The present invention relates to isolated nucleic acid molecules which restore fertility to cytoplasmic male sterile plants and modify expression of toxic mitochondria proteins by the plant. The present invention also relates to methods of identifying a candidate plant suitable for breeding with a cytoplasmic male sterile plant and methods of identifying a candidate gene restoring fertility in plants by analyzing for the candidate plant and candidate gene, respectively, for the presence of the nucleic acid molecule of the present invention. Also disclosed are methods of producing hybrid plant seed, methods of directing gene expression to plant mitochondria, and method of expressing a gene preferentially in roots of a plant. Promoters and terminators from plant genes which restore fertility to cytoplasmic male sterile plants and modify expression of toxic mitochondria proteins are also disclosed. Finally, methods of producing plants with a cytoplasmic male sterile plant restoration system are disclosed.