A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria

  1. John C Whitney
  2. S Brook Peterson
  3. Jungyun Kim
  4. Manuel Pazos
  5. Adrian J Verster
  6. Matthew C Radey
  7. Hemantha D Kulasekara
  8. Mary Q Ching
  9. Nathan P Bullen
  10. Diane Bryant
  11. Young Ah Goo
  12. Michael G Surette
  13. Elhanan Borenstein
  14. Waldemar Vollmer
  15. Joseph D Mougous  Is a corresponding author
  1. McMaster University, Canada
  2. University of Washington, United States
  3. Newcastle University, United Kingdom
  4. Advanced Light Source, United States
  5. Northwestern University, United States

Abstract

The Firmicutes are a phylum of bacteria that dominate numerous polymicrobial habitats of importance to human health and industry. Although these communities are often densely colonized, a broadly distributed contact-dependent mechanism of interbacterial antagonism utilized by Firmicutes has not been elucidated. Here we show that proteins belonging to the LXG polymorphic toxin family present in Streptococus intermedius mediate cell contact- and Esx secretion pathway-dependent growth inhibition of diverse Firmicute species. The structure of one such toxin revealed a previously unobserved protein fold that we demonstrate directs the degradation of a uniquely bacterial molecule required for cell wall biosynthesis, lipid II. Consistent with our functional data linking LXG toxins to interbacterial interactions in S. intermedius, we show that LXG genes are prevalent in the human gut microbiome, a polymicrobial community dominated by Firmicutes. We speculate that interbacterial antagonism mediated by LXG toxins plays a critical role in shaping Firmicute-rich bacterial communities.

Article and author information

Author details

  1. John C Whitney

    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
    Competing interests
    The authors declare that no competing interests exist.
  2. S Brook Peterson

    Department of Microbiology, School of Medicine, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Jungyun Kim

    Department of Microbiology, School of Medicine, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3793-4264
  4. Manuel Pazos

    Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Adrian J Verster

    Department of Genome Sciences, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Matthew C Radey

    Department of Microbiology, School of Medicine, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Hemantha D Kulasekara

    Department of Microbiology, School of Medicine, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Mary Q Ching

    Department of Microbiology, School of Medicine, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Nathan P Bullen

    Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
    Competing interests
    The authors declare that no competing interests exist.
  10. Diane Bryant

    Experimental Systems Group, Advanced Light Source, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Young Ah Goo

    Northwestern Proteomics Core Facility, Northwestern University, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Michael G Surette

    Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
    Competing interests
    The authors declare that no competing interests exist.
  13. Elhanan Borenstein

    Department of Genome Sciences, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Waldemar Vollmer

    Centre for Bacterial Cell Biology, Newcastle University, Newcastle, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  15. Joseph D Mougous

    Department of Microbiology, University of Washington, Seattle, United States
    For correspondence
    mougous@uw.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5417-4861

Funding

Canadian Institutes of Health Research

  • John C Whitney

Natural Sciences and Engineering Research Council of Canada

  • Adrian J Verster

Wellcome (101824/Z/13/Z)

  • Waldemar Vollmer

National Cancer Institute (CCSG P30 CA060553)

  • Young Ah Goo

National Institutes of Health (AI080609)

  • Joseph D Mougous

Howard Hughes Medical Institute

  • Joseph D Mougous

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

Reviewing Editor

  1. Michael T Laub, Massachusetts Institute of Technology, United States

Version history

  1. Received: March 20, 2017
  2. Accepted: July 10, 2017
  3. Accepted Manuscript published: July 11, 2017 (version 1)
  4. Accepted Manuscript updated: July 12, 2017 (version 2)
  5. Version of Record published: August 14, 2017 (version 3)
  6. Version of Record updated: August 24, 2017 (version 4)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 6,924
    views
  • 1,182
    downloads
  • 133
    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. John C Whitney
  2. S Brook Peterson
  3. Jungyun Kim
  4. Manuel Pazos
  5. Adrian J Verster
  6. Matthew C Radey
  7. Hemantha D Kulasekara
  8. Mary Q Ching
  9. Nathan P Bullen
  10. Diane Bryant
  11. Young Ah Goo
  12. Michael G Surette
  13. Elhanan Borenstein
  14. Waldemar Vollmer
  15. Joseph D Mougous
(2017)
A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria
eLife 6:e26938.
https://doi.org/10.7554/eLife.26938

Share this article

https://doi.org/10.7554/eLife.26938

Further reading

    1. Microbiology and Infectious Disease
    Alejandro Prieto, Luïsa Miró ... Antonio Juarez
    Research Article

    Antimicrobial resistance (AMR) poses a significant threat to human health. Although vaccines have been developed to combat AMR, it has proven challenging to associate specific vaccine antigens with AMR. Bacterial plasmids play a crucial role in the transmission of AMR. Our recent research has identified a group of bacterial plasmids (specifically, IncHI plasmids) that encode large molecular mass proteins containing bacterial immunoglobulin-like domains. These proteins are found on the external surface of the bacterial cells, such as in the flagella or conjugative pili. In this study, we show that these proteins are antigenic and can protect mice from infection caused by an AMR Salmonella strain harboring one of these plasmids. Furthermore, we successfully generated nanobodies targeting these proteins, that were shown to interfere with the conjugative transfer of IncHI plasmids. Considering that these proteins are also encoded in other groups of plasmids, such as IncA/C and IncP2, targeting them could be a valuable strategy in combating AMR infections caused by bacteria harboring different groups of AMR plasmids. Since the selected antigens are directly linked to AMR itself, the protective effect extends beyond specific microorganisms to include all those carrying the corresponding resistance plasmids.

    1. Microbiology and Infectious Disease
    Hideo Fukuhara, Kohei Yumoto ... Katsumi Maenaka
    Research Article

    Canine distemper virus (CDV) belongs to morbillivirus, including measles virus (MeV) and rinderpest virus, which causes serious immunological and neurological disorders in carnivores, including dogs and rhesus monkeys, as recently reported, but their vaccines are highly effective. The attachment glycoprotein hemagglutinin (CDV-H) at the CDV surface utilizes signaling lymphocyte activation molecule (SLAM) and Nectin-4 (also called poliovirus-receptor-like-4; PVRL4) as entry receptors. Although fusion models have been proposed, the molecular mechanism of morbillivirus fusion entry is poorly understood. Here, we determined the crystal structure of the globular head domain of CDV-H vaccine strain at 3.2 Å resolution, revealing that CDV-H exhibits a highly tilted homodimeric form with a six-bladed β-propeller fold. While the predicted Nectin-4-binding site is well conserved with that of MeV-H, that of SLAM is similar but partially different, which is expected to contribute to host specificity. Five N-linked sugars covered a broad area of the CDV-H surface to expose receptor-binding sites only, supporting the effective production of neutralizing antibodies. These features are common to MeV-H, although the glycosylation sites are completely different. Furthermore, real-time observation using high-speed atomic force microscopy revealed highly mobile features of the CDV-H dimeric head via the connector region. These results suggest that sugar-shielded tilted homodimeric structure and dynamic conformational changes are common characteristics of morbilliviruses and ensure effective fusion entry and vaccination.