Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protease activities induced in the apoplast of the resistant tomato cultivar Hawaii 7996 in response to Ralstonia solanacearum infection

ABSTRACT: In the work presented here we aimed to identify the active proteases secreted in the apoplast of the resistant tomato Hawaii 7996 when challenged with R. solanacearum and compared it with that of the susceptible cultivar Marmande. Using ABPP we characterized a variety-specific induction of papain-like cysteine proteases and serine hydrolases.. Altogether this work denotes the importance of novel proteomic approaches –such as ABPP– to provide new insights on old yet elusive questions regarding the molecular basis of resistance to R. solanacearum.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Ralstonia Solanacearum (strain Gmi1000) (pseudomonas Solanacearum) Solanum Lycopersicum

TISSUE(S): Leaf

SUBMITTER: Farnusch Kaschani

LAB HEAD: Farnusch Kaschani

PROVIDER: PXD005603 | Pride | 2018-05-18

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ACE_0183_MP01.raw	Raw
	ACE_0183_MP02.raw	Raw
	ACE_0183_MP03.raw	Raw
	ACE_0183_MP04.raw	Raw
	ACE_0183_MP05.raw	Raw

Items per page:

1 - 5 of 28

Publications

Protease Activities Triggered by <i>Ralstonia solanacearum</i> Infection in Susceptible and Tolerant Tomato Lines.

Planas-Marquès Marc M Bernardo-Faura Martí M Paulus Judith J Kaschani Farnusch F Kaiser Markus M Valls Marc M van der Hoorn Renier A L RAL Coll Núria S NS

Molecular & cellular proteomics : MCP 20180309 6

Activity-based protein profiling (ABPP) is a powerful proteomic technique to display protein activities in a proteome. It is based on the use of small molecular probes that react with the active site of proteins in an activity-dependent manner. We used ABPP to dissect the protein activity changes that occur in the intercellular spaces of tolerant (Hawaii 7996) and susceptible (Marmande) tomato plants in response to <i>R. solanacearum</i>, the causing agent of bacterial wilt, one of the most dest ...[more]

PMID: 29523767

Similar Datasets

Arabidopsis Col-5 challenged with Ralstonia solanacearum BCCF401

Project description:Arabidopsis plants were challenged with Ralstonia solanacearum isolate BCCF401 and expression profiles investigated during early and late wilt symptom development. Keywords: Disease state analysis A direct comparison was performed. Two replicate biological experiments were performed and two technical replicates with dye swap were included in each biological replicate.

2010-11-22 | E-GEOD-19178 | biostudies-arrayexpress

Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins:Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins:Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins:Mass Spectrometry (MS)-based quantitative profiling of Se-probes-reactive proteins

Project description:We performed MS-based quantitative profiling of Se-probes-reactive proteins by ABPP using stable isotope reductive dimethylation method.

2023-12-07 | PXD046856 | Pride

Identification of sulfhydryl-containing proteins and further evaluation of the selenium- tagged redox homeostasis-regulating proteins:Identification of cysteine sites using tandem orthogonal proteolysis strategy (TOP-ABPP).

Project description:We sought to identify exact modified cysteine sites by Se-probes using TOP-ABPP strategy and the acid cleavable azide-biotin tag was used to enrich and release the modified peptides for LC-MS/MS analys

2023-12-07 | PXD046852 | Pride

comparative genomic hybridization by array of Ralstonia solanacearum different phyloptypes.

Project description:Natural transformation between different phylotypes in Ralstonia solanacearum species complex

2010-10-01 | E-MEXP-2660 | biostudies-arrayexpress

Activity-based protein profiling assay for functional biocatalyst screening in white rot fungus Phanerochaete chrysosporium grown on beech wood chips

Project description:Activity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications mainly in the field of biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from Phanerochaete chrysosporium suspension cultures grown on beech wood chips. P. chrysosporium is a thermophilic white rot fungus that expresses a large enzyme repertoire for efficient lignocellulose hydrolysis. By employing a comparative ABPP approach, we could preselect lignocellulose-degrading serine and glycoside hydrolases from this enzyme repertoire for further biochemical characterization. In addition to the supernatant, also a substrate-bound protein fraction isolated from wood chips was screened for active enzymes. As heterologous expression of fungal enzymes remains challenging, our ABPP-mediated preselection procedure allows to focus experimental efforts on the most promising biocatalysts. Besides, we show that this approach can also be used to functionally annotate domains-of-unknown functions (DUFs). ABPP-based biocatalyst screening may thus allow the elucidation of biocatalysts with novel gene sequences, and we anticipate that the presented ABPP approach will find wider applications both in the discovery of novel biocatalysts and in revealing the catalytic activity of hitherto unknown enzymes.

2023-03-11 | PXD030618 | Pride

Comparative genomic hybridization of 17 strains of Ralstonia solanacearum, one strain of R. syzygii and one strain of R. pickettii

Project description:comparison of gene content between 17 strains of Ralstonia solanacearum, one strain of R. syzygii and one strain of R. pickettii

2006-11-25 | E-MEXP-851 | biostudies-arrayexpress

Comparative genomic hybridization of Ralstonia solanacearum strains to detect horizontal gene transfer

Project description:Comparison of gene content between R. solanacearum strains GMI1000, NCPPB332, GMI1000::NCPPB332 recombinants, CFBP2968 and GMI1000::CFBP2968 recombinants

2009-04-09 | E-MEXP-2012 | biostudies-arrayexpress

ABPP-HT* - Deep meets fast for activity-based profiling of deubiquitylating enzymes using advanced DIA mass spectrometry methodsABPP-HT* - Deep meets fast for activity-based profiling of deubiquitylating enzymes using advanced DIA mass spectrometry methods

Project description:Activity-based protein profiling (ABPP) uses a combination of activity-based chemical probes with mass spectrometry (MS) to selectively characterise a particular enzyme or enzyme class. ABPP has proven invaluable for profiling enzymatic inhibitors in drug discovery. When applied to cell extracts and cells, challenging the ABP-enzyme complex formation with a small molecule can simultaneously inform on potency, selectivity, reversibility/binding affinity, permeability, and stability. ABPP can also be applied to pharmacodynamic studies to inform on cellular target engagement within specific organs when applied to in vivo models. Recently, we established separate high depth and high throughput ABPP (ABPP-HT) protocols for the profiling of deubiquitylating enzymes (DUBs). However, the combination of the two, deep and fast, in one method has been elusive. To further increase the sensitivity of the current ABPP-HT workflow we implemented state-of-the-art data-independent acquisition (DIA) and data-dependent acquisition (DDA) MS analysis tools. Hereby, we describe an improved methodology, ABPP-HT* (enhanced high-throughput-compatible activity-based protein profiling), that in combination with DIA MS methods allowed for the consistent profiling of 35-40 DUBs and provided a reduced number of missing values, whilst maintaining a throughput of 100 samples per day.

2022-04-04 | PXD031848 | Pride

SITE-SPECIFIC ACTIVITY-BASED PROTEIN PROFILING USING PHOSPHONATE HANDLES

Project description:Most drug molecules target proteins. Identification of the exact drug binding sites on these proteins is essential to understand and predict how drugs affect protein structure and function. To address this challenge, we developed a strategy that uses IMAC-enrichable phosphonate affinity tags, for efficient and selective enrichment of peptides bound to an activity-based probe (ABP), enabling the identification of the exact drug binding site. As a proof of concept, using this approach, termed PhosID–ABPP (Activity-based protein profiling), over 500 unique binding sites were reproducibly identified of an alkynylated Afatinib derivative (PF-06672131). As PhosID–ABPP is compatible with intact cell inhibitor treatment, we investigated the quantitative differences in approachable binding sites in intact cells and in lysates of the same cell line and observed and quantified substantial differences. Moreover, an alternative protease digestion approach was used to capture the previously reported binding site on the epidermal growth factor receptor (EGFR), which turned out to remain elusive when using solely trypsin as protease. Overall, we find that PhosID–ABPP is highly complementary to biotin-based enrichment strategies in activity-based protein profiling studies, with PhosID–ABPP providing the advantage of direct ABP-interaction site identification.

2023-01-10 | PXD036569 | Pride

Transcriptome analysis of neuromuscular junction during degeneration and regeneration of axon terminal

Project description:The neuromuscular junction (NMJ) is a specialized tripartite synapse composed of the motor axon terminal, covered by perisynaptic Schwann cells (PSCs), and the muscle fibre, separated by a basal lamina. It is exposed to different kind of injures such as mechanical traumas, pathogens including neurotoxins, and neuromuscular diseases such as amyotrophic lateral sclerosis and immune-mediated disorders, and has retained throughout vertebrate evolution an intrinsic ability for repair and regeneration, at variance from central synapses1. Following peripheral nerve injury, an intense but poorly defined crosstalk takes place at the NMJ among its components, functional to nerve terminal regeneration. To identify crucial factors released by PSCs and the muscle to induce nerve regrowth, we performed a transcriptome analysis of the NMJ at different time points after injection of -latrotoxin, a presynaptic neurotoxin isolated from the venom of the black widow spider. This toxin is a simple and controlled method to induce an acute, localized and reversible nerve terminal degeneration not blurred by inflammation, and can help to identify molecules involved in the intra- and inter-cellular signalling governing NMJ regeneration.

2017-05-30 | E-MTAB-5730 | biostudies-arrayexpress

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