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 J 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

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.

Data availability

The following data sets were generated

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 J 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 J 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

  • 5,159
    Page views
  • 827
    Downloads
  • 41
    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)

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. Didi He
  2. Sam Hughes
  3. Sally Vanden-Hehir
  4. Atanas Georgiev
  5. Kirsten Altenbach
  6. Emma J Tarrant
  7. C Logan Mackay
  8. Kevin J Waldron
  9. David J Clarke
  10. Jon Marles-Wright
(2016)
Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments
eLife 5:e18972.
https://doi.org/10.7554/eLife.18972

Further reading

    1. Biochemistry and Chemical Biology
    Layla Drwesh et al.
    Research Article Updated

    Signal-anchored (SA) proteins are anchored into the mitochondrial outer membrane (OM) via a single transmembrane segment at their N-terminus while the bulk of the proteins is facing the cytosol. These proteins are encoded by nuclear DNA, translated on cytosolic ribosomes, and are then targeted to the organelle and inserted into its OM by import factors. Recently, research on the insertion mechanisms of these proteins into the mitochondrial OM have gained a lot of attention. In contrast, the early cytosolic steps of their biogenesis are unresolved. Using various proteins from this category and a broad set of in vivo, in organello, and in vitro assays, we reconstituted the early steps of their biogenesis. We identified a subset of molecular (co)chaperones that interact with newly synthesized SA proteins, namely, Hsp70 and Hsp90 chaperones and co-chaperones from the Hsp40 family like Ydj1 and Sis1. These interactions were mediated by the hydrophobic transmembrane segments of the SA proteins. We further demonstrate that interfering with these interactions inhibits the biogenesis of SA proteins to a various extent. Finally, we could demonstrate direct interaction of peptides corresponding to the transmembrane segments of SA proteins with the (co)chaperones and reconstitute in vitro the transfer of such peptides from the Hsp70 chaperone to the mitochondrial Tom70 receptor. Collectively, this study unravels an array of cytosolic chaperones and mitochondrial import factors that facilitates the targeting and membrane integration of mitochondrial SA proteins.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Rajesh Sharma et al.
    Research Article

    Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cGMP signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs, complementing drugs that target nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation by cGMP is not well understood. Here we present a crystal structure of PKG Iβ in which the auto-inhibitory sequence and the cyclic nucleotide binding domains are bound to the catalytic domain, providing a snapshot of the auto-inhibited state. Specific contacts between the PKG Iβ auto-inhibitory sequence and the enzyme active site help explain isoform-specific activation constants and the effects of phosphorylation in the linker. We also present a crystal structure of a PKG I cyclic nucleotide binding domain with an activating mutation linked to Thoracic Aortic Aneurysms and Dissections. Similarity of this structure to wild type cGMP-bound domains and differences with the auto-inhibited enzyme provide a mechanistic basis for constitutive activation. We show that PKG Iβ auto-inhibition is mediated by contacts within each monomer of the native full-length dimeric protein, and using the available structural and biochemical data we develop a model for the regulation and cooperative activation of PKGs.