Coevolution predicts direct interactions between mtDNA-encoded and nDNA-encoded subunits of oxidative phosphorylation complex I

Moran Gershoni, Angelika Fuchs, Naama Shani, Yearit Fridman, Marisol Corral-Debrinski, Amir Aharoni, Dmitrij Frishman, Dan Mishmar

Research output: Contribution to journalArticlepeer-review

51 Scopus citations


Despite years of research, the structure of the largest mammalian oxidative phosphorylation (OXPHOS) complex, NADH-ubiquinone oxidoreductase (complex I), and the interactions among its 45 subunits are not fully understood. Since complex I harbors subunits encoded by mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) genomes, with the former evolving ~. 10 times faster than the latter, tight cytonuclear coevolution is expected and observed. Recently, we identified three nDNA-encoded complex I subunits that underwent accelerated amino acid replacement, suggesting their adjustment to the elevated mtDNA rate of change. Hence, they constitute excellent candidates for binding mtDNA-encoded subunits.Here, we further disentangle the network of physical cytonuclear interactions within complex I by analyzing subunits coevolution. Firstly, relying on the bioinformatic analysis of 10 protein complexes possessing solved structures, we show that signals of coevolution identified physically interacting subunits with nearly 90% accuracy, thus lending support to our approach. When applying this approach to cytonuclear interaction within complex I, we predict that the 'rate-accelerated' nDNA-encoded subunits of complex I, NDUFC2 and NDUFA1, likely interact with the mtDNA-encoded subunits ND5/. ND4 and ND5/ND4/ND1, respectively. Furthermore, we predicted interactions among mtDNA-encoded complex I subunits. Using the yeast two-hybrid system, we experimentally confirmed the predicted interactions of human NDUFC2 with ND4, the interactions of human NDUFA1 with ND1 and ND4, and the lack of interaction of NDUFC2 with ND3 and NDUFA1, thus providing a proof of concept for our approach.Our study shows, for the first time, evidence for direct interactions between nDNA-encoded and mtDNA-encoded subunits of human OXPHOS complex I and paves the path towards deciphering subunit interactions within complexes lacking three-dimensional structures. Our subunit-interactions-predicting method, ComplexCorr, is available at

Original languageEnglish
Pages (from-to)158-171
Number of pages14
JournalJournal of Molecular Biology
Issue number1
StatePublished - 19 Nov 2010


  • Coevolution
  • Complex I
  • Correlated mutation analysis
  • Mitochondria
  • Mitochondrial DNA

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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