1. Chromosomes and Gene Expression
  2. Genetics and Genomics
Download icon

A genetic selection reveals functional metastable structures embedded in a toxin-encoding mRNA

  1. Sara Masachis
  2. Nicolas J Tourasse
  3. Claire Lays
  4. Marion Faucher
  5. Sandrine Chabas
  6. Isabelle Iost
  7. Fabien Darfeuille  Is a corresponding author
  1. INSERM U1212, CNRS UMR5320, University of Bordeaux, France
Research Article
  • Cited 8
  • Views 1,200
  • Annotations
Cite this article as: eLife 2019;8:e47549 doi: 10.7554/eLife.47549

Abstract

Post-transcriptional regulation plays important roles to finely tune gene expression in bacteria. In particular, regulation of type I toxin-antitoxin (TA) systems is achieved through sophisticated mechanisms involving toxin mRNA folding. Here, we set up a genetic approach to decipher the molecular underpinnings behind the regulation of a type I TA in Helicobacter pylori. We used the lethality induced by chromosomal inactivation of the antitoxin to select mutations that suppress toxicity. We found that single point mutations are sufficient to allow cell survival. Mutations located either in the 5' untranslated region or within the open reading frame of the toxin hamper its translation by stabilizing stem-loop structures that sequester the Shine-Dalgarno sequence. We propose that these short hairpins correspond to metastable structures that are transiently formed during transcription to avoid premature toxin expression. This work uncovers the co-transcriptional inhibition of translation as an additional layer of TA regulation in bacteria.

Data availability

Sequencing data have been deposited in GEO under accession code GSE121423

The following data sets were generated

Article and author information

Author details

  1. Sara Masachis

    ARNA laboratory, INSERM U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Nicolas J Tourasse

    ARNA laboratory, INSERM U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France
    Competing interests
    The authors declare that no competing interests exist.
  3. Claire Lays

    ARNA laboratory, INSERM U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France
    Competing interests
    The authors declare that no competing interests exist.
  4. Marion Faucher

    ARNA laboratory, INSERM U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Sandrine Chabas

    ARNA laboratory, INSERM U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Isabelle Iost

    ARNA laboratory, INSERM U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Fabien Darfeuille

    ARNA laboratory, INSERM U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France
    For correspondence
    fabien.darfeuille@inserm.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1167-6113

Funding

Agence Nationale de la Recherche (ANR-12-BSV5-0025-Bactox1)

  • Sandrine Chabas
  • Isabelle Iost
  • Fabien Darfeuille

H2020 Marie Skłodowska-Curie Actions (642738)

  • Sara Masachis
  • Fabien Darfeuille

Agence Nationale de la Recherche (ANR-12-BSV6-007- asSUPYCO)

  • Sandrine Chabas
  • Isabelle Iost
  • Fabien Darfeuille

Institut National de la Santé et de la Recherche Médicale (U1212)

  • Sara Masachis
  • Nicolas J Tourasse
  • Marion Faucher
  • Sandrine Chabas
  • Isabelle Iost
  • Fabien Darfeuille

Centre National de la Recherche Scientifique (UMR 5320)

  • Isabelle Iost
  • Fabien Darfeuille

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

Reviewing Editor

  1. Gisela Storz, National Institute of Child Health and Human Development, United States

Publication history

  1. Received: April 9, 2019
  2. Accepted: August 14, 2019
  3. Accepted Manuscript published: August 14, 2019 (version 1)
  4. Version of Record published: September 9, 2019 (version 2)

Copyright

© 2019, Masachis 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

  • 1,200
    Page views
  • 151
    Downloads
  • 8
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Chromosomes and Gene Expression
    Alessandro Stirpe et al.
    Research Article

    The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast Schizosaccharomyces pombe, and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remain to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to clr4 deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbors a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.

    1. Chromosomes and Gene Expression
    2. Microbiology and Infectious Disease
    Michele Felletti et al.
    Research Article

    The ability to regulate DNA replication initiation in response to changing nutrient conditions is an important feature of most cell types. In bacteria, DNA replication is triggered by the initiator protein DnaA, which has long been suggested to respond to nutritional changes; nevertheless, the underlying mechanisms remain poorly understood. Here, we report a novel mechanism that adjusts DnaA synthesis in response to nutrient availability in Caulobacter crescentus. By performing a detailed biochemical and genetic analysis of the dnaA mRNA, we identified a sequence downstream of the dnaA start codon that inhibits DnaA translation elongation upon carbon exhaustion. Our data show that the corresponding peptide sequence, but not the mRNA secondary structure or the codon choice, is critical for this response, suggesting that specific amino acids in the growing DnaA nascent chain tune translational efficiency. Our study provides new insights into DnaA regulation and highlights the importance of translation elongation as a regulatory target. We propose that translation regulation by nascent chain sequences, like the one described, might constitute a general strategy for modulating the synthesis rate of specific proteins under changing conditions.