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Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones

Author

Listed:
  • Hyeong Jin Kim

    (University of Alberta)

  • Mazzen Black

    (University of Alberta)

  • Ross A. Edwards

    (University of Alberta)

  • Flora Peillard-Fiorente

    (Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université de Lyon)

  • Rashmi Panigrahi

    (University of Alberta)

  • David Klingler

    (University of Innsbruck)

  • Reiner Eidelpes

    (University of Innsbruck)

  • Ricarda Zeindl

    (University of Innsbruck)

  • Shiyun Peng

    (University of Alberta)

  • Jikun Su

    (University of Alberta)

  • Ayat R. Omar

    (University of Alberta)

  • Andrew M. MacMillan

    (University of Alberta)

  • Christoph Kreutz

    (University of Innsbruck)

  • Martin Tollinger

    (University of Innsbruck)

  • Xavier Charpentier

    (Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université de Lyon)

  • Laetitia Attaiech

    (Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université de Lyon)

  • J. N. Mark Glover

    (University of Alberta)

Abstract

The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. The structure reveals specific recognition of the 3’ nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila. Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3’ ssRNA tail.

Suggested Citation

  • Hyeong Jin Kim & Mazzen Black & Ross A. Edwards & Flora Peillard-Fiorente & Rashmi Panigrahi & David Klingler & Reiner Eidelpes & Ricarda Zeindl & Shiyun Peng & Jikun Su & Ayat R. Omar & Andrew M. Mac, 2022. "Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34875-5
    DOI: 10.1038/s41467-022-34875-5
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    References listed on IDEAS

    as
    1. Saskia Bauriedl & Milan Gerovac & Nadja Heidrich & Thorsten Bischler & Lars Barquist & Jörg Vogel & Christoph Schoen, 2020. "The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
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