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Bioinformatics 2005 21(Suppl 2):ii144-ii150; doi:10.1093/bioinformatics/bti1124
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes

Toni Gabaldón * and Martijn A. Huynen

Center for Molecular and Biomolecular Informatics (CMBI) and Nijmegen Center for Molecular Life Sciences (NCMLS), Radboud University of Nijmegen Medical Center Toernooiveld 1, 6525 ED Nijmegen, the Netherlands

*To whom correspondence should be addressed.

Motivation: 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.

Contact: T.Gabaldon{at}cmbi.ru.nl

Supplementary information: Sequences and trees for the selected orthologous groups can be accessed at http://www.cmbi.kun.nl/~jagabald/table_groupsb.html


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