Origin and evolution of the mitochondrial proteome

The endosymbiotic theory for the origin of mitochondria requires substantia l modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha -proteobacter ia symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from alpha -proteobacteria. Random mutations in the form of deletions large and small seem to have elim inated nonessential genes from the endosymbiont-mitochondrial genome lineag es. This process, together with the transfer of genes from the endosymbiont -mitochondrial genome to nuclei, has led to a marked reduction in the size of mitochondrial genomes. All proteins of bacterial descent that are encode d by nuclear genes were probably transferred by the same mechanism, involvi ng the disintegration of mitochondria ol bacteria by the intracellular memb ranous vacuoles of cells to release nucleic acid fragments that transform t he nuclear genome. This ongoing process has intermittently introduced bacte rial genes to nuclear. genomes. The genomes of the last common ancestor of all organisms, in particular of mitochondria, encoded cytochrome oxidase ho mologues. There are no phylogenetic indications either in the mitochondrial proteome ol in the nuclear genomes that the initial or subsequent function of the ancestor to the mitochondria was anaerobic. In contrast there are i ndications that relatively advanced eukaryotes adapted to anaerobiosis by d ismantling their mitochondria and refitting them as hydrogenosomes. Accordi ngly, a continuous history of aerobic respiration seems to have been the fa te of most mitochondrial lineages. The initial phases of this history may h ave involved aerobic respiration by the symbiont functioning as a scavenger of toxic oxygen. The transition to mitochondria capable of active ATP expo rt to the host cell seems to have required recruitment of eukaryotic ATP tr ansport proteins from the nucleus. The identity of the ancestral host of th e alpha -proteobacterial endosymbiont is unclear; but there is no indicatio n that it was an autotroph. There are no indications of a specific alpha -p roteobacterial origin to genes for glycolysis. In the absence of data to th e contrary it is assumed that the ancestral host cell was a heterotroph.