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Quantification on NOD1 ubiquitination sites with ubiquitin and SspH2 co-overexpression

ABSTRACT: HEK293T cells were transiently transfected with NOD1-FLAG, HA-SspH2 WT/HA-SspH2 C580/empty vector, and Myc-Ubiquitin. Following anti-FLAG automated immunoprecipitation and in-gel trypsin digestion, fractionated samples were injected onto LC-MS/MS. Quantitation was performed on diglycyl-lysine sites on NOD1, on identical peptides with highest intensity across samples.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Olivier Julien Amit Bhavsar

PROVIDER: MSV000087693 | MassIVE | Wed Jun 23 16:43:00 BST 2021

REPOSITORIES: MassIVE

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Publications

The <i>Salmonella</i> Effector SspH2 Facilitates Spatially Selective Ubiquitination of NOD1 to Enhance Inflammatory Signaling.

Delyea Cole J CJ Forster Malcolm D MD Luo Shu S Dubrule Bradley E BE Julien Olivier O Bhavsar Amit P AP

Biochemistry 20240827 18

As part of its pathogenesis, <i>Salmonella enterica</i> serovar Typhimurium delivers effector proteins into host cells. One effector is SspH2, a member of the so-called novel E3 ubiquitin ligase family, that interacts with and enhances, NOD1 pro-inflammatory signaling, though the underlying mechanisms are unclear. Here, we report that SspH2 interacts with multiple members of the NLRC family to enhance pro-inflammatory signaling by targeted ubiquitination. We show that SspH2 modulates host innate ...[more]

PMID: 39189508

Similar Datasets

Quantification on NOD1 ubiquitination sites with SspH2 co-overexpression

Project description:HEK293T cells were transiently transfected with NOD1-FLAG and HA-SspH2 WT/HA-SspH2 C580/empty vector. Following anti-FLAG automated immunoprecipitation and in-gel trypsin digestion, fractionated samples were injected onto LC-MS/MS. Quantitation was performed on diglycyl-lysine sites on NOD1, on identical peptides with highest intensity across samples.

2021-06-24 | MSV000087700 | MassIVE

Huntingtin contains an ubiquitin-binding domain and regulates lysosomal targeting of mitochondrial and RNA-binding proteins

Project description:Evaluating the identity of ubiquitinated and ubiquitin-associated proteins tandem co-purifying non-covalently with wild-type (17 glutamine) human Huntingtin fragment, amino acids 1-502 C-terminally tagged with the HA peptide epitope, basally expressed from the CMV promoter within vector pcDNA3.1 transiently transfected into striatal precursor cell line St14A, significantly elevated above cells transfected with empty pcDNA3.1 vector negative control, in cells co-transfected with human FLAG-ubiquitin.

2024-07-31 | PXD053980 | Pride

Gene expression profiling of FaDu cells overexpressing TINCR-HA-FLAG

Project description:Differential gene expression analysis of FaDu cells overexpressing TINCR-HA-FLAG or an empty vector.

2024-07-16 | GSE180301 | GEO

MS analysis of STING linear ubiquitinated sites

Project description:HEK293T cells transiently transfected with plasmids encoding Flag-STING, Myc-HOIP and HA-HOIL-1L, were lysed with buffer (20 mM Na2HPO4, 20 mM NaH2PO4, 1% NP-40, 2 mM EDTA) supplemented with 1 mM DTT, 5 mM NEM, complete protease inhibitor cocktail, PhosSTOP and 0.1% SDS. The lysates were incubated with Anti-Flag M2 Affinity Gel. The bound material was eluted with 0.1 M glycine-HCl pH 2.7, separated by electrophoresis in a 10% gel, and stained with Bio-Safe Coomassie and then for mass spectrometry analysis

2023-10-26 | PXD046415 |

Affinity purification MS of human Ubiquitin-tagged RIT1

Project description:Human RIT1 was tagged with HA tag + N or C terminal ubiquitin (HA-Ubiqutin-RIT1 and HA-RIT1-Ubiqutin) and compared with empty vector (EV) or S35N/M90I RIT1 mutant (HA-RIT1 S35N/M90I). The constructs were expressed in human 293T cells and affinity purified using HA beads. RIT1 interacting proteins were compared by quantifying MS1 extracted chromatograms of peptides identified in conventional target-decoy database search.

2024-07-09 | PXD047228 | Pride

Bulk RNA-Seq to study the effects of CENP-A overexpression, p53 status, and X- irradiation treatment in MCF-10-2A cells

Project description:We performed bulk RNA-Seq to investigate global transcriptional changes upon overexpression of the centromeric H3 variant CenH3/CENP-A in p53 wild-type and defective cells, and after X-irradiation treatment. We established clonal MCF-10-2A TetOn-CENPA-FLAG-HA cell lines where CENP-A can be reversibly induced by Doxycycline (Dox) treatment. Upon CENP-A overexpression, these cells exhibit different radiosensitivity depending on p53 status. In order to profile global changes in expression, we compared MCF-10-2A TetOn-CENPA-FLAG-HA cells expressing either empty vector (p53-WT) or dominant-negative p53 (p53-DN) with 0X Dox (no Dox), 1X Dox (10 ng/ml), or 10X Dox (100 ng/ml) for 24h. At time 0, we irradiated one set of cells by X-ray generator (4gy) while a control set remained un-irradiated (0gy). 6h later, we extracted RNA for RNA-seq.

2021-03-01 | E-MTAB-9867 | biostudies-arrayexpress

Quantitative Proteomic Identification of Proteins that are Responsive to RNF12 E3 Ligase Ubiquitin Activity

Project description:Rlim-/y mouse embryonic stem cells (mESCs) were transfected with either empty pCAGGS vector, HA-RNF12 or HA-RNF12 (H569A/C572A). Experiment was performed in biological triplicate (9 samples in total).

2022-06-30 | PXD032317 | Pride

RIT1 oncoproteins escape LZTR1-mediated proteolysis

Project description:These data accompany our publication "RIT1 oncoproteins escape LZTR1-mediated proteolysis" (Castel P., et al. Science, 2019). Experiment 1: Identification of LZTR1 as an interacting partner of RIT1 Q Exactive Plus P20161208-02 FLAG GFP P20161208-03 FLAG RIT1 LTQ Orbitrap Velos V20170407-01 GST empty vector V20170407-03 GST RIT1 V20170407-06 HA empty vector V20170407-07 HA RIT1 Experiment 2: Identification of K135 and K187 ubiquitination sites in RIT1 Q Exactive Plus P20180408-01 FLAG-RIT1 / empty vector / empty vector (replicate 1) P20180408-02 FLAG-RIT1 / LZTR1 / empty vector (replicate 1) P20180408-03 FLAG-RIT1 / empty vector / TUBE (replicate 1) P20180408-04 FLAG-RIT1 / LZTR1 / TUBE (replicate 1) P20180408-06 GST-RIT1 / empty vector / empty vector (replicate 1) P20180408-07 GST-RIT1 / LZTR1 / empty vector (replicate 1) P20180408-08 GST-RIT1 / empty vector / TUBE (replicate 1) P20180408-09 GST-RIT1 / LZTR1 / TUBE (replicate 1) P20180408-11 GST-RIT1 / empty vector / empty vector (replicate 2) P20180408-12 GST-RIT1 / LZTR1 / empty vector (replicate 2) P20180408-13 GST-RIT1 / empty vector / TUBE (replicate 2) P20180408-14 GST-RIT1 / LZTR1 / TUBE (replicate 2) P20180408-16 FLAG-RIT1 / empty vector / empty vector (replicate 2) P20180408-17 FLAG-RIT1 / LZTR1 / empty vector (replicate 2) P20180408-18 FLAG-RIT1 / empty vector / TUBE (replicate 2) P20180408-32 FLAG-RIT1 / LZTR1 / TUBE (replicate 2)

2019-02-14 | MSV000083444 | MassIVE

Ubiquitin-dependent turnover of MYC promotes loading of the PAF complex on RNA Polymerase II to drive transcriptional elongation (ChIP-seq)

Project description:The MYC transcription factor is an unstable protein and its turnover is controlled by the ubiquitin system. Ubiquitination enhances MYC-dependent transactivation, but the underlying mechanism remains unresolved. Here we show that proteasomal turnover of MYC is dispensable for recruitment of RNA polymerase II (RNAPII), but is required to promote transcriptional elongation at MYC target genes. Degradation of MYC stimulates histone acetylation and recruitment of BRD4 and P-TEFb to target promoters, leading to phosphorylation of RNAPII CTD and the release of elongating RNAPII. In the absence of degradation, the RNA polymerase II-associated factor (PAF) complex associates with MYC via interaction of its CDC73 subunit with a conserved domain in the amino-terminus of MYC ("MYC box I"), suggesting that a MYC/PAF complex is an intermediate in transcriptional activation. Since histone acetylation depends on a second highly conserved domain in MYCs amino-terminus ("MYC box II"), we propose that both domains co-operate to transfer elongation factors onto paused RNAPII. ChIP-Seq experiments for MYC-HA (HA-IP) and RNAPII (total,Ser2p,Ser5p) performed in IMEC primary breast epithelial cells. Input-samples were sequenced as controls. The following antibodies were used: HA (Abcam; ab 9110)/ total RNAPII (Santa Cruz; sc-899x)/ Ser2p RNAPII (Abcam; ab 5095)/ Ser5p RNAPII (Covance; MMS-128P)

2016-01-04 | E-GEOD-70001 | biostudies-arrayexpress

Acetylation site mapping on TULP3

Project description:Fig. 2B: Semi-quantitative acetylation level on TULP3 in the presence of either empty pcDNA 3.1(+), Myc-p300, FLAG-PCAF or FLAG-GCN5 following immunoprecipitation.

2020-10-22 | MSV000086358 | MassIVE

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