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.
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Abbreviations
- TAIR:
-
(the Arabidopsis information database)
- PPDB:
-
(plant plastid database)
- MS:
-
(mass spectrometry)
- PSI:
-
(photosystem I)
- PSII:
-
(photosystem II)
- LHC I:
-
(light-harvesting complex of photosystem I)
- LHC II:
-
(light-harvesting complex of photosystem II)
- GO:
-
(gene ontology)
- GFP:
-
(green fluorescent protein)
- GOM:
-
(global optimization method)
- FDR:
-
(false discovery rate)
- CCs:
-
(correlation coefficients)
- BLAST:
-
(basic local alignment search tool)
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Acknowledgements
We thank the RIKEN BRC in Japan for provision of all full-length cDNA in this study. National Natural Science Foundation of China (grants numbers 30530100 and 90408010), the State Key Program of Basic Research of China (grant numbers 2007CB947600 and 2007CB108800), and Hi-Tech Research and Development Program of China (grant number 2006AA02Z313) supported this project.
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Supplementary information
Supplementary information, Figure S1
The flowchart to construct chloroplast protein interaction network in Arabidopsis thaliana. (PDF 81 kb)
Supplementary information, Table S1
7,592 putative chloroplast proteins from nine different methods. (XLS 1390 kb)
Supplementary information, Table S2
1,720 chloroplast core proteins encoded by the nuclear genome obtained in this work. (XLS 308 kb)
Supplementary information, Table S3
Chloroplast protein interactions integrated by the naive Bayesian Method. (XLS 1455 kb)
Supplementary information, Table S4
Chloroplast protein interactions predicted based on microarray data (Pearson Coefficient >= 0.95) (XLS 534 kb)
Supplementary information, Table S5
Function Annotation With Arabidopsis chloroplast protein interaction network. (TXT 7 kb)
Supplementary information, Table S6
12 predicted protein interactions selected for Yeast two-hybrid experiment (DOC 26 kb)
Supplementary information, Table S7
The Pearson correlation coefficients (CCs) between each comparison pair of nine data sets (XLS 26 kb)
Supplementary information, Table S8
GSP/GSN- the number of protein pairs in given classes that were present in the gold standard positive/negative set of interactions (DOC 42 kb)
Supplementary information, Table S9
The Primers used in this study (DOC 41 kb)
Supplementary information, Data S1
Nine genome-scale data sets of putative chloroplast proteins (DOC 70 kb)
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Yu, QB., Li, G., Wang, G. et al. Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana. Cell Res 18, 1007–1019 (2008). https://doi.org/10.1038/cr.2008.286
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DOI: https://doi.org/10.1038/cr.2008.286
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