Abstract
Protein-protein interactions are critical for most cellular processes; however, many remain to be identified. Here, to comprehensively identify protein complexes in photosynthetic organisms, we applied the recently developed approach of blue native PAGE (BN-PAGE) coupled with LC-MS/MS to the thylakoid proteins of Arabidopsis thaliana and the whole cell proteins of whole cell proteins of Synechocystis sp. PCC 6803. We identified 245 proteins from the purified Arabidopsis thylakoid membranes and 1,458 proteins from the whole cells of Synechocystis using the method. Next, we generated protein migration profiles that were assessed by plotting the label-free estimations of protein abundances versus migration distance in BN-PAGE. Comparisons between the migration profiles of the major photosynthetic complexes and their band patterns showed that the protein migration profiles were well correlated. Thus, the protein migration profiles allowed us to estimate the molecular size of each protein complex and to identify co-migrated proteins with the proteins of interest by determining the protein pairs that contained peaks in the same gel slice. Finally, we built the protein co-migration database for photosynthetic organisms (PCoM-DB: http://pcomdb.lowtem.hokudai.ac.jp/proteins/top) to make our data publicly accessible online, which stores the analyzed data with a user-friendly interface to compare the migration profiles of proteins of interest. It helps users to find unidentified protein complexes in Arabidopsis thylakoids and Synechocystis cells. The accumulation of the data from the BN-PAGE coupled with LC-MS/MS should reveal unidentified protein complexes and should aid in understanding the adaptation and the evolution of photosynthetic organisms.