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Phylointeractomics reconstructs functional evolution of protein binding

Author

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  • Dennis Kappei

    (Cancer Science Institute of Singapore, National University of Singapore
    Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden)

  • Marion Scheibe

    (Institute of Molecular Biology (IMB) gGmbH
    Max Planck Institute of Biochemistry)

  • Maciej Paszkowski-Rogacz

    (Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden)

  • Alina Bluhm

    (Institute of Molecular Biology (IMB) gGmbH)

  • Toni Ingolf Gossmann

    (University of Sheffield, Western Bank, Sheffield S10 2TN, UK)

  • Sabrina Dietz

    (Institute of Molecular Biology (IMB) gGmbH)

  • Mario Dejung

    (Institute of Molecular Biology (IMB) gGmbH)

  • Holger Herlyn

    (Institute of Anthropology, University of Mainz)

  • Frank Buchholz

    (Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden
    Max Planck Institute of Molecular Cell Biology and Genetics
    German Cancer Research Center (DKFZ), Neuenheimer Feld 280, 69120 Heidelberg, Germany
    German Cancer Consortium (DKTK) partner site)

  • Matthias Mann

    (Max Planck Institute of Biochemistry)

  • Falk Butter

    (Institute of Molecular Biology (IMB) gGmbH)

Abstract

Molecular phylogenomics investigates evolutionary relationships based on genomic data. However, despite genomic sequence conservation, changes in protein interactions can occur relatively rapidly and may cause strong functional diversification. To investigate such functional evolution, we here combine phylogenomics with interaction proteomics. We develop this concept by investigating the molecular evolution of the shelterin complex, which protects telomeres, across 16 vertebrate species from zebrafish to humans covering 450 million years of evolution. Our phylointeractomics screen discovers previously unknown telomere-associated proteins and reveals how homologous proteins undergo functional evolution. For instance, we show that TERF1 evolved as a telomere-binding protein in the common stem lineage of marsupial and placental mammals. Phylointeractomics is a versatile and scalable approach to investigate evolutionary changes in protein function and thus can provide experimental evidence for phylogenomic relationships.

Suggested Citation

  • Dennis Kappei & Marion Scheibe & Maciej Paszkowski-Rogacz & Alina Bluhm & Toni Ingolf Gossmann & Sabrina Dietz & Mario Dejung & Holger Herlyn & Frank Buchholz & Matthias Mann & Falk Butter, 2017. "Phylointeractomics reconstructs functional evolution of protein binding," Nature Communications, Nature, vol. 8(1), pages 1-9, April.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14334
    DOI: 10.1038/ncomms14334
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    Cited by:

    1. Sile F. Yang & Christopher B. Nelson & Jadon K. Wells & Madushan Fernando & Robert Lu & Joshua A. M. Allen & Lisa Malloy & Noa Lamm & Vincent J. Murphy & Joel P. Mackay & Andrew J. Deans & Anthony J. , 2024. "ZNF827 is a single-stranded DNA binding protein that regulates the ATR-CHK1 DNA damage response pathway," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Frances Karla Kusuma & Aishvaryaa Prabhu & Galen Tieo & Syed Moiz Ahmed & Pushkar Dakle & Wai Khang Yong & Elina Pathak & Vikas Madan & Yan Yi Jiang & Wai Leong Tam & Dennis Kappei & Peter Dröge & H. , 2023. "Signalling inhibition by ponatinib disrupts productive alternative lengthening of telomeres (ALT)," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Hanna Braun & Ziyan Xu & Fiona Chang & Nikenza Viceconte & Grishma Rane & Michal Levin & Liudmyla Lototska & Franziska Roth & Alexia Hillairet & Albert Fradera-Sola & Vartika Khanchandani & Zi Wayne S, 2023. "ZNF524 directly interacts with telomeric DNA and supports telomere integrity," Nature Communications, Nature, vol. 14(1), pages 1-17, December.

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