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.

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  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

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