Mitochondria contain their own DNA, as well as the transcription and translation machinery necessary to express the genes encoded in this DNA. The size of the mitochondrial genome varies dramatically and most mitochondrial DNAs, regardless of size, encode a common subset of the proteins required for the ETS. These include a few of the most hydrophobic subunits of complexes I, III, and IV, and the mitochondrial ATP synthase. In addition, the mitochondrial genome carries genes for the ribosomal RNAs and many (in some cases all) of the tRNAs required for mitochondrial protein synthesis. A large majority of the subunits of the respiratory complexes, however, are encoded in nuclear DNA, synthesized on cytoplasmic ribosomes, and subsequently transported into the mitochondrion. The nuclear-encoded mitochondrial protein genes were presumably transferred there from an ancestral endosymbiont's genome. The retention of the entire mitochondrial genetic apparatus just to synthesize a small set of mitochondrial polypeptides is curious.
Many mitochondrial genes possess peculiar features that would prevent their translation in the cytoplasm of the cell. In human mitochondria, the codon UGA, normally a stop codon in the so-called universal genetic code, is translated as tryptophan, and the codon AUA, normally an isoleucine codon, is translated as methionine. In mitochondrial DNA
from baker's yeast, Saccharomyces cerevisiae, in addition to the same deviations from the genetic code observed in human mitochondria, CUA, CUC, CUG, and CUU codons (normally leucine) are translated as the amino acid threonine. Furthermore, numerous mitochondrial mRNAs (e.g., in plant and trypanosome mitochondria) are edited, some through the conversion of specific cytidines to uridines and others through the insertion and deletion of uridines, in both cases altering the resulting polypeptide sequence. Finally, mitochondrial genes in many organisms (other than vertebrates) contain introns that are spliced out of the RNA by mechanisms that differ significantly from the predominant mechanism of nuclear mRNA splicing. Such variations in coding sequences would most likely impede any further transfer of genes from the mitochondrial genome to the nuclear genome.
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