Cytoplasmic regulation of the accumulation of nuclear-encoded proteins in the mitochondrial proteome of maize

Mitochondria from normal (NA)- and Texas (T)-cytoplasm maize (Zea mays L.) were purified from unpollinated ears via Percoll centrifugation. Approximately 300 mitochondrial proteins were resolved using two-dimensional (2-D) electrophoresis. The 197 most abundant proteins were analyzed by matrix-assisted laser desorption lonization time-of-flight (MALDI-ToF) mass spectrometry involving overlapping pH gradients (pH 4-7 and 6-9). Database searches identified 58 genes that encode 100 of these protein spots. Functions could be predicted for 38 of the 58 genes (66%). All but one of these genes are located in the nuclear genome. Thirteen per cent of the analyzed protein spots (25 out of 197) exhibited at least a threefold difference in accumulation between the mitochondrial proteomes of NA- or T-cytoplasm maize plants that had essentially identical nuclear genomes. As most of these proteins were nuclear-encoded, these findings demonstrate that the genotype of a mitochondrion can regulate the accumulation of the nuclear-encoded fraction of its proteome. About half (27 out of 58) of the maize mitochondrial proteins identified in this study were not recovered in previous analyses of the Arabidopsis and rice mitochondrial proteomes.