Publication Information
Zhang et al., 2015
Abstract
Proteomics. 2015 Jul;15(14):2447-57. doi: 10.1002/pmic.201400530. Epub 2015 Apr
17.
Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted
degradation in Arabidopsis roots.
Zhang H(1)(2), Deery MJ(2), Gannon L(1), Powers SJ(3), Lilley KS(2), Theodoulou
FL(1).
Author information:
(1)Biological Chemistry and Crop Protection Department, Rothamsted Research,
Harpenden, UK.
(2)Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University
of Cambridge, Cambridge, UK.
(3)Computational and Systems Biology Department, Rothamsted Research, Harpenden,
UK.
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
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. All MS data have
been deposited in the ProteomeXchange with identifier PXD001719
(http://proteomecentral.proteomexchange.org/dataset/PXD001719).
© 2015 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA,
Weinheim.
DOI: 10.1002/pmic.201400530
PMCID: PMC4692092
PMID: 25728785 [Indexed for MEDLINE]
