1. Biochemistry and Chemical Biology
  2. Evolutionary Biology
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Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes

  1. Xinyu Zhu
  2. Aren Boulet
  3. Katherine M Buckley
  4. Casey B Phillips
  5. Micah G Gammon
  6. Laura E Oldfather
  7. Stanley A Moore
  8. Scot C Leary
  9. Paul A Cobine  Is a corresponding author
  1. Auburn University, United States
  2. University of Saskatchewan, Canada
  3. University Saskatchewan, Canada
Research Article
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Cite this article as: eLife 2021;10:e64690 doi: 10.7554/eLife.64690

Abstract

The mitochondrial carrier family protein SLC25A3 transports both copper and phosphate in mammals yet in Saccharomyces cerevisiae the transport of these substrates is partitioned across two paralogs: PIC2 and MIR1. To understand the ancestral state of copper and phosphate transport in mitochondria, we explored the evolutionary relationships of PIC2 and MIR1 orthologs across the eukaryotic tree of life. Phylogenetic analyses revealed that PIC2-like and MIR1-like orthologs are present in all major eukaryotic supergroups, indicating an ancient gene duplication created these paralogs. To link this phylogenetic signal to protein function, we used structural modelling and site-directed mutagenesis to identify residues involved in copper and phosphate transport. Based on these analyses, we generated a L175A variant of mouse SLC25A3 that retains the ability to transport copper but not phosphate. This work highlights the utility of using an evolutionary framework to uncover amino acids involved in substrate recognition by mitochondrial carrier family proteins.

Data availability

All data generated or analyzed during this study are included in the manuscript, supplemental file, and available on GenBank.

The following previously published data sets were used
    1. Alasdair C Ivens 1
    2. Christopher S Peacock
    3. Elizabeth A Worthey
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    8. Marie-Adele Rajandream
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    10. Rita Aert
    11. Atashi Anupama
    12. Zina Apostolou
    13. Philip Attipoe
    14. Nathalie Bason
    15. Christopher Bauser
    16. Alfred Beck
    17. Stephen M Beverley
    18. Gabriella Bianchettin
    19. Katja Borzym
    20. Gordana Bothe
    21. Carlo V Bruschi
    22. Matt Collins
    23. Eithon Cadag
    24. Laura Ciarloni
    25. Christine Clayton
    26. Richard M R Coulson
    27. Ann Cronin
    28. Angela K Cruz
    29. Robert M Davies
    30. Javier De Gaudenzi
    31. Deborah E Dobson
    32. Andreas Duesterhoeft
    33. Gholam Fazelina
    34. Nigel Fosker
    35. Alberto Carlos Frasch
    36. Audrey Fraser
    37. Monika Fuchs
    38. Claudia Gabel
    39. Arlette Goble
    40. André Goffeau
    41. David Harris
    42. Christiane Hertz-Fowler
    43. Helmut Hilbert
    44. David Horn
    45. Yiting Huang
    46. Sven Klages
    47. Andrew Knights
    48. Michael Kube
    49. Natasha Larke
    50. Lyudmila Litvin
    51. Angela Lord
    52. Tin Louie
    53. Marco Marra
    54. David Masuy
    55. Keith Matthews
    56. Shulamit Michaeli
    57. Jeremy C Mottram
    58. Silke Müller-Auer
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    61. Halina Norbertczak
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    73. Johan Robben
    74. Laura Robertson
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    80. David C Schwartz
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    83. Sarah Sharp
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    85. Dhileep Sivam
    86. Rob Squares
    87. Steve Squares
    88. Valentina Tosato
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    91. Rolf Wambutt
    92. Tim Warren
    93. Holger Wedler
    94. John Woodward
    95. Shiguo Zhou
    96. Wolfgang Zimmermann
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    (2011) ASM272v2
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Article and author information

Author details

  1. Xinyu Zhu

    Biological Sciences, Auburn University, Auburn, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Aren Boulet

    Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Katherine M Buckley

    Biological Sciences, Auburn University, Auburn, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Casey B Phillips

    Biological Sciences, Auburn University, Auburn, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Micah G Gammon

    Biological Sciences, Auburn University, Auburn, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Laura E Oldfather

    Biological Sciences, Auburn University, Auburn, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Stanley A Moore

    Biochemistry, Microbiology and Immunology, University Saskatchewan, Saskatoon, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Scot C Leary

    Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
    Competing interests
    The authors declare that no competing interests exist.
  9. Paul A Cobine

    Biological Sciences, Auburn University, Auburn, United States
    For correspondence
    paul.cobine@auburn.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6012-0985

Funding

National Institutes of Health (R01GM120211)

  • Scot C Leary
  • Paul A Cobine

National Science Foundation (EF 2021886)

  • Katherine M Buckley

Alabama Agricultural Experiment Station

  • Paul A Cobine

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Randy B Stockbridge, University of Michigan, United States

Publication history

  1. Received: November 7, 2020
  2. Accepted: February 15, 2021
  3. Accepted Manuscript published: February 16, 2021 (version 1)
  4. Version of Record published: March 2, 2021 (version 2)

Copyright

© 2021, Zhu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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