PXD001719

PXD001719 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots
Description	According to the Arg/N-end rule pathway, proteins with basic N-termini are targeted for degradation by the Arabidopsis thaliana E3 ligase, PROTEOLYSIS6 (PRT6). Proteins can also become PRT6 substrates following post-translational arginylation by arginyltransferases ATE1 and 2. Here, we undertook a quantitative proteomics study of Arg/N-end rule mutants, ate1/2 and prt6, to investigate the impact of this pathway on the root proteome. Tandem mass tag (TMT) labelling identified a small number of proteins with increased abundance in the mutants, some of which represent downstream targets of transcription factors known to be N-end rule substrates. Isolation of N-terminal peptides using terminal amine isotope labelling of samples (TAILS) combined with triple dimethyl labelling identified 1465 unique N-termini. Stabilising residues were over-represented among the free neo-N-termini, but destabilising residues were not markedly enriched in N-end rule mutants. The majority of free neo-N-termini were revealed following cleavage of organellar targeting signals, thus compartmentation may account in part for the presence of destabilising residues in the wild type N-terminome. Our data suggest that PRT6 does not have a marked impact on the global proteome of Arabidopsis roots and is likely involved in the controlled degradation of relatively few regulatory proteins.
HostingRepository	PRIDE
AnnounceDate	2015-03-26
AnnouncementXML	Submission_2015-03-26_07:56:57.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hongtao Zhang
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	deamidated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; dimethylated residue; 4x(2)H labeled dimethylated residue; TMT6plex-126 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-01-21 08:15:09	ID requested
⏵ 1	2015-03-26 07:56:58	announced

Zhang H, Deery MJ, Gannon L, Powers SJ, Lilley KS, Theodoulou FL, Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots. Proteomics, 15(14):2447-57(2015) [pubmed]

curator keyword: Biological

submitter keyword: N-end rule, quantitative proteomics, root, TMT, TAILS

Frederica L. Theodoulou
contact affiliation	Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
contact email	freddie.theodoulou@rothamsted.ac.uk
lab head
Hongtao Zhang
contact affiliation	Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
contact email	hongtao.zhang@rothamsted.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001719
     1. Label: PRIDE project
     2. Name: Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots