MBE Advance Access originally published online on April 6, 2009
Molecular Biology and Evolution 2009 26(7):1533-1548; doi:10.1093/molbev/msp068
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Research Articles |
A Proteomic Survey of Chlamydomonas reinhardtii Mitochondria Sheds New Light on the Metabolic Plasticity of the Organelle and on the Nature of the 
-Proteobacterial Mitochondrial Ancestor
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* Laboratoire de Physiologie Cellulaire Végétale, CNRS, UMR5168 Grenoble, France
CEA, DSV, iRTSV, Grenoble, France
INRA, UMR1200, Grenoble, France
Université Joseph Fourier, Grenoble, France
|| Unité de Bioénergétique et Ingénierie des Protéines, CNRS, UPR9036-IFR 88, Marseille, France
¶ Laboratoire d'Etude de la Dynamique des Protéomes, INSERM, U880, Grenoble, France
# Institute of Botany, University of Düsseldorf, Germany
E-mail: ariane.atteia{at}ifr88.cnrs-mrs.fr.
Accepted for publication March 24, 2009.
Mitochondria play a key role in the life and death of eukaryotic cells, yet the full spectrum of mitochondrial functions is far from being fully understood, especially in photosynthetic organisms. To advance our understanding of mitochondrial functions in a photosynthetic cell, an extensive proteomic survey of Percoll-purified mitochondria from the metabolically versatile, hydrogen-producing green alga Chlamydomonas reinhardtii was performed. Different fractions of purified mitochondria from Chlamydomonas cells grown under aerobic conditions were analyzed by nano-liquid chromatography–electrospray ionization–mass spectrometry after protein separation on sodium dodecyl sulfate polyacrylamide gel electrophoresis or on blue-native polyacrylamide gel electrophoresis. Of the 496 nonredundant proteins identified, 149 are known or predicted to reside in other cellular compartments and were thus excluded from the molecular and evolutionary analyses of the Chlamydomonas proteome. The mitochondrial proteome of the photosynthetic alga reveals important lineage-specific differences with other mitochondrial proteomes, reflecting the high metabolic diversity of the organelle. Some mitochondrial metabolic pathways in Chlamydomonas appear to combine typical mitochondrial enzymes and bacterial-type ones, whereas others are unknown among mitochondriate eukaryotes. The comparison of the Chlamydomonas proteins to their identifiable homologs predicted from 354 sequenced genomes indicated that Arabidopsis is the most closely related nonalgal eukaryote. Furthermore, this phylogenomic analysis shows that free-living 
-proteobacteria from the metabolically versatile orders Rhizobiales and Rhodobacterales better reflect the gene content of the ancestor of the chlorophyte mitochondria than parasitic -proteobacteria with reduced and specialized genomes.
Key Words: Chlamydomonas • endosymbiont • metabolism • phylogeny • proteome
Martin Embley, Associate Editor