Publication Information
Rowland et al., 2015
Abstract
Plant Physiol. 2015 Nov;169(3):1881-96. doi: 10.1104/pp.15.01214. Epub 2015 Sep
14.
The Arabidopsis Chloroplast Stromal N-Terminome: Complexities of Amino-Terminal
Protein Maturation and Stability.
Rowland E(1), Kim J(1), Bhuiyan NH(1), van Wijk KJ(2).
Author information:
(1)Department of Plant Biology, Cornell University, Ithaca, New York 14850.
(2)Department of Plant Biology, Cornell University, Ithaca, New York 14850
kv35@cornell.edu.
Protein amino (N) termini are prone to modifications and are major determinants
of protein stability in bacteria, eukaryotes, and perhaps also in chloroplasts.
Most chloroplast proteins undergo N-terminal maturation, but this is poorly
understood due to insufficient experimental information. Consequently, N termini
of mature chloroplast proteins cannot be accurately predicted. This motivated an
extensive characterization of chloroplast protein N termini in Arabidopsis
(Arabidopsis thaliana) using terminal amine isotopic labeling of substrates and
mass spectrometry, generating nearly 14,000 tandem mass spectrometry spectra
matching to protein N termini. Many nucleus-encoded plastid proteins accumulated
with two or three different N termini; we evaluated the significance of these
different proteoforms. Alanine, valine, threonine (often in N-α-acetylated
form), and serine were by far the most observed N-terminal residues, even after
normalization for their frequency in the plastid proteome, while other residues
were absent or highly underrepresented. Plastid-encoded proteins showed a
comparable distribution of N-terminal residues, but with a higher frequency of
methionine. Infrequent residues (e.g. isoleucine, arginine, cysteine, proline,
aspartate, and glutamate) were observed for several abundant proteins (e.g. heat
shock proteins 70 and 90, Rubisco large subunit, and ferredoxin-glutamate
synthase), likely reflecting functional regulation through their N termini. In
contrast, the thylakoid lumenal proteome showed a wide diversity of N-terminal
residues, including those typically associated with instability (aspartate,
glutamate, leucine, and phenylalanine). We propose that, after cleavage of the
chloroplast transit peptide by stromal processing peptidase, additional
processing by unidentified peptidases occurs to avoid unstable or otherwise
unfavorable N-terminal residues. The possibility of a chloroplast N-end rule is
discussed.
© 2015 American Society of Plant Biologists. All Rights Reserved.
DOI: 10.1104/pp.15.01214
PMCID: PMC4634096
PMID: 26371235 [Indexed for MEDLINE]
