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

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. MacMillan, Christoph Kreutz, Martin Tollinger, Xavier Charpentier, Laetitia Attaiech () and J. N. Mark Glover ()
Additional contact information
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

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-34875-5

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