Structure-function analysis of Lactiplantibacillus plantarum DltE& reveals D-alanylated lipoteichoic acids as direct cues supporting Drosophila juvenile growth

  1. Nikos Nikolopoulos
  2. Renata Matos
  3. Stephanie Ravaud
  4. Pascal Courtin
  5. Houssam Akherraz
  6. Simon Palussiere
  7. Virginie Gueguen-Chaignon
  8. Marie Salomon-Mallet
  9. Alain Guillot
  10. Yann Guerardel
  11. Marie-Pierre Chapot-Chartier  Is a corresponding author
  12. Christophe Grangeasse  Is a corresponding author
  13. François Leulier  Is a corresponding author
  1. CNRS UMR 5086, Universite Claude Bernard, France
  2. Ecole Normale Supérieure de Lyon, France
  3. Universite Paris-Saclay, INRAE, France
  4. CNRS UAR3444, INSERM US8, Universite Claude Bernard, France
  5. Univ Lille, CNRS, UMR 8576, France

Abstract

Metazoans establish mutually beneficial interactions with their resident microorganisms. However, our understanding of the microbial cues contributing to host physiology remains elusive. Previously, we identified a bacterial machinery encoded by the dlt operon involved in Drosophila melanogaster's juvenile growth promotion by Lactiplantibacillus plantarum. Here, using crystallography combined with biochemical and cellular approaches, we investigate the physiological role of an uncharacterized protein (DltE) encoded by this operon. We show that lipoteichoic acids (LTAs) but not wall teichoic acids are D-alanylated in Lactiplantibacillus plantarumNC8 cell envelope and demonstrate that DltE is a D-Ala carboxyesterase removing D-Ala from LTA. Using the mutualistic association of L. plantarumNC8 and Drosophila melanogaster as a symbiosis model, we establish that D-alanylated LTAs (D-Ala-LTAs) are direct cues supporting intestinal peptidase expression and juvenile growth in Drosophila. Our results pave the way to probing the contribution of D-Ala-LTAs to host physiology in other symbiotic models.

Data availability

-Diffraction data have been deposited in PDB under the accession codes 8AGR/8AIK/8AJI/8AKH-All data generated during this study are included in the manuscript and supporting file and a single Source Data file has been provided.

The following data sets were generated

Article and author information

Author details

  1. Nikos Nikolopoulos

    Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Universite Claude Bernard, Lyon, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Renata Matos

    Institut de Génomique Fonctionnelle d eLyon, Ecole Normale Supérieure de Lyon, Lyon, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7480-6099
  3. Stephanie Ravaud

    Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Universite Claude Bernard, Lyon, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5867-0785
  4. Pascal Courtin

    Micalis Institute, Universite Paris-Saclay, INRAE, Jouy-en-Josas, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Houssam Akherraz

    Institut de Genomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Simon Palussiere

    Micalis Institute, Universite Paris-Saclay, INRAE, Jouy-en-Josas, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Virginie Gueguen-Chaignon

    Protein Science Facility, CNRS UAR3444, INSERM US8, Universite Claude Bernard, Lyon, France
    Competing interests
    The authors declare that no competing interests exist.
  8. Marie Salomon-Mallet

    Micalis Institute, Universite Paris-Saclay, INRAE, Jouy-en-Josas, France
    Competing interests
    The authors declare that no competing interests exist.
  9. Alain Guillot

    Micalis Institute, Universite Paris-Saclay, INRAE, Jouy-en-Josas, France
    Competing interests
    The authors declare that no competing interests exist.
  10. Yann Guerardel

    Unite de Glycobiologie Structurale et Fonctionnelle, Univ Lille, CNRS, UMR 8576, Lille, France
    Competing interests
    The authors declare that no competing interests exist.
  11. Marie-Pierre Chapot-Chartier

    Micalis Institute, Universite Paris-Saclay, INRAE, Jouy-en-Josas, France
    For correspondence
    marie-pierre.chapot-chartier@inrae.fr
    Competing interests
    The authors declare that no competing interests exist.
  12. Christophe Grangeasse

    Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Universite Claude Bernard, Lyon, France
    For correspondence
    christophe.grangeasse@ibcp.fr
    Competing interests
    The authors declare that no competing interests exist.
  13. François Leulier

    Institut de Génomique Fonctionnelle d eLyon, Ecole Normale Supérieure de Lyon, Lyon, France
    For correspondence
    francois.leulier@ens-lyon.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4542-3053

Funding

Agence Nationale de la Recherche (ANR-18-CE15-0011)

  • Nikos Nikolopoulos
  • Renata Matos
  • Stephanie Ravaud
  • Pascal Courtin
  • Houssam Akherraz
  • Simon Palussiere
  • Virginie Gueguen-Chaignon
  • Marie Salomon-Mallet
  • Alain Guillot
  • Yann Guerardel
  • Marie-Pierre Chapot-Chartier
  • Christophe Grangeasse
  • François Leulier

Fondation pour la Recherche Médicale (DEQ20180839196)

  • Renata Matos
  • Houssam Akherraz
  • François Leulier

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

Copyright

© 2023, Nikolopoulos 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

  • 1,282
    views
  • 213
    downloads
  • 7
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

Share this article

https://doi.org/10.7554/eLife.84669

Further reading

    1. Microbiology and Infectious Disease
    Carley N Gray, Manickam Ashokkumar ... Michael Emerman
    Research Article

    The latent HIV reservoir is a major barrier to HIV cure. Combining latency reversal agents (LRAs) with differing mechanisms of action such as AZD5582, a non-canonical NF-kB activator, and I-BET151, a bromodomain inhibitor is appealing toward inducing HIV-1 reactivation. However, even this LRA combination needs improvement as it is inefficient at activating proviruses in cells of people living with HIV (PLWH). We performed a CRISPR screen in conjunction with AZD5582 & I-BET151 and identified a member of the Integrator complex as a target to improve this LRA combination, specifically Integrator complex subunit 12 (INTS12). Integrator functions as a genome-wide attenuator of transcription that acts on elongation through its RNA cleavage and phosphatase modules. Knockout of INTS12 improved latency reactivation at the transcriptional level and is more specific to the HIV-1 provirus than AZD5582 & I-BET151 treatment alone. We found that INTS12 is present on chromatin at the promoter of HIV and therefore its effect on HIV may be direct. Additionally, we observed more RNAPII in the gene body of HIV only with the combination of INTS12 knockout with AZD5582 & I-BET151, indicating that INTS12 induces a transcriptional elongation block to viral reactivation. Moreover, knockout of INTS12 increased HIV-1 reactivation in CD4 T cells from virally suppressed PLWH ex vivo, and we detected viral RNA in the supernatant from CD4 T cells of all three virally suppressed PLWH tested upon INTS12 knockout, suggesting that INTS12 prevents full-length HIV RNA production in primary T cells. Finally, we found that INTS12 more generally limits the efficacy of a variety of LRAs with different mechanisms of action.

    1. Microbiology and Infectious Disease
    McKenna Harpring, Junghoon Lee ... John V Cox
    Research Article

    Chlamydia trachomatis serovar L2 (Ct), an obligate intracellular bacterium that does not encode FtsZ, divides by a polarized budding process. In the absence of FtsZ, we show that FtsK, a chromosomal translocase, is critical for divisome assembly in Ct. Chlamydial FtsK forms discrete foci at the septum and at the base of the progenitor mother cell, and our data indicate that FtsK foci at the base of the mother cell mark the location of nascent divisome complexes that form at the site where a daughter cell will emerge in the next round of division. The divisome in Ct has a hybrid composition, containing elements of the divisome and elongasome from other bacteria, and FtsK is recruited to nascent divisomes prior to the other chlamydial divisome proteins assayed, including the PBP2 and PBP3 transpeptidases, and MreB and MreC. Knocking down FtsK prevents divisome assembly in Ct and inhibits cell division and septal peptidoglycan synthesis. We further show that MreB does not function like FtsZ and serve as a scaffold for the assembly of the Ct divisome. Rather, MreB is one of the last proteins recruited to the chlamydial divisome, and it is necessary for the formation of septal peptidoglycan rings. Our studies illustrate the critical role of chlamydial FtsK in coordinating divisome assembly and peptidoglycan synthesis in this obligate intracellular bacterial pathogen.