Experimental Analysis of the Rice Mitochondrial Proteome, Its Biogenesis, and Heterogeneity

Mitochondria in rice (Oryza sativa) are vital in expanding our understanding of the cellular response to reoxygenation of tissuesafter anaerobiosis, the crossroads of carbon and nitrogen metabolism, and the role of respiratory energy generation incytoplasmic male sterility. We have combined density gradient and surface charge purification techniques with proteomics toprovide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. Quantitativecomparisons of mitochondria purified by density gradients and after further surface charge purification have been used toensure that the proteins identified copurify with mitochondria and to remove contaminants from the analysis. This rigorousapproach to defining a subcellular proteome has yielded 322 nonredundant rice proteins and highlighted contaminants inpreviously reported rice mitochondrial proteomes. Comparative analysis with the Arabidopsis (Arabidopsis thaliana) mitochondrialproteome reveals conservation of a broad range of known and unknown function proteins in plant mitochondria,with only approximately 20% not having a clear homolog in the Arabidopsis mitochondrial proteome. As in Arabidopsis, onlyapproximately 60% of the rice mitochondrial proteome is predictable using current organelle-targeting prediction tools. Use ofthe rice protein data set to explore rice transcript data provided insights into rice mitochondrial biogenesis during seedgermination, leaf development, and heterogeneity in the expression of nucleus-encoded mitochondrial components in differentrice tissues. Highlights include the identification of components involved in thiamine synthesis, evidence for coexpressed andunregulated expression of specific components of protein complexes, a selective anther-enhanced subclass of the decarboxylatingsegment of the tricarboxylic acid cycle, the differential expression of DNA and RNA replication components, andenhanced expression of specific metabolic components in photosynthetic tissues.