Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots

A - Papers appearing in refereed journals

Zhang, H., Deery, M. J., Gannon, L., Powers, S. J., Lilley, K. S. and Theodoulou, F. L. 2015. Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots. Proteomics. 15 (14), pp. 2447-2457.

AuthorsZhang, H., Deery, M. J., Gannon, L., Powers, S. J., Lilley, K. S. and Theodoulou, F. L.
Abstract

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 ().

KeywordsBiochemical Research Methods; Biochemistry & Molecular Biology
Year of Publication2015
JournalProteomics
Journal citation15 (14), pp. 2447-2457
Digital Object Identifier (DOI)doi:10.1002/pmic.201400530
PubMed ID25728785
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeDesigning Seeds for Nutrition and Health (DS)
Publisher's version
Publication process dates
Accepted24 Feb 2015
PublisherWiley
Grant IDBB/J017647/1
BB/J016276/1
ISSN1615-9853

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