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Prediction of Mitochondrial Protein Function by Comparative Physiology and Phylogenetic Profiling

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1264)

Abstract

According to the endosymbiotic theory, mitochondria originate from a free-living alpha-proteobacteria that established an intracellular symbiosis with the ancestor of present-day eukaryotic cells. During the bacterium-to-organelle transformation, the proto-mitochondrial proteome has undergone a massive turnover, whereby less than 20 % of modern mitochondrial proteomes can be traced back to the bacterial ancestor. Moreover, mitochondrial proteomes from several eukaryotic organisms, for example, yeast and human, show a rather modest overlap, reflecting differences in mitochondrial physiology. Those differences may result from the combination of differential gain and loss of genes and retargeting processes among lineages. Therefore, an evolutionary signature, also called “phylogenetic profile”, could be generated for every mitochondrial protein. Here, we present two evolutionary biology approaches to study mitochondrial physiology: the first strategy, which we refer to as “comparative physiology,” allows the de novo identification of mitochondrial proteins involved in a physiological function; the second, known as “phylogenetic profiling,” allows to predict protein functions and functional interactions by comparing phylogenetic profiles of uncharacterized and known components.

Key words

Mitochondrial evolution Comparative genomics Comparative physiology Phylogenetic profiling Orthology 

Notes

Acknowledgment

This work was supported by Deutsche Forschungsgemeinschaft Emmy Noether Programme Grant PE 2053/1-1 and the Bavarian State Ministry of Education, Science and the Arts.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Gene CenterLudwig-Maximilians-UniversitätMunichGermany
  2. 2.Institute of Human Genetics, Helmholtz Zentrum MunichMunichGermany
  3. 3.Genzentrum/Ludwig-Maximilians-UniversitaetMunichGermany

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