Hierarchical mechanism of amino acid sensing by the T-box riboswitch

Krishna C. Suddala, Javier Cabello-Villegas, Malgorzata Michnicka, Collin Marshall, Edward P. Nikonowicz () and Nils G. Walter ()
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Krishna C. Suddala: University of Michigan
Javier Cabello-Villegas: University of Michigan
Malgorzata Michnicka: Rice University
Collin Marshall: University of Michigan
Edward P. Nikonowicz: Rice University
Nils G. Walter: University of Michigan

Nature Communications, 2018, vol. 9, issue 1, 1-14

Abstract: Abstract In Gram-positive bacteria, T-box riboswitches control gene expression to maintain the cellular pools of aminoacylated tRNAs essential for protein biosynthesis. Co-transcriptional binding of an uncharged tRNA to the riboswitch stabilizes an antiterminator, allowing transcription read-through, whereas an aminoacylated tRNA does not. Recent structural studies have resolved two contact points between tRNA and Stem-I in the 5′ half of the T-box riboswitch, but little is known about the mechanism empowering transcriptional control by a small, distal aminoacyl modification. Using single-molecule fluorescence microscopy, we have probed the kinetic and structural underpinnings of tRNA binding to a glycyl T-box riboswitch. We observe a two-step mechanism where fast, dynamic recruitment of tRNA by Stem-I is followed by ultra-stable anchoring by the downstream antiterminator, but only without aminoacylation. Our results support a hierarchical sensing mechanism wherein dynamic global binding of the tRNA body is followed by localized readout of its aminoacylation status by snap-lock-based trapping.

Date: 2018
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DOI: 10.1038/s41467-018-04305-6

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