, ER-Golgi transport, and protein translation. It i ...[more]

PMID: 33655243

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Dynamic profiling of the protein life cycle in response to pathogens (protein)

Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.

2015-03-06 | E-GEOD-59792 | biostudies-arrayexpress

Glucose dissociates DDX21 dimers to regulate mRNA splicing and promote epidermal differentiation

Project description:We discovered that glucose directly bind to DDX21, induced the conformation change of the proteins and inhibit its helicase activity. Glucose also inhibits the dimerization of DDX21, re-localize DDX21 from nucleolus to nucleoplasm and reassemble DDX21 to RNA splicing complex. DDX21 is essential for epidermal differentiation while with normal glucose condition, DDX21 was re-localized from nucleolus to nucleoplasm, bind to splicing factors and mRNA introns more to regulate splicing of key differentiation factors and promote epidermal differentiation.

2023-01-05 | PXD028561 | Pride

The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted host antiviral signaling and translation

Project description:To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 SARS-CoV-2 viral proteins using proximity proteomics.

2022-02-16 | PXD023239 | Pride

Global Proteome Analysis of the NCI-60 Cell Line Panel

Project description:The NCI-60 cell line collection is a very widely used panel for the study of cellular mechanisms of cancer in general and in vitro drug action in particular. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. Here, we present a quantitative proteome and kinome profile of the NCI-60 panel covering, in total, 10,350 proteins (including 375 protein kinases) and including a core cancer proteome of 5,578 proteins that were consistently quantified across all tissue types. Bioinformatic analysis revealed strong cell line clusters according to tissue type and disclosed hundreds of differentially regulated proteins representing potential biomarkers for numerous tumor properties. Integration with public transcriptome data showed considerable similarity between mRNA and protein expression. Modeling of proteome and drug-response profiles for 108 FDA-approved drugs identified known and potential protein markers for drug sensitivity and resistance. To enable community access to this unique resource, we incorporated it into a public database for comparative and integrative analysis (http://wzw.tum.de/proteomics/nci60).

2017-03-31 | PXD005940 | Pride

Global Proteome Analysis of the NCI-60 Cell Line Panel, part 3

2017-09-25 | PXD005946 | Pride

Global Proteome Analysis of the NCI-60 Cell Line Panel, part 2

2017-03-31 | PXD005942 | Pride

SILAC-based Quantitative Proteomic Analysis Unveiled the Arsenite-induced Perturbation of Multiple Pathways in Human Skin Fibroblast Cells

Project description:Humans are exposed to arsenic species through inhalation, ingestion and dermal contact, which may lead to skin, liver, and bladder cancers as well as cardiovascular and neurological diseases. The mechanisms underlying the cytotoxic and carcinogenic effects of arsenic species, however, remain incompletely understood. To exploit the mechanisms of toxicity of As(III), we employed stable isotope labeling by amino acids in cell culture (SILAC) together with LC-MS/MS analysis to assess quantitatively the As(III)-induced perturbation of the entire proteome of cultured human skin fibroblast cells. Shotgun proteomic analysis on an LTQ-Orbitrap Velos mass spectrometer facilitated the quantification of more than 3800 proteins, 250 of which displayed significant alternations (> 1.5 fold) upon arsenite treatment. Targeted analysis on a triple-quadrupole mass spectrometer in the multiple-reaction monitoring (MRM) mode confirmed the quantification results of some select proteins. Ingenuity pathway analysis revealed the arsenite-induced alteration of more than 10 biological pathways, including the Nrf2-mediated oxidative stress response pathway as reflected by the up-regulation of 9 proteins in this pathway. In addition, arsenite induced changes in expression levels of a number of selenoproteins and metallothioneins. Together, the results from the present study painted a more complete picture about the biological pathways that are altered in human skin fibroblast cells upon arsenite exposure.

2018-10-26 | PXD005646 | Pride

Identification of dI-binding proteins

Project description:The dI-binding proteins were enriched and analysed by LC-MS/MS.

2023-02-03 | PXD033424 | Pride

Project description:The objectives of this study were 2-fold: 1) to compare the expression profiles at specific ages of blood leukocytes from foals stimulated with virulent R. equi with those of unstimulated leukocytes; and, 2) to characterize the age-related changes in the gene expression profile associated with blood leukocytes in response to stimulation with virulent R. equi. Peripheral blood leukocytes were obtained from 6 foals within 24 hours (h) of birth (day 1) and 2, 4, and 8 weeks after birth. The samples were split, such that half were stimulated with live virulent R. equi, and the other half served as unstimulated control. For one hyb design: we hybridized 6 samples stimulated and 6 unstimulated at each time point (30 mL of blood was treated with live virulent R. equi (Strain ATCC 33701) and the remaining 30 mL of blood with PBS ). For time course: 6 samples from day1 stimulated hybridized to week2 stimulated; day1 stimulated hyb to week 4 stimulated and day1 stimulated hyb to week8 stimulated. RNA was extracted and the generated cDNA was labeled with fluorescent dyes for microarray hybridizations using an equine microarray.

2013-05-31 | E-GEOD-45004 | biostudies-arrayexpress

Saccharomyces cerevisiae mutant strain with R1158 strain background: Fold change after doxycycline treatment

Project description:To understand the extent that Heat shock protein 90 (Hsp90) regulated its target proteins at the transcription level, transcriptomic change was profiled in yeast cells upon Hsp90 compromising. We genetically modified the R1158 strain (resulting genotype of mutant strain: TETp-HSC82 hsp82Δ arg4Δ lys5Δ car2Δ::URA3) and then reduced the Hsp90 amount with doxycycline treatment. Fold change of mRNA from untreated to treated cells indicated the transcriptomic change. Totally, we identified 1104 genes mis-regulated with a fold change of no less than 1.5 (P <0.05) upon Hsp90 compromising. Two-condition experiment, treated vs. untreated cells. Biological duplicates, independently grown and harvested. Technical triplicates for RNA isolation.

2014-03-26 | E-GEOD-56186 | biostudies-arrayexpress

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