Bacterial flagellar capping proteins adopt diverse oligomeric states

  1. Sandra Postel
  2. Daniel Deredge
  3. Daniel A Bonsor
  4. Xiong Yu
  5. Kay Diederichs
  6. Saskia Helmsing
  7. Aviv Vromen
  8. Assaf Friedler
  9. Michael Hust
  10. Edward H Egelman
  11. Dorothy Beckett
  12. Patrick L Wintrode
  13. Eric J Sundberg  Is a corresponding author
  1. University of Maryland School of Medicine, United States
  2. University of Maryland School of Pharmacy, United States
  3. University of Virginia, United States
  4. University of Konstanz, Germany
  5. Technische Universitaet Braunschweig, Germany
  6. The Hebrew University of Jerusalem, Israel
  7. Technische Universität Braunschweig, Germany
  8. University of Maryland College Park, United States

Abstract

Flagella are critical for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD from Pseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. In combination with a multitude of biophysical and functional analyses, we find that Pseudomonas FliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary between bacteria in protofilament number, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies.

Article and author information

Author details

  1. Sandra Postel

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6717-1870
  2. Daniel Deredge

    Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, United States
    Competing interests
    No competing interests declared.
  3. Daniel A Bonsor

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, United States
    Competing interests
    No competing interests declared.
  4. Xiong Yu

    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, United States
    Competing interests
    No competing interests declared.
  5. Kay Diederichs

    Department of Biology, University of Konstanz, Konstanz, Germany
    Competing interests
    No competing interests declared.
  6. Saskia Helmsing

    Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universitaet Braunschweig, Braunschweig, Germany
    Competing interests
    No competing interests declared.
  7. Aviv Vromen

    Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
    Competing interests
    No competing interests declared.
  8. Assaf Friedler

    Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
    Competing interests
    No competing interests declared.
  9. Michael Hust

    Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
    Competing interests
    No competing interests declared.
  10. Edward H Egelman

    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, United States
    Competing interests
    Edward H Egelman, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4844-5212
  11. Dorothy Beckett

    Department of Chemistry and Biochemistry, University of Maryland College Park, Baltimore, United States
    Competing interests
    No competing interests declared.
  12. Patrick L Wintrode

    Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, United States
    Competing interests
    No competing interests declared.
  13. Eric J Sundberg

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, United States
    For correspondence
    ESundberg@ihv.umaryland.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0478-3033

Funding

National Center for Research Resources (NIH S10 RR15899)

  • Dorothy Beckett

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

Copyright

© 2016, Postel 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

  • 2,446
    views
  • 537
    downloads
  • 42
    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. Sandra Postel
  2. Daniel Deredge
  3. Daniel A Bonsor
  4. Xiong Yu
  5. Kay Diederichs
  6. Saskia Helmsing
  7. Aviv Vromen
  8. Assaf Friedler
  9. Michael Hust
  10. Edward H Egelman
  11. Dorothy Beckett
  12. Patrick L Wintrode
  13. Eric J Sundberg
(2016)
Bacterial flagellar capping proteins adopt diverse oligomeric states
eLife 5:e18857.
https://doi.org/10.7554/eLife.18857

Share this article

https://doi.org/10.7554/eLife.18857

Further reading

    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics
    Liza Dahal, Thomas GW Graham ... Xavier Darzacq
    Research Article

    Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Angel D'Oliviera, Xuhang Dai ... Jeffrey S Mugridge
    Research Article

    The SARS-CoV-2 main protease (Mpro or Nsp5) is critical for production of viral proteins during infection and, like many viral proteases, also targets host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 is recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes cellular protein synthesis and redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain. Evolutionary analysis shows the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 is likely resistant to cleavage. TRMT1 proteolysis results in reduced tRNA binding and elimination of tRNA methyltransferase activity. We also determined the structure of an Mpro-TRMT1 peptide complex that shows how TRMT1 engages the Mpro active site in an uncommon substrate binding conformation. Finally, enzymology and molecular dynamics simulations indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis following substrate binding. Together, these data provide new insights into substrate recognition by SARS-CoV-2 Mpro that could help guide future antiviral therapeutic development and show how proteolysis of TRMT1 during SARS-CoV-2 infection impairs both TRMT1 tRNA binding and tRNA modification activity to disrupt host translation and potentially impact COVID-19 pathogenesis or phenotypes.