Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogen Acinetobacter baumannii

  1. Lucile Moynie
  2. Ilaria Serra
  3. Mariano A Scorciapino
  4. Emilia Oueis
  5. Malcolm GP Page
  6. Matteo Ceccarelli
  7. James H Naismith  Is a corresponding author
  1. Wellcome Trust Centre of Human Genomics, United Kingdom
  2. University of Cagliari, Italy
  3. The University of St Andrews, United Kingdom
  4. Jacobs University, Germany

Abstract

New strategies are urgently required to develop antibiotics. The siderophore uptake system has attracted considerable attention but rational design of siderophore antibiotic conjugates requires knowledge of recognition by the cognate outer membrane transporter. Acinetobacter baumannii is a serious pathogen, which utilizes (pre)acinetobactin to scavenge iron from the host. We report the structure of the (pre)acinetobactin transporter BauA bound to the siderophore, identifying the structural determinants of recognition. Detailed biophysical analysis confirms that BauA recognises preacinetobactin. We show that acinetobactin is not recognised by the protein thus preacinetobactin is essential for iron uptake. The structure shows and NMR confirms that under physiological conditions a molecule of acinetobactin will bind to two free coordination sites on the iron preacinetobactin complex. The ability to recognise a heterotrimeric iron preacinetobactin acinetobactin complex may rationalize contradictory reports in the literature. These results open new avenues for the design of novel antibiotic conjugates (trojan horse) antibiotics.

Data availability

Diffraction data have been deposited in PDB under the accession codes 6H7F, 6H7V, 6HCP.

The following data sets were generated

Article and author information

Author details

  1. Lucile Moynie

    Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Ilaria Serra

    Department of Physics, University of Cagliari, Cagliari, Italy
    Competing interests
    The authors declare that no competing interests exist.
  3. Mariano A Scorciapino

    Department of Physics, University of Cagliari, Cagliari, Italy
    Competing interests
    The authors declare that no competing interests exist.
  4. Emilia Oueis

    The University of St Andrews, St Andrews, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0228-6394
  5. Malcolm GP Page

    Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Matteo Ceccarelli

    Department of Physics, University of Cagliari, Cagliari, Italy
    Competing interests
    The authors declare that no competing interests exist.
  7. James H Naismith

    Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Oxford, United Kingdom
    For correspondence
    naismith@strubi.ox.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6744-5061

Funding

European Union (115525)

  • Lucile Moynie
  • Ilaria Serra
  • Mariano A Scorciapino
  • Malcolm GP Page
  • Matteo Ceccarelli
  • James H Naismith

Wellcome (100209/Z/12/Z)

  • Lucile Moynie
  • James H Naismith

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

Copyright

© 2018, Moynie 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

  • 2,221
    views
  • 333
    downloads
  • 47
    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. Lucile Moynie
  2. Ilaria Serra
  3. Mariano A Scorciapino
  4. Emilia Oueis
  5. Malcolm GP Page
  6. Matteo Ceccarelli
  7. James H Naismith
(2018)
Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogen Acinetobacter baumannii
eLife 7:e42270.
https://doi.org/10.7554/eLife.42270

Share this article

https://doi.org/10.7554/eLife.42270

Further reading

    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology
    A Sofia F Oliveira, Fiona L Kearns ... Adrian J Mulholland
    Short Report

    The spike protein is essential to the SARS-CoV-2 virus life cycle, facilitating virus entry and mediating viral-host membrane fusion. The spike contains a fatty acid (FA) binding site between every two neighbouring receptor-binding domains. This site is coupled to key regions in the protein, but the impact of glycans on these allosteric effects has not been investigated. Using dynamical nonequilibrium molecular dynamics (D-NEMD) simulations, we explore the allosteric effects of the FA site in the fully glycosylated spike of the SARS-CoV-2 ancestral variant. Our results identify the allosteric networks connecting the FA site to functionally important regions in the protein, including the receptor-binding motif, an antigenic supersite in the N-terminal domain, the fusion peptide region, and another allosteric site known to bind heme and biliverdin. The networks identified here highlight the complexity of the allosteric modulation in this protein and reveal a striking and unexpected link between different allosteric sites. Comparison of the FA site connections from D-NEMD in the glycosylated and non-glycosylated spike revealed that glycans do not qualitatively change the internal allosteric pathways but can facilitate the transmission of the structural changes within and between subunits.

    1. Biochemistry and Chemical Biology
    2. Genetics and Genomics
    Conor J Howard, Nathan S Abell ... Nathan B Lubock
    Research Article

    Deep Mutational Scanning (DMS) is an emerging method to systematically test the functional consequences of thousands of sequence changes to a protein target in a single experiment. Because of its utility in interpreting both human variant effects and protein structure-function relationships, it holds substantial promise to improve drug discovery and clinical development. However, applications in this domain require improved experimental and analytical methods. To address this need, we report novel DMS methods to precisely and quantitatively interrogate disease-relevant mechanisms, protein-ligand interactions, and assess predicted response to drug treatment. Using these methods, we performed a DMS of the melanocortin-4 receptor (MC4R), a G-protein-coupled receptor (GPCR) implicated in obesity and an active target of drug development efforts. We assessed the effects of >6600 single amino acid substitutions on MC4R’s function across 18 distinct experimental conditions, resulting in >20 million unique measurements. From this, we identified variants that have unique effects on MC4R-mediated Gαs- and Gαq-signaling pathways, which could be used to design drugs that selectively bias MC4R’s activity. We also identified pathogenic variants that are likely amenable to a corrector therapy. Finally, we functionally characterized structural relationships that distinguish the binding of peptide versus small molecule ligands, which could guide compound optimization. Collectively, these results demonstrate that DMS is a powerful method to empower drug discovery and development.