PXD002476

PXD002476 is an original dataset announced via ProteomeXchange.

Title	Arabidopsis chloroplast N-terminome
Description	Protein N-termini are prone to post translational modification 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 and the N-termini of mature chloroplast proteins cannot be accurately predicted. This motivated an extensive characterization of chloroplast protein N-termini using terminal amine isotopic labeling of substrates (TAILS). Many nuclear-encoded plastid proteins accumulated with two or three different N-termini; we evaluated the significance of these different proteoforms. Ala, Val, Thr (often in N-α acetylated form) and Ser were the most frequently observed N-terminal residues, even after normalization for their frequency in the plastid proteome, while other residues were absent or highly under-represented. Plastid-encoded proteins showed a similar distribution of N-terminal residues, but with a higher frequency of Met. Infrequent residues such as Ile, Arg, Cys, Pro, Asp and Glu were observed for several abundant proteins 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 (Asp, Glu, Leu, Phe). 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. This work provides a baseline for understanding N-terminal processing and maturation of chloroplast proteins.
HostingRepository	PRIDE
AnnounceDate	2015-10-22
AnnouncementXML	Submission_2015-10-22_08:04:14.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002476
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Elden Rowland
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deaminated residue; 4x(2)H labeled alpha-dimethylamino N-terminal residue; dimethylated residue; 4x(2)H labeled dimethylated L-lysine; 4x(2)H labeled dimethylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-06 01:18:35	ID requested
⏵ 1	2015-10-22 08:04:15	announced

Rowland E, Kim J, Bhuiyan NH, van Wijk KJ, The Arabidopsis Chloroplast Stromal N-Terminome: Complexities of Amino-Terminal Protein Maturation and Stability. Plant Physiol, 169(3):1881-96(2015) [pubmed]

curator keyword: Biological

submitter keyword: N-terminome, Arabidopsis thaliana, proteolysis, protein maturation, protein processing, chloroplast protein import, chloroplast transit peptide, TAILS

Klaas van Wijk
contact affiliation	Dept. Plant Biology Cornell University
contact email	kv35@cornell.edu
lab head
Elden Rowland
contact affiliation	Cornell University
contact email	eer55@cornell.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002476
     1. Label: PRIDE project
     2. Name: Arabidopsis chloroplast N-terminome