Lili Liu, Li Jiang and Ming Chen Pages 583 - 590 ( 8 )
Protein subcellular localization has been a long-standing key problem in investigating proteins’ function, which provides important clues for revealing their functions and aids in understanding their interactions with other biomolecules at the cellular level. Here, we systematically defined the organelle-focused proteomes and interactomes in Oryza sativa. A total of 83.42% of the whole rice proteome obtained their subcellular localizations based on manual annotation, manual adjustment and predictors’ cross validation. The final organelle-focused interactomes were located in nine organelles. Furthermore, we discussed the cross talk bias between different organelles and the function organization accounting for nine organelles. Motif analysis illustrated the protein interaction bias in different organelles to implement certain biology functions. We exemplified the connection between functions and the overrepresented motifs in the organelle-focused interactomes and exemplified how to infer the functions of unknown proteins via expanding the overrepresented motifs.
Function enrichment analysis, motif analysis, organelle-focused interactome, organelle-focused proteome, rice.
Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.