Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana.
Chloroplast is a typical plant cell organelle where photosynthesis takes place. In this study, a total of 1,808 chloroplast core proteins in Arabidopsis thaliana were reliably identified by combining the results of previously published studies and our own predictions. We then constructed a chloroplast protein interaction network primarily based on these core protein interactions. The network had 22,925 protein interaction pairs which involved 2,214 proteins. A total of 160 previously uncharacterized proteins were annotated in this network. The subunits of the photosynthetic complexes were modularized, and the functional relationships among photosystem I (PSI), photosystem II (PSII), light harvesting complex of photosystem I (LHC I) and light harvesting complex of photosystem I (LHC II) could be deduced from the predicted protein interactions in this network. We further confirmed an interaction between an unknown protein AT1G52220 and a photosynthetic subunit PSI-D2 by yeast two-hybrid analysis. Our chloroplast protein interaction network should be useful for functional mining of photosynthetic proteins and investigation of chloroplast-related functions at the systems biology level in Arabidopsis.
Yu
Qing-Bo
QB
College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
Li
Guang
G
Wang
Guan
G
Sun
Jing-Chun
JC
Wang
Peng-Cheng
PC
Wang
Chen
C
Mi
Hua-Ling
HL
Ma
Wei-Min
WM
Cui
Jian
J
Cui
Yong-Lan
YL
Chong
Kang
K
Li
Yi-Xue
YX
Li
Yu-Hua
YH
Zhao
Zhongming
Z
Shi
Tie-Liu
TL
Yang
Zhong-Nan
ZN
D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D002736:Chloroplasts / Q000235:genetics* / Q000378:metabolism; D049452:Green Fluorescent Proteins / Q000032:analysis / Q000096:biosynthesis; D010788:Photosynthesis; D045322:Photosynthetic Reaction Center Complex Proteins / Q000235:genetics* / Q000378:metabolism; D045331:Photosystem I Protein Complex / Q000235:genetics / Q000378:metabolism; D045332:Photosystem II Protein Complex / Q000235:genetics / Q000378:metabolism; D020798:Two-Hybrid System Techniques
D029681:Arabidopsis Proteins; D045322:Photosynthetic Reaction Center Complex Proteins; D045331:Photosystem I Protein Complex; D045332:Photosystem II Protein Complex; D049452:Green Fluorescent Proteins