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Published on November 14, 2008; 10.1104/pp.108.131300

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Received October 15, 2008
Accepted November 12, 2008

Experimental analysis of the rice mitochondrial proteome, its biogenesis and heterogeneity

Shaobai Huang , Nicolas L. Taylor , Reena Narsai , Holger Eubel , James Whelan , and A. Harvey Millar *

ARC Centre of Excellence in Plant Energy Biology, M316, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia

* Corresponding author; email: hmillar{at}cyllene.uwa.edu.au.

Mitochondria in rice are vital in expanding our understanding of cellular response to reoxygenation of tissues after anaerobiosis, the cross-roads of carbon and nitrogen metabolism, and the role of respiratory energy generation in cytoplasmic male sterility. We have combined density gradient and surface change purification techniques with proteomics to provide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. Quantitative comparisons of mitochondria purified by density gradients and after further surface charge purification has been used to ensure the proteins identified co-purify with mitochondria and to remove contaminants from the analysis. This rigorous approach to defining a sub-cellular proteome has yielded 322 non-redundant rice proteins and highlighted contaminants in previously reported rice mitochondrial proteomes. Comparative analysis to the Arabidopsis mitochondrial proteome reveals conservation of a broad range of known and unknown function proteins in plant mitochondria with only ~20% not having a clear homolog in the Arabidopsis mitochondrial proteome. Like in Arabidopsis, only ~60% of the rice mitochondrial proteome is predictable using current organelle targeting prediction tools. Use of the rice protein dataset to explore rice transcript data provided insights into rice mitochondrial biogenesis during seed germination, leaf development and heterogeneity in the expression of nuclear-encoded mitochondrial components in different rice tissues. Highlights include identification of components involved in thiamine synthesis, evidence for co-expressed and unregulated expression of specific components of protein complexes, a selective anther-enhanced subclass of the decarboxylating segment of the TCA cycle, the differential expression of DNA and RNA replication components, and enhanced expression of specific metabolic components in photosynthetic tissues.




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