PXD004550

PXD004550 is an original dataset announced via ProteomeXchange.

Title	Arabidopsis, protein turnover, plastid, leaf growth and development-15N progressive labelling
Description	In order to characterize plant protein degradation rates and understand their determinants as they relate to plant growth rate, we have applied 15N labelling approaches in leaves of the Arabidopsis rosette. We found a series of leaves in Arabidopsis plants for which the proteome was stable over time and degradation rates of individual proteins could thus be measured by considering the dilution of total protein abundance through growth. By progressively labelling new peptides with 15N and measuring the decrease in the abundance of over 60,000 peptides with natural isotope abundance profiles we determined the degradation rate of 1228 proteins. The exponential constant of the decay rate (KD) for each protein calculated from the relative isotope abundance of each peptide and the fold change in protein abundance during growth showed a wide distribution, ranging from 0 to 2 per day. This showed Arabidopsis protein half-lives vary from several hours to several months. In assessing intrinsic factors to explain these protein degradation rates, little effect of the N-end amino acid of proteins or of protein aggregation propensity were found, however protein complex membership and specific protein domains were strong predictors of degradation rate. We found new rapidly degrading subunits in a variety of protein complexes in plastids, identified the set of plant proteins whose degradation rate changes in different leaves of the rosette and correlated with leaf growth rate, and calculated the protein turnover energy costs in different leaves and their key determinants within the proteome.
HostingRepository	PRIDE
AnnounceDate	2017-02-01
AnnouncementXML	Submission_2017-02-01_04:59:01.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lei Li
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	6520 Quadrupole Time-of-Flight LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2016-07-11 05:53:27	ID requested
⏵ 1	2017-02-01 04:59:02	announced

Li L, Nelson CJ, Tr, ö, sch J, Castleden I, Huang S, Millar AH, Leaf Growth and Development. Plant Cell, 29(2):207-228(2017) [pubmed]

curator keyword: Biological

submitter keyword: Arabidopsis, protein turnover, plastid, leaf growth, development

Harvey Millar
contact affiliation	ARC CoE Plant Energy Biology, The University of Western Australia
contact email	harvey.millar@uwa.edu.au
lab head
Lei Li
contact affiliation	The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia
contact email	lei.li@uwa.edu.au
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/2017/02/PXD004550

PRIDE project URI

• PRIDE
  1. PXD004550
     1. Label: PRIDE project
     2. Name: Arabidopsis, protein turnover, plastid, leaf growth and development-15N progressive labelling