The Arthropoda-specific Tramtrack group BTB protein domains use previously unknown interface to form hexamers

Abstract

BTB (Bric-a-brack, Tramtrack and Broad Complex) is a diverse group of protein-protein interaction domains found within metazoan proteins. Transcription factors contain a dimerizing BTB subtype with a characteristic N-terminal extension. The Tramtrack group (TTK) is a distinct type of BTB domain, which can multimerize. Single-particle cryo-EM microscopy revealed that the TTK-type BTB domains assemble into a hexameric structure consisting of three canonical BTB dimers connected through a previously uncharacterized interface. We demonstrated that the TTK-type BTB domains are found only in Arthropods and have undergone lineage-specific expansion in modern insects. The Drosophila genome encodes 24 transcription factors with TTK-type BTB domains, whereas only four have non‑TTK‑type BTB domains. Yeast two-hybrid analysis revealed that the TTK-type BTB domains have an unusually broad potential for heteromeric associations presumably through dimer-dimer interaction interface. Thus, the TTK-type BTB domains are a structurally and functionally distinct group of protein domains specific to Arthropodan transcription factors.

Data availability

The cryo-EM maps (blushed-regularized and normal regularization) and PDB model files have been deposited in the Protein Data Bank under the PDB entry code 8RC6 and in the EMDB with entry code EMD-19049. SAXS data have been deposited in the Small Angle Scattering Biological Data Bank (www.sasbdb.org) under accession codes SASDP59 (merged data for LOLA1-120 at 1.0 mg/ml and 3.0 mg/ml), SASDP49 (CG67651-133 at 1.5 mg/ml). Atomic models (both native and exactly corresponding to expression constructs) and reports of SAXS approximation are provided as Supplemental files. Results of bioinformatic analysis are provided as Supplemental tables.

Article and author information

Author details

  1. Artem N Bonchuk

    Department of the Control of Genetic Processes, Russian Academy of Sciences, Moscow, Russian Federation
    For correspondence
    echinaceus@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0948-0640
  2. Konstantin I Balagurov

    Department of the Control of Genetic Processes, Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8650-1839
  3. Rozbeh Baradaran

    CryoEM Structural Biology Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.
  4. Konstantin M Boyko

    Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8229-189X
  5. Nikolai N Sluchanko

    Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8608-1416
  6. Anastasia M Khrustaleva

    Department of the Control of Genetic Processes, Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
  7. Anna D Burtseva

    Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0675-1043
  8. Olga V Arkova

    Department of the Control of Genetic Processes, Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5353-0748
  9. Karina K Khalisova

    Department of the Control of Genetic Processes, Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
  10. Vladimir O Popov

    Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
  11. Andreas Naschberger

    CryoEM Structural Biology Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    For correspondence
    andreas.naschberger@kaust.edu.sa
    Competing interests
    The authors declare that no competing interests exist.
  12. Pavel G Georgiev

    Department of the Control of Genetic Processes, Russian Academy of Sciences, Moscow, Russian Federation
    For correspondence
    georgiev_p@mail.ru
    Competing interests
    The authors declare that no competing interests exist.

Funding

Russian Science Foundation (19-74-10099-P)

  • Artem N Bonchuk
  • Konstantin I Balagurov
  • Konstantin M Boyko
  • Anna D Burtseva

Russian Science Foundation (19-74-30026-Р)

  • Artem N Bonchuk
  • Konstantin I Balagurov
  • Anastasia M Khrustaleva
  • Olga V Arkova
  • Karina K Khalisova
  • Pavel G Georgiev

Ministry of Science and Higher Education of the Russian Federation (075-15-2019-1661)

  • Artem N Bonchuk
  • Konstantin I Balagurov
  • Olga V Arkova

KAUST Baseline Grant (BAS/1/1107-01-01)

  • Rozbeh Baradaran
  • Andreas Naschberger

This work was supported by the Russian Science Foundation - project 19-74-10099-P to A.B. (expression and purification of proteins and their mutants), project 19-74-30026-Р to P.G. (analysis of protein-protein interactions) and by Ministry of Science and Higher Education of the Russian Federation - grant 075-15-2019-1661 (structural and bioinformatic analysis). Funding for open access charge: Ministry of Science and Higher Education of the Russian Federation and Russian Science Foundation. The single-particle cryo-EM work was financially supported by the KAUST Baseline Grant BAS/1/1107-01-01. N.N.S. and K.M.B. acknowledges that SEC-MALS work was supported by the Ministry of Science and Higher Education of the Russian Federation.

Copyright

© 2024, Bonchuk 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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  1. Artem N Bonchuk
  2. Konstantin I Balagurov
  3. Rozbeh Baradaran
  4. Konstantin M Boyko
  5. Nikolai N Sluchanko
  6. Anastasia M Khrustaleva
  7. Anna D Burtseva
  8. Olga V Arkova
  9. Karina K Khalisova
  10. Vladimir O Popov
  11. Andreas Naschberger
  12. Pavel G Georgiev
(2024)
The Arthropoda-specific Tramtrack group BTB protein domains use previously unknown interface to form hexamers
eLife 13:e96832.
https://doi.org/10.7554/eLife.96832

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https://doi.org/10.7554/eLife.96832

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