Homologue replacement in the import motor of the mitochondrial inner membrane of trypanosomes

  1. Corinne von Känel
  2. Sergio A Muñoz-Gómez
  3. Silke Oeljeklaus
  4. Christoph Wenger
  5. Bettina Warscheid
  6. Jeremy G Wideman  Is a corresponding author
  7. Anke Harsman  Is a corresponding author
  8. Andre Schneider  Is a corresponding author
  1. University of Berne, Switzerland
  2. Arizona State University, United States
  3. University of Freiburg, Germany

Abstract

Many mitochondrial proteins contain N-terminal presequences that direct them to the organelle. The main driving force for their translocation across the inner membrane is provided by the presequence translocase-associated motor (PAM) which contains the J-protein Pam18. Here, we show that in the PAM of Trypanosoma brucei the function of Pam18 has been replaced by the non-orthologous euglenozoan-specific J-protein TbPam27. TbPam27 is specifically required for the import of mitochondrial presequence-containing but not for carrier proteins. Similar to yeast Pam18, TbPam27 requires an intact J-domain to function. Surprisingly, T. brucei still contains a bona fide Pam18 orthologue that, while essential for normal growth, is not involved in protein import. Thus, during evolution of kinetoplastids, Pam18 has been replaced by TbPam27. We propose that this replacement is linked to the transition from two ancestral and functionally distinct TIM complexes, found in most eukaryotes, to the single bifunctional TIM complex present in trypanosomes.

Data availability

All produced data are contained within the manuscript (e.g. Data Source files)

Article and author information

Author details

  1. Corinne von Känel

    Department of Chemistry and Biochemistry, University of Berne, Bern, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  2. Sergio A Muñoz-Gómez

    Center for Mechanisms of Evolution, Arizona State University, Arizona, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Silke Oeljeklaus

    Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Christoph Wenger

    Department of Chemistry and Biochemistry, University of Berne, Bern, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  5. Bettina Warscheid

    Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5096-1975
  6. Jeremy G Wideman

    Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, United States
    For correspondence
    Jeremy.Wideman@asu.edu
    Competing interests
    The authors declare that no competing interests exist.
  7. Anke Harsman

    Department of Chemistry and Biochemistry, University of Berne, Bern, Switzerland
    For correspondence
    anke.harsman@web.de
    Competing interests
    The authors declare that no competing interests exist.
  8. Andre Schneider

    Department of Chemistry and Biochemistry, University of Berne, Bern, Switzerland
    For correspondence
    andre.schneider@dcb.unibe.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5421-0909

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (175563)

  • Andre Schneider

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (NCCR RNA and Disease)

  • Andre Schneider

ERC Consolidator grant (648235)

  • Bettina Warscheid

Deutsche Forschungsgemeinschaft (403222702/SFB 1381)

  • Bettina Warscheid

Germany's Excellence Strategy (CIBSS - EXC-2189 - Project ID 390939984)

  • Bettina Warscheid

Excellence Initiative of the German Federal and State Governments (EXC 294 BIOSS)

  • Bettina Warscheid

Peter und Traudl Engelhorn foundation

  • Anke Harsman

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

Reviewing Editor

  1. Agnieszka Chacinska, University of Warsaw, Poland

Version history

  1. Received: October 8, 2019
  2. Accepted: February 26, 2020
  3. Accepted Manuscript published: February 27, 2020 (version 1)
  4. Version of Record published: March 10, 2020 (version 2)

Copyright

© 2020, von Känel 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.

Metrics

  • 1,232
    views
  • 188
    downloads
  • 18
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Corinne von Känel
  2. Sergio A Muñoz-Gómez
  3. Silke Oeljeklaus
  4. Christoph Wenger
  5. Bettina Warscheid
  6. Jeremy G Wideman
  7. Anke Harsman
  8. Andre Schneider
(2020)
Homologue replacement in the import motor of the mitochondrial inner membrane of trypanosomes
eLife 9:e52560.
https://doi.org/10.7554/eLife.52560

Share this article

https://doi.org/10.7554/eLife.52560

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Marian Brenner, Christoph Zink ... Antje Gohla
    Research Article

    Vitamin B6 deficiency has been linked to cognitive impairment in human brain disorders for decades. Still, the molecular mechanisms linking vitamin B6 to these pathologies remain poorly understood, and whether vitamin B6 supplementation improves cognition is unclear as well. Pyridoxal 5’-phosphate phosphatase (PDXP), an enzyme that controls levels of pyridoxal 5’-phosphate (PLP), the co-enzymatically active form of vitamin B6, may represent an alternative therapeutic entry point into vitamin B6-associated pathologies. However, pharmacological PDXP inhibitors to test this concept are lacking. We now identify a PDXP and age-dependent decline of PLP levels in the murine hippocampus that provides a rationale for the development of PDXP inhibitors. Using a combination of small-molecule screening, protein crystallography, and biolayer interferometry, we discover, visualize, and analyze 7,8-dihydroxyflavone (7,8-DHF) as a direct and potent PDXP inhibitor. 7,8-DHF binds and reversibly inhibits PDXP with low micromolar affinity and sub-micromolar potency. In mouse hippocampal neurons, 7,8-DHF increases PLP in a PDXP-dependent manner. These findings validate PDXP as a druggable target. Of note, 7,8-DHF is a well-studied molecule in brain disorder models, although its mechanism of action is actively debated. Our discovery of 7,8-DHF as a PDXP inhibitor offers novel mechanistic insights into the controversy surrounding 7,8-DHF-mediated effects in the brain.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Thomas RM Germe, Natassja G Bush ... Anthony Maxwell
    Research Article

    DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to form the active complex. DNA gyrase can loop DNA around the C-terminal domains (CTDs) of GyrA and pass one DNA duplex through a transient double-strand break (DSB) established in another duplex. This results in the conversion from a positive (+1) to a negative (–1) supercoil, thereby introducing negative supercoiling into the bacterial genome by steps of 2, an activity essential for DNA replication and transcription. The strong protein interface in the GyrA dimer must be broken to allow passage of the transported DNA segment and it is generally assumed that the interface is usually stable and only opens when DNA is transported, to prevent the introduction of deleterious DSBs in the genome. In this paper, we show that DNA gyrase can exchange its DNA-cleaving interfaces between two active heterotetramers. This so-called interface ‘swapping’ (IS) can occur within a few minutes in solution. We also show that bending of DNA by gyrase is essential for cleavage but not for DNA binding per se and favors IS. Interface swapping is also favored by DNA wrapping and an excess of GyrB. We suggest that proximity, promoted by GyrB oligomerization and binding and wrapping along a length of DNA, between two heterotetramers favors rapid interface swapping. This swapping does not require ATP, occurs in the presence of fluoroquinolones, and raises the possibility of non-homologous recombination solely through gyrase activity. The ability of gyrase to undergo interface swapping explains how gyrase heterodimers, containing a single active-site tyrosine, can carry out double-strand passage reactions and therefore suggests an alternative explanation to the recently proposed ‘swivelling’ mechanism for DNA gyrase (Gubaev et al., 2016).