Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter (original) (raw)

Nature volume 476, pages 341–345 (2011)Cite this article

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Abstract

Mitochondria from diverse organisms are capable of transporting large amounts of Ca2+ via a ruthenium-red-sensitive, membrane-potential-dependent mechanism called the uniporter1,2,3,4. Although the uniporter’s biophysical properties have been studied extensively, its molecular composition remains elusive. We recently used comparative proteomics to identify MICU1 (also known as CBARA1), an EF-hand-containing protein that serves as a putative regulator of the uniporter5. Here, we use whole-genome phylogenetic profiling, genome-wide RNA co-expression analysis and organelle-wide protein coexpression analysis to predict proteins functionally related to MICU1. All three methods converge on a novel predicted transmembrane protein, CCDC109A, that we now call ‘mitochondrial calcium uniporter’ (MCU). MCU forms oligomers in the mitochondrial inner membrane, physically interacts with MICU1, and resides within a large molecular weight complex. Silencing MCU in cultured cells or in vivo in mouse liver severely abrogates mitochondrial Ca2+ uptake, whereas mitochondrial respiration and membrane potential remain fully intact. MCU has two predicted transmembrane helices, which are separated by a highly conserved linker facing the intermembrane space. Acidic residues in this linker are required for its full activity. However, an S259A point mutation retains function but confers resistance to Ru360, the most potent inhibitor of the uniporter. Our genomic, physiological, biochemical and pharmacological data firmly establish MCU as an essential component of the mitochondrial Ca2+ uniporter.

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References

  1. DeLuca, H. F. & Engstrom, G. W. Calcium uptake by rat kidney mitochondria. Proc. Natl Acad. Sci. USA 47, 1744–1750 (1961)
    Article ADS CAS Google Scholar
  2. Vasington, F. D. & Murphy, J. V. Ca++ ion uptake by rat kidney mitochondria and its dependence on respiration and phosphorylation. J. Biol. Chem. 237, 2670–2677 (1962)
    CAS PubMed Google Scholar
  3. Carafoli, E. & Lehninger, A. L. A survey of the interaction of calcium ions with mitochondria from different tissues and species. Biochem. J. 122, 681–690 (1971)
    Article CAS Google Scholar
  4. Gunter, K. & Gunter, T. E. Transport of calcium by mitochondria. J. Bioenerg. Biomembr. 26, 471–485 (1994)
    Article CAS Google Scholar
  5. Perocchi, F. et al. MICU1 encodes a mitochondrial EF hand protein required for Ca2+ uptake. Nature 467, 291–296 (2010)
    Article ADS CAS Google Scholar
  6. Pagliarini, D. J. et al. A mitochondrial protein compendium elucidates complex I disease biology. Cell 134, 112–123 (2008)
    Article CAS Google Scholar
  7. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA 96, 4285–4288 (1999)
    Article ADS CAS Google Scholar
  8. Lattin, J. E. et al. Expression analysis of G Protein-Coupled Receptors in mouse macrophages. Immunome Res. 4, 5 (2008)
    Article Google Scholar
  9. Rizzuto, R., Simpson, A. W., Brini, M. & Pozzan, T. Rapid changes of mitochondrial Ca2+ revealed by specifically targeted recombinant aequorin. Nature 358, 325–327 (1992)
    Article ADS CAS Google Scholar
  10. Denton, R. M. & McCormack, J. G. The role of calcium in the regulation of mitochondrial metabolism. Biochem. Soc. Trans. 8, 266–268 (1980)
    Article CAS Google Scholar
  11. Territo, P. R., Mootha, V. K., French, S. A. & Balaban, R. S. Ca2+ activation of heart mitochondrial oxidative phosphorylation: role of the F0/F1-ATPase. Am. J. Physiol. Cell Physiol. 278, C423–C435 (2000)
    Article CAS Google Scholar
  12. Chance, B. & Williams, G. R. Respiratory enzymes in oxidative phosphorylation. I. Kinetics of oxygen utilization. J. Biol. Chem. 217, 383–393 (1955)
    CAS PubMed Google Scholar
  13. Musunuru, K. et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 466, 714–719 (2010)
    Article ADS CAS Google Scholar
  14. Akinc, A. et al. A combinatorial library of lipid-like materials for delivery of RNAi therapeutics. Nature Biotechnol. 26, 561–569 (2008)
    Article CAS Google Scholar
  15. Akinc, A. et al. Targeted delivery of RNAi therapeutics with endogenous and exogenous ligand-based mechanisms. Mol. Ther. 18, 1357–1364 (2010)
    Article CAS Google Scholar
  16. Claros, M. G. & Vincens, P. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241, 779–786 (1996)
    Article CAS Google Scholar
  17. Bernsel, A., Viklund, H., Hennerdal, A. & Elofsson, A. TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res. 37, W465–W468 (2009)
    Article CAS Google Scholar
  18. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001)
    Article CAS Google Scholar
  19. Moore, C. L. Specific inhibition of mitochondrial Ca++ transport by ruthenium red. Biochem. Biophys. Res. Commun. 42, 298–305 (1971)
    Article ADS CAS Google Scholar
  20. Ying, W. L., Emerson, J., Clarke, M. J. & Sanadi, D. R. Inhibition of mitochondrial calcium ion transport by an oxo-bridged dinuclear ruthenium ammine complex. Biochemistry 30, 4949–4952 (1991)
    Article CAS Google Scholar
  21. Bernardi, P. Mitochondrial transport of cations: channels, exchangers, and permeability transition. Physiol. Rev. 79, 1127–1155 (1999)
    Article CAS Google Scholar
  22. Kirichok, Y., Krapivinsky, G. & Clapham, D. E. The mitochondrial calcium uniporter is a highly selective ion channel. Nature 427, 360–364 (2004)
    Article ADS CAS Google Scholar
  23. Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283–1298 (2006)
    Article CAS Google Scholar
  24. Semple, S. C. et al. Rational design of cationic lipids for siRNA delivery. Nature Biotechnol. 28, 172–176 (2010)
    Article CAS Google Scholar
  25. Rebres, R. A. et al. Synergistic Ca2+ responses by Gαi- and Gαq-coupled G-protein-coupled receptors require a single PLCβ isoform that is sensitive to both Gβγ and Gαq . J. Biol. Chem. 286, 942–951 (2011)
    Article CAS Google Scholar
  26. Gohil, V. M. et al. Nutrient-sensitized screening for drugs that shift energy metabolism from mitochondrial respiration to glycolysis. Nature Biotechnol. 28, 249–255 (2010)
    Article CAS Google Scholar
  27. Ryan, M. T., Voos, W. & Pfanner, N. Assaying protein import into mitochondria. Methods Cell Biol. 65, 189–215 (2001)
    Article CAS Google Scholar
  28. Schagger, H. & von Jagow, G. Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal. Biochem. 199, 223–231 (1991)
    Article CAS Google Scholar

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Acknowledgements

We thank R. Nilsson, J. Engreitz and S. Calvo for bioinformatics assistance; D. Root and S. Silver for assistance in lentiviral RNAi; B. R. Bettencourt, K. Charisse, S. Kuchimanchi and L. Speciner for siRNA design, synthesis and formulation; M. Blower, J. Avruch and R. Ward for advice; and members of the Mootha laboratory for valuable feedback. J.M.B. and L.S. were supported by graduate student fellowships from the National Science Foundation. This work was supported by grants from the National Institutes of Health (GM0077465, DK080261) awarded to V.K.M.

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Author notes

  1. Joshua M. Baughman and Fabiana Perocchi: These authors contributed equally to this work.

Authors and Affiliations

  1. Departments of Systems Biology and Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, 02114, Massachusetts, USA
    Joshua M. Baughman, Fabiana Perocchi, Hany S. Girgis, Molly Plovanich, Casey A. Belcher-Timme, Yasemin Sancak, X. Robert Bao, Laura Strittmatter, Olga Goldberger & Vamsi K. Mootha
  2. Broad Institute, Cambridge, 02142, Massachusetts, USA
    Joshua M. Baughman, Fabiana Perocchi, Hany S. Girgis, Molly Plovanich, Casey A. Belcher-Timme, Yasemin Sancak, X. Robert Bao, Laura Strittmatter, Olga Goldberger & Vamsi K. Mootha
  3. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA
    Roman L. Bogorad
  4. Alnylam Pharmaceuticals, Inc., Cambridge, 02142, Massachusetts, USA
    Victor Koteliansky

Authors

  1. Joshua M. Baughman
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  2. Fabiana Perocchi
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  3. Hany S. Girgis
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  4. Molly Plovanich
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  5. Casey A. Belcher-Timme
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  6. Yasemin Sancak
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  7. X. Robert Bao
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  8. Laura Strittmatter
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  9. Olga Goldberger
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  10. Roman L. Bogorad
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  11. Victor Koteliansky
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  12. Vamsi K. Mootha
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Contributions

J.M.B., F.P. and V.K.M. conceived of the project and its design. J.M.B., F.P., H.S.G., M.P., O.G., L.S., C.A.B.-T., X.R.B., Y.S. and R.L.B. performed experiments and data analysis. V.K. aided in experimental design. V.K.M., J.M.B., F.P. and M.P. wrote the manuscript.

Corresponding author

Correspondence toVamsi K. Mootha.

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Baughman, J., Perocchi, F., Girgis, H. et al. Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter.Nature 476, 341–345 (2011). https://doi.org/10.1038/nature10234

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Editorial Summary

Mitochondrial Ca2+ channel identified

Central to the role of the mitochondrion in cellular metabolism is its ability to control the fluxes of the key signalling ion, Ca2+. This is done by a highly selective ion channel known as the mitochondrial calcium uniporter. The molecular nature of this channel has remained elusive, but now two groups report the identification of a 40-kilodalton protein in the inner membrane of mitochondria as the active channel of the uniporter. This protein contains two transmembrane domains and exhibits calcium-channel activity in vitro and in vivo.