Glutamine synthetase mRNA releases sRNA from its 3´UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae

  1. Masatoshi Miyakoshi  Is a corresponding author
  2. Teppei Morita
  3. Asaki Kobayashi
  4. Anna Berger
  5. Hiroki Takahashi
  6. Yasuhiro Gotoh
  7. Tetsuya Hayashi
  8. Kan Tanaka
  1. University of Tsukuba, Japan
  2. Keio University, Japan
  3. Chiba University, Japan
  4. Kyushu University, Japan
  5. Tokyo Institute of Technology, Japan

Abstract

Glutamine synthetase (GS) is the key enzyme of nitrogen assimilation induced under nitrogen limiting conditions. The carbon skeleton of glutamate and glutamine, 2-oxoglutarate, is supplied from the TCA cycle, but how this metabolic flow is controlled in response to nitrogen availability remains unknown. We show that the expression of the E1o component of 2-oxoglutarate dehydrogenase, SucA, is repressed under nitrogen limitation in Salmonella enterica and E coli. The repression is exerted at the post-transcriptional level by an Hfq-dependent sRNA GlnZ generated from the 3´UTR of the GS-encoding glnA mRNA. Enterobacterial GlnZ variants contain a conserved seed sequence and primarily regulate sucA through base-pairing far upstream of the translation initiation region. During growth on glutamine as the nitrogen source, the glnA 3´UTR deletion mutants expressed SucA at higher levels than the S. enterica and E. coli wild-type strains, respectively. In E. coli, the transcriptional regulator Nac also participates in the repression of sucA. Lastly, this study clarifies that the release of GlnZ from the glnA mRNA by RNase E is essential for the post-transcriptional regulation of sucA. Thus the mRNA coordinates the two independent functions to balance the supply and demand of the fundamental metabolites.

Data availability

The RNA-seq data have been deposited in DDBJ DRA under accession number DRA012682.

The following data sets were generated

Article and author information

Author details

  1. Masatoshi Miyakoshi

    Department of Infection Biology, University of Tsukuba, Tsukuba, Japan
    For correspondence
    mmiyakoshi@md.tsukuba.ac.jp
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4901-2809
  2. Teppei Morita

    Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
    Competing interests
    The authors declare that no competing interests exist.
  3. Asaki Kobayashi

    Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
    Competing interests
    The authors declare that no competing interests exist.
  4. Anna Berger

    International Joint Degree Master's Program in Agro-Biomedical Science in Food and Health, University of Tsukuba, Tsukuba, Japan
    Competing interests
    The authors declare that no competing interests exist.
  5. Hiroki Takahashi

    Medical Mycology Research Center, Chiba University, Chiba, Japan
    Competing interests
    The authors declare that no competing interests exist.
  6. Yasuhiro Gotoh

    Department of Bacteriology, Kyushu University, Fukuoka, Japan
    Competing interests
    The authors declare that no competing interests exist.
  7. Tetsuya Hayashi

    Department of Bacteriology, Kyushu University, Fukuoka, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6366-7177
  8. Kan Tanaka

    Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama, Japan
    Competing interests
    The authors declare that no competing interests exist.

Funding

Japan Society for the Promotion of Science (JP19H03464)

  • Masatoshi Miyakoshi

Japan Society for the Promotion of Science (JP19KK0406)

  • Masatoshi Miyakoshi

Japan Society for the Promotion of Science (JP21K19063)

  • Masatoshi Miyakoshi

Japan Society for the Promotion of Science (JP22H02236)

  • Kan Tanaka

Japan Society for the Promotion of Science (JP16H06279)

  • Hiroki Takahashi
  • Tetsuya Hayashi

Waksman Foundation of Japan

  • Masatoshi Miyakoshi

Takeda Medical Research Foundation

  • Masatoshi Miyakoshi

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

Copyright

© 2022, Miyakoshi 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

  • 1,580
    views
  • 231
    downloads
  • 8
    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. Masatoshi Miyakoshi
  2. Teppei Morita
  3. Asaki Kobayashi
  4. Anna Berger
  5. Hiroki Takahashi
  6. Yasuhiro Gotoh
  7. Tetsuya Hayashi
  8. Kan Tanaka
(2022)
Glutamine synthetase mRNA releases sRNA from its 3´UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae
eLife 11:e82411.
https://doi.org/10.7554/eLife.82411

Share this article

https://doi.org/10.7554/eLife.82411

Further reading

    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease
    Axelle Amen, Randy Yoo ... Matthijs M Jore
    Research Article

    Circulating sexual stages of Plasmodium falciparum (Pf) can be transmitted from humans to mosquitoes, thereby furthering the spread of malaria in the population. It is well established that antibodies can efficiently block parasite transmission. In search for naturally acquired antibodies targets on sexual stages, we established an efficient method for target-agnostic single B cell activation followed by high-throughput selection of human monoclonal antibodies (mAbs) reactive to sexual stages of Pf in the form of gametes and gametocyte extracts. We isolated mAbs reactive against a range of Pf proteins including well-established targets Pfs48/45 and Pfs230. One mAb, B1E11K, was cross-reactive to various proteins containing glutamate-rich repetitive elements expressed at different stages of the parasite life cycle. A crystal structure of two B1E11K Fab domains in complex with its main antigen, RESA, expressed on asexual blood stages, showed binding of B1E11K to a repeating epitope motif in a head-to-head conformation engaging in affinity-matured homotypic interactions. Thus, this mode of recognition of Pf proteins, previously described only for Pf circumsporozoite protein (PfCSP), extends to other repeats expressed across various stages. The findings augment our understanding of immune-pathogen interactions to repeating elements of the Plasmodium parasite proteome and underscore the potential of the novel mAb identification method used to provide new insights into the natural humoral immune response against Pf.

    1. Microbiology and Infectious Disease
    Nicolas Flaugnatti, Loriane Bader ... Melanie Blokesch
    Research Article Updated

    The type VI secretion system (T6SS) is a sophisticated, contact-dependent nanomachine involved in interbacterial competition. To function effectively, the T6SS must penetrate the membranes of both attacker and target bacteria. Structures associated with the cell envelope, like polysaccharides chains, can therefore introduce spatial separation and steric hindrance, potentially affecting the efficacy of the T6SS. In this study, we examined how the capsular polysaccharide (CPS) of Acinetobacter baumannii affects T6SS’s antibacterial function. Our findings show that the CPS confers resistance against T6SS-mediated assaults from rival bacteria. Notably, under typical growth conditions, the presence of the surface-bound capsule also reduces the efficacy of the bacterium’s own T6SS. This T6SS impairment is further enhanced when CPS is overproduced due to genetic modifications or antibiotic treatment. Furthermore, we demonstrate that the bacterium adjusts the level of the T6SS inner tube protein Hcp according to its secretion capacity, by initiating a degradation process involving the ClpXP protease. Collectively, our findings contribute to a better understanding of the dynamic relationship between T6SS and CPS and how they respond swiftly to environmental challenges.