PerTurboID, A targeted in situ method reveals the impact of kinase deletion on its local protein environment in the cytoadhesion complex of malaria causing parasites

  1. Heledd Davies
  2. Hugo Belda
  3. Malgorzata Broncel
  4. Jill Dalimot
  5. Moritz Treeck  Is a corresponding author
  1. The Francis Crick Institute, United Kingdom

Abstract

Reverse genetics is key to understanding protein function, but the mechanistic connection between a gene of interest and the observed phenotype is not always clear. Here we describe the use of proximity labeling using TurboID and site-specific quantification of biotinylated peptides to measure changes to the local protein environment of selected targets upon perturbation. We apply this technique, which we call PerTurboID, to understand how the P. falciparum exported kinase, FIKK4.1, regulates the function of the major virulence factor of the malaria causing parasite, PfEMP1. We generated independent TurboID fusions of 2 proteins that are predicted substrates of FIKK4.1 in a FIKK4.1 conditional KO parasite line. Comparing the abundance of site-specific biotinylated peptides between wildtype and kinase deletion lines reveals the differential accessibility of proteins to biotinylation, indicating changes to localization, protein-protein interactions, or protein structure which are mediated by FIKK4.1 activity. We further show that FIKK4.1 is likely the only FIKK kinase that controls surface levels of PfEMP1, but not other surface antigens, on the infected red blood cell under standard culture conditions. We believe PerTurboID is broadly applicable to study the impact of genetic or environmental perturbation on a selected cellular niche.

Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (62) partner repository with the dataset identifier PXD039125.Source data for all Western Blots and PCRs is shown in two separate Source data files.

The following data sets were generated

Article and author information

Author details

  1. Heledd Davies

    The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3475-0080
  2. Hugo Belda

    The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Malgorzata Broncel

    The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2991-3500
  4. Jill Dalimot

    The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1306-093X
  5. Moritz Treeck

    The Francis Crick Institute, London, United Kingdom
    For correspondence
    moritz.treeck@crick.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9727-6657

Funding

Francis Crick Institute (CC2132)

  • Heledd Davies
  • Hugo Belda
  • Malgorzata Broncel
  • Jill Dalimot
  • Moritz Treeck

Francis Crick Institute (CC0199)

  • Malgorzata Broncel
  • Moritz Treeck

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

Reviewing Editor

  1. Dominique Soldati-Favre, University of Geneva, Switzerland

Version history

  1. Received: January 23, 2023
  2. Preprint posted: February 3, 2023 (view preprint)
  3. Accepted: September 21, 2023
  4. Accepted Manuscript published: September 22, 2023 (version 1)
  5. Version of Record published: October 10, 2023 (version 2)

Copyright

© 2023, Davies 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. Heledd Davies
  2. Hugo Belda
  3. Malgorzata Broncel
  4. Jill Dalimot
  5. Moritz Treeck
(2023)
PerTurboID, A targeted in situ method reveals the impact of kinase deletion on its local protein environment in the cytoadhesion complex of malaria causing parasites
eLife 12:e86367.
https://doi.org/10.7554/eLife.86367

Share this article

https://doi.org/10.7554/eLife.86367

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