1. ¹College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
2. ²Shanghai Information Center for Life Science, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai 200032, China
3. ³National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, The Chinese Academy of Sciences, Shanghai 200032, China
4. ⁴College of Life Sciences, The Northeast Forestry University, Harbin, Heilongjiang 150040, China
5. 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
6. ⁶Department of Psychiatry and Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298, USA
7. ⁷Bioinformation Center, Key Laboratory of System Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai 200232, China

Correspondence: Zhong-Nan Yang, Tel: +86-2164324650; Fax: +86-2164322142 E-mail: znyang@shnu.edu.cn; Tie-Liu Shi, Tel: +86-2154922980; E-mail: tlshi@sibs.ac.cn

^*These three authors contributed equally to this work.

Received 15 October 2007; Revised 10 January 2008; Accepted 7 April 2008.

Abstract

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.