Hyeong Jin Kim 1, Mazzen Black 1, Ross A. Edwards1, Flora Peillard-Fiorente 2, Rashmi Panigrahi 1, David Klingler 3, Reiner Eidelpes 3, Ricarda Zeindl 3, Shiyun Peng1, Jikun Su1, Ayat R. Omar1, Andrew M. MacMillan1, Christoph Kreutz 3, Martin Tollinger 3, Xavier Charpentier 2, Laetitia Attaiech 2 & J. N. Mark Glover 1
1Department of Biochemistry, University of Alberta, Edmonton, AB T6G2H7, Canada. 2CIRI, Centre International de Recherche en Infectiologie, Team “Horizontal gene transfer in bacterial pathogens”, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université de Lyon, 69100 Villeurbanne, France. 3Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
Corresponding author:Laetitia Attaiech & J. N. Mark Glover
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.