Reconstruction of the proto-mitochondrial metabolism

  • Gabaldón T
  • Huynen M
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Two new hypotheses explain the initial relationship between the alpha-proteobacterial ancestor (1, 2) of the mitochondrion (the proto-mitochondrion) and its host, one in which the proto-mitochondrion would have been an oxygen scavenger (3) and the other in which it would have been a hydrogen-producing, facultatively anaerobic species (4). Previous studies on the proto-mitochondrion's metabolism have been based on ~50 yeast mitochondrial proteins of alpha-proteobacterial origin (5). To also detect nonmitochondrial proteins of alpha-proteobacterial origin, we compared the proteins encoded by six alpha-proteobacterial genomes to a total of 77 genomes including nine eukaryotes, and derived their phylogenies. In the 22.525 reconstructed phylogenies, 630 orthologous groups showed a close evolutionary relationship between alpha-proteobacterial and eukaryotic proteins and did not indicate more recent horizontal transfer (6). We consider this a minimal estimate of the proto-mitochondrial proteome, because many of its genes have likely been lost from the sequenced eukaryotic genomes or do not have a strong enough phylogenetic signal to be detected in large-scale analyses. This is apparent in the mitochondrial genome of Reclinomonas americana for which our method retrieved 61% of the nonribosomal proteins

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