1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
Download icon

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments

  1. Didi He
  2. Sam Hughes
  3. Sally Vanden-Hehir
  4. Atanas Georgiev
  5. Kirsten Altenbach
  6. Emma Tarrant
  7. C Logan Mackay
  8. Kevin J Waldron
  9. David J Clarke  Is a corresponding author
  10. Jon Marles-Wright  Is a corresponding author
  1. The University of Edinburgh, United Kingdom
  2. Newcastle University, United Kingdom
Research Article
  • Cited 16
  • Views 3,866
  • Annotations
Cite this article as: eLife 2016;5:e18972 doi: 10.7554/eLife.18972

Abstract

Ferritins are ubiquitous proteins that oxidise and store iron within a protein shell to protect cells from oxidative damage. We have characterized the structure and function of a new member of the ferritin superfamily that is sequestered within an encapsulin capsid. We show that this encapsulated ferritin (EncFtn) has two main alpha helices, which assemble in a metal dependent manner to form a ferroxidase center at a dimer interface. EncFtn adopts an open decameric structure that is topologically distinct from other ferritins. While EncFtn acts as a ferroxidase, it cannot mineralize iron. Conversely, the encapsulin shell associates with iron, but is not enzymatically active, and we demonstrate that EncFtn must be housed within the encapsulin for iron storage. This encapsulin nanocompartment is widely distributed in bacteria and archaea and represents a distinct class of iron storage system, where the oxidation and mineralization of iron are distributed between two proteins.

Article and author information

Author details

  1. Didi He

    Institute of Quantitative Biology, Biochemistry and Biotechnology, The University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Sam Hughes

    The School of Chemistry, The University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Sally Vanden-Hehir

    The School of Chemistry, The University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Atanas Georgiev

    Institute of Quantitative Biology, Biochemistry and Biotechnology, The University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Kirsten Altenbach

    Institute of Quantitative Biology, Biochemistry and Biotechnology, The University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Emma Tarrant

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcasle upon Tyne, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. C Logan Mackay

    The School of Chemistry, The University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Kevin J Waldron

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5577-7357
  9. David J Clarke

    The School of Chemistry, The University of Edinburgh, Edinburgh, United Kingdom
    For correspondence
    dave.clarke@ed.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
  10. Jon Marles-Wright

    Institute of Quantitative Biology, Biochemistry and Biotechnology, The University of Edinburgh, Edinburgh, United Kingdom
    For correspondence
    jon.marles-wright1@ncl.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9156-3284

Funding

Royal Society (RG130585)

  • Jon Marles-Wright

China Scholarship Council

  • Didi He

Biotechnology and Biological Sciences Research Council (BB/N005570/1)

  • David J Clarke
  • Jon Marles-Wright

Wellcome Trust (098375/Z/12/Z)

  • Emma Tarrant
  • Kevin J Waldron

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

Reviewing Editor

  1. Richard Losick, Harvard University, United States

Publication history

  1. Received: June 24, 2016
  2. Accepted: August 14, 2016
  3. Accepted Manuscript published: August 16, 2016 (version 1)
  4. Accepted Manuscript updated: August 24, 2016 (version 2)
  5. Version of Record published: September 6, 2016 (version 3)

Copyright

© 2016, He 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

  • 3,866
    Page views
  • 710
    Downloads
  • 16
    Citations

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

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
    2. Neuroscience
    Nami Kitajima et al.
    Research Article Updated

    Adenosine 5’ triphosphate (ATP) is a ubiquitous extracellular signaling messenger. Here, we describe a method for in-vivo imaging of extracellular ATP with high spatiotemporal resolution. We prepared a comprehensive set of cysteine-substitution mutants of ATP-binding protein, Bacillus FoF1-ATP synthase ε subunit, labeled with small-molecule fluorophores at the introduced cysteine residue. Screening revealed that the Cy3-labeled glutamine-105 mutant (Q105C-Cy3; designated ATPOS) shows a large fluorescence change in the presence of ATP, with submicromolar affinity, pH-independence, and high selectivity for ATP over ATP metabolites and other nucleotides. To enable in-vivo validation, we introduced BoNT/C-Hc for binding to neuronal plasma membrane and Alexa Fluor 488 for ratiometric measurement. The resulting ATPOS complex binds to neurons in cerebral cortex of living mice, and clearly visualized a concentrically propagating wave of extracellular ATP release in response to electrical stimulation. ATPOS should be useful to probe the extracellular ATP dynamics of diverse biological processes in vivo.

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression
    Syafiq Abd Wahab, Dirk Remus
    Research Article Updated

    Eukaryotic replication origins are licensed by the loading of the replicative DNA helicase, Mcm2-7, in inactive double hexameric form around DNA. Subsequent origin activation is under control of multiple protein kinases that either promote or inhibit origin activation, which is important for genome maintenance. Using the reconstituted budding yeast DNA replication system, we find that the flexible N-terminal extension (NTE) of Mcm2 promotes the stable recruitment of Dbf4-dependent kinase (DDK) to Mcm2-7 double hexamers, which in turn promotes DDK phosphorylation of Mcm4 and −6 and subsequent origin activation. Conversely, we demonstrate that the checkpoint kinase, Rad53, inhibits DDK binding to Mcm2-7 double hexamers. Unexpectedly, this function is not dependent on Rad53 kinase activity, suggesting steric inhibition of DDK by activated Rad53. These findings identify critical determinants of the origin activation reaction and uncover a novel mechanism for checkpoint-dependent origin inhibition.