Protein degradation rate in Arabidopsis thaliana leaf growth and development

Lei Li, Clark J. Nelson, Josua Trösch, Ian Castleden, Shaobai Huang, A. Harvey Millar

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

We applied 15N labeling approaches to leaves of the Arabidopsis thaliana rosette to characterize their protein degradation rate and understand its determinants. The progressive labeling of new peptides with 15N and measuring the decrease in the abundance of >60,000 existing peptides over time allowed us to define the degradation rate of 1228 proteins in vivo. We show that Arabidopsis protein half-lives vary from several hours to several months based on the exponential constant of the decay rate for each protein. This rate was calculated from the relative isotope abundance of each peptide and the fold change in protein abundance during growth. Protein complex membership and specific protein domains were found to be strong predictors of degradation rate, while N-end amino acid, hydrophobicity, or aggregation propensity of proteins were not. We discovered rapidly degrading subunits in a variety of protein complexes in plastids and identified the set of plant proteins whose degradation rate changed in different leaves of the rosette and correlated with leaf growth rate. From this information, we have calculated the protein turnover energy costs in different leaves and their key determinants within the proteome.

Original languageEnglish
Pages (from-to)207-228
Number of pages22
JournalThe Plant Cell
Volume29
Issue number2
DOIs
Publication statusPublished - 1 Feb 2017

Fingerprint

protein degradation
Growth and Development
Arabidopsis
Proteolysis
growth and development
Arabidopsis thaliana
leaves
Proteins
proteins
peptides
Peptides
Arabidopsis Proteins
Plant Proteins
Plastids
Proteome
Growth
degradation
Hydrophobic and Hydrophilic Interactions
Isotopes
energy costs

Cite this

Li, Lei ; Nelson, Clark J. ; Trösch, Josua ; Castleden, Ian ; Huang, Shaobai ; Millar, A. Harvey. / Protein degradation rate in Arabidopsis thaliana leaf growth and development. In: The Plant Cell. 2017 ; Vol. 29, No. 2. pp. 207-228.
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Protein degradation rate in Arabidopsis thaliana leaf growth and development. / Li, Lei; Nelson, Clark J.; Trösch, Josua; Castleden, Ian; Huang, Shaobai; Millar, A. Harvey.

In: The Plant Cell, Vol. 29, No. 2, 01.02.2017, p. 207-228.

Research output: Contribution to journalArticle

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