This Article Full Text Full Text (PDF) Supplemental Data All Versions of this Article: 20/6/1603    most recent tpc.108.060541v1 Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via CrossRef Google Scholar Articles by Lee, D. W. Articles by Hwang, I. PubMed PubMed Citation Articles by Lee, D. W. Articles by Hwang, I. Agricola Articles by Lee, D. W. Articles by Hwang, I.

Arabidopsis Nuclear-Encoded Plastid Transit Peptides Contain Multiple Sequence Subgroups with Distinctive Chloroplast-Targeting Sequence Motifs^[W]

^a Laboratory of Cellular Systems Biology, Division of Molecular and Life Sciences, POSTECH, Pohang 790-784, Korea
^b Department of Computer Science, POSTECH, Pohang 790-784, Korea
^c Laboratory of Structural Bioinformatics, Division of Molecular and Life Sciences, POSTECH, Pohang 790-784, Korea

² Address correspondence to sukim{at}postech.ac.kr or ihhwang{at}postech.ac.kr.

The N-terminal transit peptides of nuclear-encoded plastid proteins are necessary and sufficient for their import into plastids, but the information encoded by these transit peptides remains elusive, as they have a high sequence diversity and lack consensus sequences or common sequence motifs. Here, we investigated the sequence information contained in transit peptides. Hierarchical clustering on transit peptides of 208 plastid proteins showed that the transit peptide sequences are grouped to multiple sequence subgroups. We selected representative proteins from seven of these multiple subgroups and confirmed that their transit peptide sequences are highly dissimilar. Protein import experiments revealed that each protein contained transit peptide–specific sequence motifs critical for protein import into chloroplasts. Bioinformatics analysis identified sequence motifs that were conserved among members of the identified subgroups. The sequence motifs identified by the two independent approaches were nearly identical or significantly overlapped. Furthermore, the accuracy of predicting a chloroplast protein was greatly increased by grouping the transit peptides into multiple sequence subgroups. Based on these data, we propose that the transit peptides are composed of multiple sequence subgroups that contain distinctive sequence motifs for chloroplast targeting.