1. Biochemistry and Chemical Biology
  2. Microbiology and Infectious Disease
Download icon

Structure of dual-BON domain protein DolP identifies phospholipid binding as a new mechanism for protein localization

  1. Jack Alfred Bryant
  2. Faye C Morris
  3. Timothy J Knowles
  4. Riyaz Maderbocus
  5. Eva Heinz
  6. Gabriela Boelter
  7. Dema Alodaini
  8. Adam Colyer
  9. Peter J Wotherspoon
  10. Kara A Staunton
  11. Mark Jeeves
  12. Douglas F Browning
  13. Yanina R Sevastsyanovich
  14. Timothy J Wells
  15. Amanda E Rossiter
  16. Vassiliy N Bavro
  17. Pooja Sridhar
  18. Douglas G Ward
  19. Zhi-Soon Chong
  20. Emily C A Goodall
  21. Christopher Icke
  22. Alvin Teo
  23. Shu-Sin Chng
  24. David I Roper
  25. Trevor Lithgow
  26. Adam F Cunningham
  27. Manuel Banzhaf
  28. Michael Overduin  Is a corresponding author
  29. Ian R Henderson  Is a corresponding author
  1. University of Birmingham, United Kingdom
  2. Monash University, Australia
  3. National University of Singapore, Singapore
  4. IMB, University of Queensland, Australia
  5. University of Warwick, United Kingdom
  6. University of Alberta, Canada
  7. University of Queensland, Australia
Research Article
  • Cited 5
  • Views 1,565
  • Annotations
Cite this article as: eLife 2020;9:e62614 doi: 10.7554/eLife.62614

Abstract

The Gram-negative outer membrane envelops the bacterium and functions as a permeability barrier against antibiotics, detergents and environmental stresses. Some virulence factors serve to maintain the integrity of the outer membrane, including DolP (formerly YraP) a protein of unresolved structure and function. Here we reveal DolP is a lipoprotein functionally conserved among Gram-negative bacteria and that loss of DolP increases membrane fluidity. We present the NMR solution structure for Escherichia coli DolP, which is composed of two BON domains that form an interconnected opposing pair. The C-terminal BON domain binds anionic phospholipids through an extensive membrane:protein interface. This interaction is essential for DolP function and is required for sub-cellular localization of the protein to the cell division site, providing evidence of subcellular localization of these phospholipids within the outer membrane. The structure of DolP provides a new target for developing therapies that disrupt the integrity of the bacterial cell envelope.

Data availability

Structural data have been deposited in PDB under the accession code 7A2D and the BMRB 19760.All data generated or analysed during this study are included in the manuscript and supporting files. We have supplied original images for Figures 1, 4, S1, S5, S9, and S10 in Additional Data File 1. We have also supplied raw data for Figure S10 in Additional Data File 2.

Article and author information

Author details

  1. Jack Alfred Bryant

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7912-2144
  2. Faye C Morris

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9021-0452
  3. Timothy J Knowles

    School of Biosciences, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Riyaz Maderbocus

    Institute of Microbiology and Infection, Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Eva Heinz

    Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology,, Monash University, Clayton, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4413-3756
  6. Gabriela Boelter

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Dema Alodaini

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Adam Colyer

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  9. Peter J Wotherspoon

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  10. Kara A Staunton

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  11. Mark Jeeves

    Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  12. Douglas F Browning

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  13. Yanina R Sevastsyanovich

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  14. Timothy J Wells

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  15. Amanda E Rossiter

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  16. Vassiliy N Bavro

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  17. Pooja Sridhar

    School of Biosciences, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  18. Douglas G Ward

    Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  19. Zhi-Soon Chong

    Department of Chemistry, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  20. Emily C A Goodall

    IMB, IMB, University of Queensland, Brisbane, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4846-6566
  21. Christopher Icke

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7815-8591
  22. Alvin Teo

    School of Life Sciences, University of Warwick, Coventry, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  23. Shu-Sin Chng

    Department of Chemistry, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5466-7183
  24. David I Roper

    School of Life Sciences, University of Warwick, Coventry, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  25. Trevor Lithgow

    Department of Microbiology, Monash University, Melbourne, Australia
    Competing interests
    The authors declare that no competing interests exist.
  26. Adam F Cunningham

    Institute of Microbiology and Infection, Institute of Inflammation and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  27. Manuel Banzhaf

    Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  28. Michael Overduin

    Department of Biochemistry, University of Alberta, Edmonton, Canada
    For correspondence
    overduin@ualberta.ca
    Competing interests
    The authors declare that no competing interests exist.
  29. Ian R Henderson

    Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    For correspondence
    i.henderson@imb.uq.edu.au
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9954-4977

Funding

Biotechnology and Biological Sciences Research Council (BB/M00810X/1)

  • Michael Overduin
  • Ian R Henderson

Biotechnology and Biological Sciences Research Council (BB/L00335X/1)

  • Michael Overduin
  • Ian R Henderson

Biotechnology and Biological Sciences Research Council (BB/P009840/1)

  • Timothy J Knowles

Natural Sciences and Engineering Research Council of Canada (RCP-12-002C)

  • Michael Overduin

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

Reviewing Editor

  1. Sonja V Albers, University of Freiburg, Germany

Publication history

  1. Received: August 31, 2020
  2. Accepted: December 11, 2020
  3. Accepted Manuscript published: December 14, 2020 (version 1)
  4. Version of Record published: January 13, 2021 (version 2)

Copyright

© 2020, Bryant 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

  • 1,565
    Page views
  • 256
    Downloads
  • 5
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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)

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

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

Further reading

    1. Biochemistry and Chemical Biology
    Xavier Portillo et al.
    Research Article Updated

    An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.

    1. Biochemistry and Chemical Biology
    Gajanan S Patil et al.
    Research Article Updated

    Fatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4′-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and accept holo-ACP unlike other members of the ANL superfamily remains elusive. We show that FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3′,5′-bisphosphate-containing CoA from holo-ACP and thus FAALs can distinguish between CoA and holo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organizations. The universal distribution of FAALs suggests that they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.