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Reconstruction of the Proto-Mitochondrial Metabolism

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Science  01 Aug 2003:
Vol. 301, Issue 5633, pp. 609
DOI: 10.1126/science.1085463

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 (6).

For a number of pathways [β-oxidation and a complete electron transport chain; fructose/mannose metabolism pathways; and for the synthesis of lipids, biotine, heme, and iron-sulfur clusters], the fraction of recovered proteins among the 630 groups is high enough to suggest they were complete in the proto-mitochondrion (Fig. 1). The citric acid cycle (7) and pentose phosphate pathway can only partially be recovered, whereas enzymes for amino acid and nucleotide metabolism, although well represented, contain relatively mainly “isolated steps.”

Fig. 1.

An overview of metabolism and transport in the proto-mitochondrion, as deduced from the orthologous groups present in its estimated proteome. Yellow boxes indicate the number of groups in that COG functional class. Boxes, arrows, and cylinders indicate pathways, enzymes, and transporters, respectively. Blue: proteins are mitochondrial in yeast or human. Orange: human and yeast orthologs have not been observed in mitochondria. Black: there is no human or yeast representative of this orthologous group.

The abundance of metabolite transporters suggests a host dependency of the proto-mitochondrion. Most significant are the finding of both a lipid transporter and a glycerol uptake protein, which can be linked to β-oxidation and glycerol metabolism, respectively. Conversely, the presence of amino acid and peptide transporters is consistent with the large number of gaps in pathways from the amino acid metabolism.

Comparing the proto-mitochondrial proteome to the largest compilation of mitochondrial proteins from yeast and human (8) indicates that mitochondrial proteins represent only a minority of the proteins of proto-mitochondrial descent (22% in human and 32% in yeast). The rest, including transporters and metabolic enzymes, have been retargeted to other parts of the cell, corroborating a prediction from (4). Our results confirm findings (5) that only a minor fraction of yeast mitochondrial proteins are of alpha-proteobacterial origin (16%) and extend this result to the human mitochondria (14%).

The reconstructed metabolism suggests an aerobic proto-mitochondrion catabolizing lipids, glycerol, and amino acids provided by the host. Although this is most compatible with the oxygen-scavenger hypothesis, in the absence of a published genome of a hydrogenosomal eukaryote this conclusion cannot be definite. More important, a multifaceted benefit of the endosymbiosis for the host seems plausible if one considers the conservation of pathways not directly related to adenosine triphosphate (ATP) production, like fructose/mannose metabolism and the synthesis of lipids, nucleotides, and vitamins. Some of these pathways have moved elsewhere in the cell, showing that modern mitochondria are not the only heritage of the ancestral symbiotic relationship between an alpha-proteobacterium and its host.

Supporting Online Material

www.sciencemag.org/cgi/content/full/301/5633/609/DC1

Materials and Methods

Fig. S1

References

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