The phylogenetic analyses of the few genes that are still encoded in the genomes of modern mitochondria suggest an alphaproteobacterial origin for this endosymbiont. Although the order Rickettsiales has been proposed as the alpha-proteobacterial sister-group of mitochondria, there is no definitive evidence as to from which alpha-proteobacterial group the proto-mitochondrion emerged. Martijn et al. found mitochondria are a possible sister-group to the alphaproteobacteria.
|Schematic ribosomal RNA phylogeny of Alphaproteobacteria|
|The cladogram of Rickettsidae has been inferred by Ferla et al.  from the comparison of 16S + 23S ribosomal RNA sequences.|
Toni Gabaldón and Martijn Huynen (2003) reconstructed the proteome (the entire set of proteins expressed by a genome) and corresponding metabolism of the proto-mitochondrion by comparing extant alpha-proteobacterial and eukaryotic genomes. They concluded that this organism was an aerobic alpha-proteobacterium catabolyzing lipids, glycerol and other compounds provided by the host. At least 630 gene families derived from this organism can still be found in the 9 eukaryotic genomes analyzed in the study.
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