Volume 18, No 10, Oct 2008
ISSN: 1001-0602
EISSN: 1748-7838 2018
impact factor 17.848*
(Clarivate Analytics, 2019)
Volume 18 Issue 10, October 2008: 1007-1019
ORIGINAL ARTICLES
Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana
Qing-Bo Yu1,5,*, Guang Li2,4,*, Guan Wang1,*, Jing-Chun Sun2,6, Peng-Cheng Wang1, Chen Wang1, Hua-Ling Mi3, Wei-Min Ma3, Jian Cui4, Yong-Lan Cui1, Kang Chong5, Yi-Xue Li7, Yu-Hua Li4, Zhongming Zhao6, Tie-Liu Shi2,7 and Zhong-Nan Yang1
1College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
2Shanghai Information Center for Life Science, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai 200032, China
3National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, The Chinese Academy of Sciences, Shanghai 200032, China
4College of Life Sciences, The Northeast Forestry University, Harbin, Heilongjiang 150040, China
5Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
6Department of Psychiatry and Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298, USA
7Bioinformation Center, Key Laboratory of System Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai 200232, China
Correspondence: Zhong-Nan Yang, Tie-Liu Shi,(znyang@shnu.edu.cn; tlshi@sibs.ac.cn )
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.
Cell Research (2008) 18:1007-1019. doi: 10.1038/cr.2008.286; published online 23 September 2008
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