PXD008305

PXD008305 is an original dataset announced via ProteomeXchange.

Title	Time-resolved inducible knock-down of Clp protease subunits in tobacco identifies putative protease substrates
Description	The Clp protease complex in plants is the one with the highest complexity through all life kingdoms. It is composed of 14 nuclear- and plastid-encoded subunits which are allocated in different rings across the complex. The proteolytic ring (P-ring; ClpP3-ClpP6) and non-proteolytic ring (R-ring; ClpR1-ClpR4 and ClpP1) form the core complex playing an essential role in protein degradation and complex stabilization, respectively. The chaperones, ClpC1, ClpC2 and ClpD are involved in substrate folding and unfolding while accessory proteins, ClpT1 and ClpT2, are important to stabilize the core complex assembly. Adaptor proteins of the complex, ClpS and ClpF, recognize protease targets. Finding substrates of proteases is one of the remaining open questions in the protease field and specifically in the Clp protease. Several attempts were made analyzing the change of protein abundance in null clp mutants by proteomic analysis. However, null clp mutants are associated with massive accumulation of pleiotropic effects, as for example impaired growth and delayed in plant development, making impossible the detection of potential Clp substrates. To address this question, we design an ethanol (EtOH) inducible strategy to silence the expression of several subunits of the Clp protease in tobacco, and follow the change in protein abundance through the EtOH time-course. In this way, we distinguish between primary and secondary effects and determine time-resolved changes in proteins stability. Time-resolved proteomic analysechloroplast processes affected by the repression of Clp activity (e.g., photosynthesis and protein homeostasis).
HostingRepository	PRIDE
AnnounceDate	2022-02-22
AnnouncementXML	Submission_2022-02-22_04:08:44.021.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008305
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Silvia Martinez Jaime
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-11-27 23:46:06	ID requested
⏵ 1	2022-02-22 04:08:44	announced

Moreno JC, Mart, í, nez-Jaime S, Schwartzmann J, Karcher D, Tillich M, Graf A, Bock R, Temporal Proteomics of Inducible RNAi Lines of Clp Protease Subunits Identifies Putative Protease Substrates. Plant Physiol, 176(2):1485-1508(2018) [pubmed]

curator keyword: Biological

submitter keyword: Clp protease

chloroplast

protein degradation

protease substrate

Nicotiana tabacum

inducible RNAi

LC-MSMS

shotgun proteomics

Ralph Bock
contact affiliation	Max-Planck-Institut für Molekulare Pflanzenphysiologie Wisenschaftspark Golm Am Mühlenberg 1 14476 Potsdam, Germany
contact email	Bock@mpimp-golm.mpg.de
lab head
Silvia Martinez Jaime
contact affiliation	MPIMP
contact email	martinez@mpimp-golm.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD008305

PRIDE project URI

• PRIDE
  1. PXD008305
     1. Label: PRIDE project
     2. Name: Time-resolved inducible knock-down of Clp protease subunits in tobacco identifies putative protease substrates