title: Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.
abstract: The endosymbiotic origin of mitochondria has resulted in a massive horizontal transfer of genetic material from an alpha-proteobacterium to the early eukaryotes. Using large-scale phylogenetic analysis we have previously identified 630 orthologous groups of proteins derived from this event. Here we show that this proto-mitochondrial protein set has undergone extensive lineage-specific gene loss in the eukaryotes, with an average of three losses per orthologous group in a phylogeny of nine species. This gene loss has resulted in a high variability of the alphaproteobacterial-derived gene content of present-day eukaryotic genomes that might reflect functional adaptation to different environments. Proteins functioning in the same biochemical pathway tend to have a similar history of gene loss events, and we use this property to predict functional interactions among proteins in our set.
authors.affiliation: Center for Molecular and Biomolecular Informatics and Nijmegen Center for Molecular Life Sciences, Radboud University of Nijmegen Medical Center, Nijmegen, The Netherlands. T.Gabaldon@cmbi.ru.nl
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.forename: Martijn A
authors.initials: MA
authors.lastname: Huynen
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D004272:DNA, Mitochondrial / Q000235:genetics*; D019143:Evolution, Molecular; D017353:Gene Deletion; D014644:Genetic Variation / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics*; D024101:Mitochondrial Proteins / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013559:Symbiosis / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial; D024101:Mitochondrial Proteins