Database Construction Of Chloroplast Proteins Interaction And Mining Functions Of Proteins Related To Photosynthesis In Arabidopsis Thaliana

Chloroplast is a very important organelle of plant cells. Besides photosynthesis,it also carries out other essential metabolism. In model plant Arabidopsis thaliana, atotal of 87 chloroplast proteins are encoded by plastomes, and about 4255nulcear-encoded proteins are predicted to be located in chloroplast. The functions ofmost chloroplast proteins are identified based on sequence homology, and about 25%of chloroplast proteins are still unknown. In this dissertation, chloroplast proteinfunctions in Arabidopsis thaliana were investigated, using both bioinformatics andmolecular biology techniques. Firstly, a chloroplast protein interaction database wasconstructed using three bioinformatics methods. A total of 8157 pairs of chloroplastprotein interactions were predicted based on protein interlogs from data of other 5species; a total of 19652 pairs were predicted based on the phylogenetic profile; and atotal of 65299 pairs were predicted based on the expression level of genes from 79gene chips data downloaded from TAIR with the coefficient of the gene co-expressionmore than 0.9000. After the chloroplast protein interactions database was constructed,protein interactions in the database were analyzed. The protein pairs in the databasewere involved in metabolic pathways such as protein transport, starches, lipidmetabolites and photosynthesis. Our database also showed that some unknownproteins interact with subunits of four major complexes in photosynthesis, and mostproteins interacting with STN7 or STN8, which are responsible for thephosphorylation in photosynthesis were protein kinases. Finally, a total of 46 proteininteraction pairs were validated by two-hybrid experiments. Our results indicated thatone unknown protein C interacts with psaD2, a protein of photosystem I. Thus, it isquite possible that the unknown protein C is involved in photosynthesis. The databasewould facilitate us the further investigation of the chloroplast systems biology andfunctional mining of proteins related to photosynthesis in Arabidopsis thaliana.