Functional and structural characterization of an ECF-type ABC transporter for vitamin B12

  1. Joana A Santos
  2. Stephan Rempel
  3. Sandra T M Mous
  4. Cristiane T Pereira
  5. Josy ter Beek
  6. Jan-Willem de Gier
  7. Albert Guskov  Is a corresponding author
  8. Dirk Slotboom  Is a corresponding author
  1. University of Groningen, Netherlands
  2. University of Campinas, Brazil
  3. Stockholm University, Sweden

Abstract

Vitamin B12 (cobalamin) is the most complex B-type vitamin and is synthetized exclusively in a limited number of prokaryotes. Its biologically active variants contain rare organometallic bonds, which are used by enzymes in a variety of central metabolic pathways such as L-methionine synthesis and ribonucleotide reduction. Although its biosynthesis and role as co-factor are well understood, knowledge about uptake of cobalamin by prokaryotic auxotrophs is scarce. Here, we characterize a cobalamin-specific ECF-type ABC transporter from Lactobacillus delbrueckii, ECF-CbrT, and demonstrate that it mediates the specific, ATP-dependent uptake of cobalamin. We solved the crystal structure of ECF-CbrT in an apo conformation to 3.4 Å resolution. Comparison with the ECF transporter for folate (ECF-FolT2) from the same organism, reveals how the identical ECF module adjusts to interact with the different substrate binding proteins FolT2 and CbrT. ECF-CbrT is unrelated to the well-characterized B12 transporter BtuCDF, but their biochemical features indicate functional convergence.

Data availability

Diffraction data have been deposited in PDB under the accession code 6FNP.

The following data sets were generated

Article and author information

Author details

  1. Joana A Santos

    Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8294-3405
  2. Stephan Rempel

    Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  3. Sandra T M Mous

    Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  4. Cristiane T Pereira

    Institute of Biology, University of Campinas, Sao Paulo, Brazil
    Competing interests
    The authors declare that no competing interests exist.
  5. Josy ter Beek

    Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  6. Jan-Willem de Gier

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  7. Albert Guskov

    Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
    For correspondence
    a.guskov@rug.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2340-2216
  8. Dirk Slotboom

    Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, Netherlands
    For correspondence
    d.j.slotboom@rug.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5804-9689

Funding

Nederlandse Organisatie voor Wetenschappelijk Onderzoek

  • Josy ter Beek
  • Albert Guskov
  • Dirk Slotboom

European Molecular Biology Organization

  • Joana A Santos
  • Stephan Rempel

Horizon 2020 Framework Programme

  • Dirk Slotboom

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

Reviewing Editor

  1. José D Faraldo-Gómez, National Heart, Lung and Blood Institute, National Institutes of Health, United States

Version history

  1. Received: February 9, 2018
  2. Accepted: May 26, 2018
  3. Accepted Manuscript published: May 29, 2018 (version 1)
  4. Version of Record published: June 12, 2018 (version 2)

Copyright

© 2018, Santos 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

  • 2,799
    views
  • 434
    downloads
  • 37
    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. Joana A Santos
  2. Stephan Rempel
  3. Sandra T M Mous
  4. Cristiane T Pereira
  5. Josy ter Beek
  6. Jan-Willem de Gier
  7. Albert Guskov
  8. Dirk Slotboom
(2018)
Functional and structural characterization of an ECF-type ABC transporter for vitamin B12
eLife 7:e35828.
https://doi.org/10.7554/eLife.35828

Share this article

https://doi.org/10.7554/eLife.35828

Further reading

    1. Biochemistry and Chemical Biology
    2. Neuroscience
    Maximilian Nagel, Marco Niestroj ... Marc Spehr
    Research Article

    In most mammals, conspecific chemosensory communication relies on semiochemical release within complex bodily secretions and subsequent stimulus detection by the vomeronasal organ (VNO). Urine, a rich source of ethologically relevant chemosignals, conveys detailed information about sex, social hierarchy, health, and reproductive state, which becomes accessible to a conspecific via vomeronasal sampling. So far, however, numerous aspects of social chemosignaling along the vomeronasal pathway remain unclear. Moreover, since virtually all research on vomeronasal physiology is based on secretions derived from inbred laboratory mice, it remains uncertain whether such stimuli provide a true representation of potentially more relevant cues found in the wild. Here, we combine a robust low-noise VNO activity assay with comparative molecular profiling of sex- and strain-specific mouse urine samples from two inbred laboratory strains as well as from wild mice. With comprehensive molecular portraits of these secretions, VNO activity analysis now enables us to (i) assess whether and, if so, how much sex/strain-selective ‘raw’ chemical information in urine is accessible via vomeronasal sampling; (ii) identify which chemicals exhibit sufficient discriminatory power to signal an animal’s sex, strain, or both; (iii) determine the extent to which wild mouse secretions are unique; and (iv) analyze whether vomeronasal response profiles differ between strains. We report both sex- and, in particular, strain-selective VNO representations of chemical information. Within the urinary ‘secretome’, both volatile compounds and proteins exhibit sufficient discriminative power to provide sex- and strain-specific molecular fingerprints. While total protein amount is substantially enriched in male urine, females secrete a larger variety at overall comparatively low concentrations. Surprisingly, the molecular spectrum of wild mouse urine does not dramatically exceed that of inbred strains. Finally, vomeronasal response profiles differ between C57BL/6 and BALB/c animals, with particularly disparate representations of female semiochemicals.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Claudia D Consalvo, Adedeji M Aderounmu ... Brenda L Bass
    Research Article

    Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, Caenorhabditis elegans Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1’s helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways.