Nitrosomonas europaea MazF specifically recognises the UGG motif and promotes selective RNA degradation

Tatsuki Miyamoto, Akiko Yokota, Yuri Ota, Masako Tsuruga, Rie Aoi, Satoshi Tsuneda, Naohiro Noda

    Research output: Contribution to journalArticle

    Abstract

    Toxin-antitoxin (TA) systems are implicated in prokaryotic stress adaptation. Previously, bioinformatics analysis predicted that such systems are abundant in some slowly growing chemolithotrophs; e.g., Nitrosomonas europaea. Nevertheless, the molecular functions of these stress-response modules remain largely unclear, limiting insight regarding their physiological roles. Herein, we show that one of the putative MazF family members, encoded at the ALW85-RS04820 locus, constitutes a functional toxin that engenders a TA pair with its cognate MazE antitoxin. The coordinate application of a specialised RNA-Seq and a fluorescence quenching technique clarified that a unique triplet, UGG, serves as the determinant for MazF cleavage. Notably, statistical analysis predicted that two transcripts, which are unique in the autotroph, comprise the prime targets of the MazF endoribonuclease: hydroxylamine dehydrogenase (hao), which is essential for ammonia oxidation, and a large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL), which plays an important role in carbon assimilation. Given that N. europaea obtains energy and reductants via ammonia oxidation and the carbon for its growth from carbon dioxide, the chemolithotroph might use the MazF endoribonuclease to modulate its translation profile and subsequent biochemical reactions.

    Original languageEnglish
    Article number2386
    JournalFrontiers in Microbiology
    Volume9
    Issue numberOCT
    DOIs
    Publication statusPublished - 2018 Oct 8

    Fingerprint

    Nitrosomonas europaea
    Antitoxins
    RNA Stability
    Endoribonucleases
    hydroxylamine dehydrogenase
    Ammonia
    Carbon
    Oxygenases
    Reducing Agents
    Computational Biology
    Carbon Dioxide
    Fluorescence
    RNA
    Growth

    Keywords

    • Ammonia oxidation
    • Carbon fixation
    • MazEF
    • Nitrosomonas europaea
    • RNase
    • Sequence-specificity
    • Toxin-antitoxin system

    ASJC Scopus subject areas

    • Microbiology
    • Microbiology (medical)

    Cite this

    Nitrosomonas europaea MazF specifically recognises the UGG motif and promotes selective RNA degradation. / Miyamoto, Tatsuki; Yokota, Akiko; Ota, Yuri; Tsuruga, Masako; Aoi, Rie; Tsuneda, Satoshi; Noda, Naohiro.

    In: Frontiers in Microbiology, Vol. 9, No. OCT, 2386, 08.10.2018.

    Research output: Contribution to journalArticle

    Miyamoto, Tatsuki ; Yokota, Akiko ; Ota, Yuri ; Tsuruga, Masako ; Aoi, Rie ; Tsuneda, Satoshi ; Noda, Naohiro. / Nitrosomonas europaea MazF specifically recognises the UGG motif and promotes selective RNA degradation. In: Frontiers in Microbiology. 2018 ; Vol. 9, No. OCT.
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