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Global proteomics of HEK293T cells treated with Val-boroPro for 48h

ABSTRACT: Global proteomics of HEK293T cells treated with Val-boroPro for 48h

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Andrew Griswold

LAB HEAD: Daniel A. Bachovchin

PROVIDER: PXD015978 | Pride | 2020-10-14

REPOSITORIES: Pride

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			Action	DRS
	1495AG_S1_1R1_i39_DBachovchin.raw	Raw
	1495AG_S1_2R1_i39_DBachovchin.raw	Raw
	1495AG_S1_3R1_i39_DBachovchin.raw	Raw
	1495AG_S1_i39_DBachovchin_Peptides.xlsx	Xlsx
	1495AG_S1_i39_DBachovchin_Proteins.xlsx	Xlsx

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Publications

Activation of the CARD8 Inflammasome Requires a Disordered Region.

Chui Ashley J AJ Griswold Andrew R AR Taabazuing Cornelius Y CY Orth Elizabeth L EL Gai Kuo K Rao Sahana D SD Ball Daniel P DP Hsiao Jeffrey C JC Bachovchin Daniel A DA

Cell reports 20201001 2

Several cytosolic pattern-recognition receptors (PRRs) form multiprotein complexes called canonical inflammasomes in response to intracellular danger signals. Canonical inflammasomes recruit and activate caspase-1 (CASP1), which in turn cleaves and activates inflammatory cytokines and gasdermin D (GSDMD), inducing pyroptotic cell death. Inhibitors of the dipeptidyl peptidases DPP8 and DPP9 (DPP8/9) activate both the human NLRP1 and CARD8 inflammasomes. NLRP1 and CARD8 have different N-terminal r ...[more]

PMID: 33053349

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DPP9 activity and not protein binding inhibits the CARD8 inflammasome

Project description:Inflammasomes are multiprotein complexes formed in response to pathogens. NLRP1 and CARD8 are related proteins that form inflammasomes, but the pathogen-associated signal(s) and the molecular mechanisms controlling their activation have not been established. Inhibitors of the serine dipeptidyl peptidases DPP8 and DPP9 (DPP8/9) were recently discovered to activate both NLRP1 and CARD8. Interestingly, DPP9 binds directly to NLRP1 and CARD8, and this interaction, in addition to DPP9’s catalytic activity, may contribute to the inhibition of NLRP1. Here, we use activity-based probes, reconstituted inflammasome assays, and mass spectrometry-based proteomics to further investigate the DPP9-CARD8 interaction. We show that the DPP9-CARD8 interaction, unlike the DPP9-NLRP1 interaction, is not disrupted by DPP9 inhibitors or mutations that block autoproteolysis. Moreover, wild-type, but not catalytically-inactive mutant, DPP9 rescues CARD8-mediated cell death in DPP9 knockout cells. Together, this work reveals DPP9 activity and not direct protein binding restrains the CARD8 inflammasome, and suggests the binding interaction likely serves some other biological purpose.

2019-10-23 | PXD015047 | Pride

Differential miRNA expression in hippocampus of hBDNF Val66Met Knockin Mice

Project description:miRNA expression profiling of adult (8 wk) hippocampus by comparing samples from Met/Met and Val/Val animals Two-genotype experiment, Met/Met vs. Val/Val. Biological replicates: 5 Met/Met, 5 Val/Val

2013-03-06 | E-GEOD-44817 | biostudies-arrayexpress

Transcriptional profile of an eca39∆ mutant fission yeast

Project description:An branched-chain amino acids auxotroph eca39∆ mutant fission yeast exhibits an unusual adaptive growth phenotype on solid minimal media containing Ile, Leu and Val when other strains are growing nearby. The transcriptional profiles of an eca39∆ mutant before and after the adaptation were determined using Affymetrix DNA microarrays. Wild-type, the eca39∆ mutant, and the adapted eca39∆ mutant fission yeasts were inoculated in YE+2mM Ile, Leu and Val, and harvested at OD ~ 1. Total RNAs were purified from the 3 samples.

2012-09-21 | E-GEOD-29355 | biostudies-arrayexpress

On the mechanism and origin of isoleucyl-tRNA synthetase editing against norvaline

Project description:Aminoacyl-tRNA synthetases (aaRSs), the enzymes responsible for coupling tRNAs to their cognate amino acids, minimize translational errors by intrinsic hydrolytic editing. Here, we compared the propensity of norvaline (Nva), a linear amino acid not coded for protein synthesis, to the proteinogenic, branched valine (Val) to mistranslate isoleucine (Ile) in proteins. We show that in the synthetic site of isoleucyl-tRNA synthetase (IleRS), aminoacylation and pre-transfer editing with Nva and Val occur at similar rates. Post-transfer editing was, however, more efficient with Nva as IleRS misaminoacylates Nva-tRNAIle at slower rate than Val-tRNAIle. Accordingly, an Escherichia coli strain lacking IleRS post-transfer editing misincorporated Nva and Val in the proteome to a similar extent and at the same Ile positions. However, Nva mistranslation inflicted higher toxicity than Val, in agreement with IleRS post-transfer editing domain being optimized for hydrolysis of Nva-tRNAIle. Furthermore, we found that the evolutionary related IleRS, leucyl- and valyl-tRNA synthetases (I/L/VRSs), all efficiently hydrolyze Nva-tRNAs even when editing of Nva seems redundant. Thus, we hypothesize that editing of Nva-tRNAs had already existed in the last common ancestor of I/L/VRSs, and that the editing domain of I/L/VRSs had primarily evolved to prevent infiltration of Nva into modern proteins.

2019-01-28 | PXD011051 | Pride

Comparative analysis from hESC from different developmental sources of derivation

Project description:Whole genome expression analysis reveals that single blastomeres from day-3 human embryos and blastocysts show unique gene signature, thus hESC derived from these two developmental sources might show differential gene expression profile. Comparative gene expression analysis has revealed that no significant differences exist between hESCs derived from blastomeres versus those obtained from ICMs, suggesting that pluripotent hESCs involve a new developmental progression. hESC derived from single blastomeres (VAL-10B and VAL-11B) and from ICM (VAL-5, -7, and -8) were compared by global gene expression

2012-11-27 | E-GEOD-42520 | biostudies-arrayexpress

Target identification of CQ31, a selective activator of the CARD8 inflammasome

Project description:Target identification of CQ31 using the photoreactive diazirine-alkyne probe, CQ73.

2021-11-17 | PXD027707 | Pride

Transcription profiling of human osteoblasts differentiated from human mesenchymal stem cells and treated with three bioactive peptides

Project description:Effects of bioactive peptides IPP(Ile-Pro-Pro), VPP (Val-Pro-Pro), and LKP(Leu-Lys-Pro) on gene expression of osteoblast differentiated from human mesenchymal stem cells. Experimental design types: compound treatment and augmented reference design.

2008-01-23 | E-MEXP-885 | biostudies-arrayexpress

Oxidized thioredoxin-1 restrains the NLRP1 inflammasome

Project description:To find cellular protein binding partners of the NLRP1 inflammasome, FLAG-tagged full length NLRP1 (or a GFP-FLAG protein control) was ectopically expressed in HEK 293T cells and affinity purified from cell lysates (Note: the NLRP1-FLAG-containing lysate samples were affinity purified in the presence or absence of excess proline) before proteins were reduced, alkylated, and trypsinized before TMT labelling and pooling of the differentially tested lysates to give three conditions (1. NLRP1-FLAG; 2. GFP-FLAG; 3. NLRP1-FLAG+proline) in duplicate. These data represent the results following sample and data processing.

2022-11-04 | PXD037391 | Pride

ProteoViz: A toolset for interactive analysis of phosphoproteomics data

Project description:Quantitative proteomics generates large datasets with increasing depth and quantitative information. Even after data processing and statistical analysis, interpreting the results and relating their significance back to the system of study remains challenging. Often, this process is performed by scientists with expertise in their field, but limited experience in proteomic or phosphoproteomic analysis. We developed a set of tools for simple, interactive exploration of phosphoproteomics data that can be easily interpreted into biological knowledge. These tools are designed to expedite the processes of reviewing raw data from statistical output, identifying and verifying enriched sequence motifs, and viewing the data from the perspective of functional pathways. Here, we present the workflow and demonstrate its functionality by analyzing a phosphoproteomic data set from two lymphoma cell lines treated with kinase inhibitors.

2020-05-07 | PXD015606 | Pride

RBM7 activates P-TEFb for a pro-survival transcriptional response to DNA damage

Project description:DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain obscure. Here we show that following DNA damage, the RNA-binding motif protein 7 (RBM7) stimulates RNA polymerase II (Pol II) elongation and increases cell viability by activating the positive transcription elongation factor b (P-TEFb). This is mediated by DNA damage-enhanced binding of RBM7 to 7SK, the scaffold of the 7SK small nuclear ribonucleoprotein (snRNP) that inhibits P-TEFb. As a result, P-TEFb relocates from 7SK snRNP to chromatin to activate transcription of key DDR genes and multiple classes of non-coding RNAs. By alleviating the inhibition of P-TEFb, RBM7 thus promotes Pol II elongation to activate a transcriptional response that is crucial for cell fate upon genotoxic insult. Our work highlights a novel paradigm in stress-dependent control of Pol II pause release, and offers the promise of combating cancer by RBM7 and P-TEFb antagonists in combination with established DNA damage-inducing chemotherapeutics.

2018-06-01 | E-MTAB-6475 | biostudies-arrayexpress