Browse
Submit Data
Databases
API
Help

Dataset Information

403 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nipped in the bud: a microbial effector destabilizes MADS-domain transcription factors

ABSTRACT: Eluates from pull down experiments were separated on an SDS gel, and bands isolated for in gel trypsin digestion. Digested samples were analysed by LCMSMS on an Orbitrap. Peaklists were generated using MaxQuant 1.3.0.5 and database searches performed using Mascot Server 2.4. Data from all gel slices from one sample were merged in one Mascot search, and the results were imported into Scaffold 4.0.4.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

SUBMITTER: Gerhard Saalbach

LAB HEAD: Gerhard Saalbach

PROVIDER: PXD000223 | Pride | 2014-05-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	130402_03.raw	Raw
	130402_04.raw	Raw
	130402_05.raw	Raw
	130402_06.raw	Raw
	130402_07.raw	Raw

Items per page:

1 - 5 of 28

Publications

Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner.

MacLean Allyson M AM Orlovskis Zigmunds Z Kowitwanich Krissana K Zdziarska Anna M AM Angenent Gerco C GC Immink Richard G H RG Hogenhout Saskia A SA

PLoS biology 20140408 4

Pathogens that rely upon multiple hosts to complete their life cycles often modify behavior and development of these hosts to coerce them into improving pathogen fitness. However, few studies describe mechanisms underlying host coercion. In this study, we elucidate the mechanism by which an insect-transmitted pathogen of plants alters floral development to convert flowers into vegetative tissues. We find that phytoplasma produce a novel effector protein (SAP54) that interacts with members of the ...[more]

PMID: 24714165

Similar Datasets

Npro protein interaction partners

Project description:The N-terminal protease Npro from pestiviruses has been shown to rapidly dismantle the innate immune response by targeting IRF3 for degradation, resulting in inhibition of apoptosis and interferon production. To understand it’s role in these different responses, we have identified multiple cellular factors that interact with this viral protein using mass spectrometry and proteomic analysis. Pull-down experiments were performed with Npro, and the samples were run on an SDS gel. Each lane was cut into 5-6 sclices and the slices were digested with trypsin. Peptides were extracted and analysed by LX-MSMS on an LTQ-Orbitrap (Thermo). Data were processed with MaxQuant (1.3.0.5) and searches performed with Mascot on the Sptrembl database (taxonomy human). All gel slices from one sample were merged in one Mascot search. Mascot results were imported into Scaffold 3.6.5.

2016-12-22 | PXD000115 | Pride

Glycosyltransferases from oat (Avena) implicated in the acylation of avenacins

Project description:To study glycosyltransferases from oat, root proteins were extracted and separated gy 1D SDS gel electrophoresis. Bands were cut out, digested with trypsin, and the resulting peptides were analysed by LCMSMS on an Orbitrap mass sepctrometer. Raw data was processed with MaxQuant 1.3.0.5, and database searches on a custom database performed using Mascot.

2013-04-24 | PXD000083 | Pride

Proteomic analysis of urine and stone matrix of patients with kidney calculi

Project description:Proteins have been extracted from kidney calculi with SDS buffer. Proteins were seperated by 1D-SDS-PAGE and stained with coomassie. Each gel lane was cut into 5 (or 6) pieces. Proteins were digested in gel with trypsin. Tryptic peptides were analysed by nanoLC-MS/MS on an ion trap instrument (6340 Ion Trap, Agilent) with CID. Peak lists were generated with Mascot Distiller, and database searching was performed with Mascot. The data from 5 (or 6) LC-MS/MS runs from one patient ware merged into one mgf file, which was searched against IPI (human) database.

2016-07-11 | PXD000302 | Pride

Arabidopsis cell LC-MSMS - Proteomics analysis reveals a highly heterogeneous proteasome composition and the post-translational regulation of peptidase activity under pathogen signaling in plants

Project description:26S proteasome was affinity-purified with anti-FLAG beads and separated by 2-DE method. Each spot was cut and digested by Trypsin enzyme, which finaly applied for LC-MS/MS nalysis using a LTQ-Orbitrap XL (Thermo Scientific). The obtained spectra were compared against 35,386 sequences in The Arabidopsis Information Resource 10 (TAIR10; http://www.arabidopsis.org/) using the MASCOT server (version 2.4; Matrix Science) with the following search parameters: threshold set-off at 0.05 in the ion-score cut-off; protein identification cut-off set to two assigned spectra per predicted protein; peptide tolerance at 10 ppm; MS/MS tolerance at +/- 0.5 Da; peptide charge of 2+ or 3+; trypsin as the enzyme and allowing up to one missed cleavage; carboxymethylation on cysteines as a fixed modification and oxidation on methionine as a variable modification.

2014-07-28 | PXD000417 | Pride

Proteome-wide purification of O-GlcNAc proteins

Project description:Global O-GlcNAc profiling: proteome-wide purification and identification of O-GlcNAc proteins using GlcNAz metabolic labeling in combination with Click chemistry and label-free LC-MS/MS-based quantification. OGA inhibition: same workflow as 'Global O-GlcNAc profiling'; inhibition of O-GlcNAcase by a small molecule inhibitor. O-GlcNAc sites: identification of O-GlcNAc sites by metabolic labeling/Click chemistry followed by beta elimination Bioinformatics workflow of Global O-GlcNAc profiling and OGA inhibition experiments: Raw mass spectrometry files have been processed using Progenesis LC-MS (4.0) and exported as Mascot generic format for subsequent Mascot (2.3) database search. Mascot search results were processed using Mascot Percolator and the results have been imported back into Progenesis as well as imported to Scaffold (3.5.1). The Progenesis peptide quantification report has been exported as Excel file. Bioinformatics workflow of O-GlcNAc site identification: Raw mass spectrometry files have been processed using Mascot Distiller 2.3 and searched with Mascot. Mascot search results were processed using the Mascot Percolator and imported into Scaffold (3.5.1). After manual validation, peptide and protein identifications (Scaffold file) were imported into Scaffold PTM 2.0 for the estimation of site localization probabilities.

2013-01-10 | PXD000061 | Pride

Identification of telomere-binding proteins by enChIP-MS

Project description:We identified the telomere associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitaion (enChIP). Purified proteins were analyzed by GeLC-MS/MS. Tandem mass spectra were extracted by Proteome Discoverer 1.2. Database searchs were submitted to an in-house Mascot server version 2.4.1. Mascot was set up to search the Swissprot database assuming the digestion enzyme as trypsin. Carbamidomethylation of cysteine was set as a fixed modification. Oxidized methionine, acetylation of N terminus and conversion of glutamine to Pyro-Glu at N terminus were set as variable modifications. The precursor mass tolerances were 10 ppm and the tolerance of the MS/MS ions was 0.8 Da. In Scaffold 3.4.5, database search results were grouped according to gel bands.

2013-11-12 | PXD000461 | Pride

Arabidopsis Wdr8 interactors identification

Project description:To identify Arabidopsis Wdr8 interactors, immunoprecipitation associated LC-MS/MS analysis was carried out. Crude proteins extracted from Wdr8-GFP expressing transgenic plants was subjected to the immuno-precipitation assay using GFP antibody magnetic beads (µMACS GFP isolation kit, Miltenyi Biotec). Co-purified proteins were separated by 10% SDS-PAGE gel and stained with SYPRO Ruby (BioRad laboratories). The stained protein bands were excised into several fraction pieces according to protein sizes, and in-gel protein digestion by trypsin was carried out. Purified protein peptides were subjected to LC-MS/MS analysis (LTQ-Orbitrap XL-HTC-PAL system). Collected MS/MS peak spectra was analyzed by the MASCOT server to identify peptide sequence.

2022-02-17 | PXD026063 | Pride

Metastasis-repressive CircRNA MASCOT Regulates Distribution of the Splicing Factor hnRNP M

Project description:Alternative splicing (AS) diversifies the transcriptome complexity and is usually hijacked by cancer cells. Here, we identified heterogeneous nuclear ribonucleoprotein M (hnRNP M) as an indispensable contributor to EMT-related AS reprogramming, whose sub-nuclear distribution of hnRNP M is altered in metastatic tumors. Upon TGFβ stimulation, hnRNP M trends to disassociate with a circRNA called MASCOT (hnRNP M-ASsociated Circular RNA Of TGFβ) that demonstrated an impressive inhibitory effect on EMT process and tumor metastasis. Mechanistically, the anti-metastatic effect of MASCOT is attributed to not only its competition with U2 RNA splicing factors to recruit hnRNP M in the nucleoplasm, but also the anchorage of hnRNP M with nucleolin into the nucleolus to cause a temporospatial separation of hnRNP M from spliceosome. Moreover, the correlation between MASCOT expression and hnRNP M sub-nuclear localization was validated in clinical specimens. Our study deciphers the regulatory codes controlling AS networks and highlights MASCOT as a promising therapeutic to treat metastasis.

2022-09-20 | GSE213677 | GEO

Metastasis-repressive CircRNA MASCOT Regulates Distribution of the Splicing Factor hnRNP M

2022-09-10 | GSE165576 | GEO

Arabidopsis drought - A reciprocal 15N-labeling proteomic analysis of expanding Arabidopsis leaves subjected to osmotic stress indicates importance of mitochondria in preserving plastid functions

Project description:Mannitol induced drought stress, metabolic labeling experiment 14N control vs 15N mannitol induced drought stress, 0mM mannitol control experiment, LCMSMS of gel slice10 of 20, 1st of 2 replicas, 14 N peptide searching

2010-12-23 | PRD000246 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data