A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

Griffin M Schroeder,Joseph E Wedekind,Jermaine L Jenkins,Maya E Blau,Chapin E Cavender,David H Mathews

doi:10.1038/s41467-021-27790-8

Griffin M Schroeder, Joseph E Wedekind + Show 4 more

Open Access

https://doi.org/10.1038/s41467-021-27790-8

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Journal: Nature Communications	Publication Date: Jan 11, 2022
Citations: 20	License type: open-access

Affiliation: University of Rochester

Abstract

Riboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs. Such RNAs regulate expression of downstream genes by recognizing a specific cellular effector. Although nearly 50 riboswitch classes are known, only a handful recognize multiple effectors. Here, we report the 2.60-Å resolution co-crystal structure of a class I type I preQ1-sensing riboswitch that reveals two effectors stacked atop one another in a single binding pocket. These effectors bind with positive cooperativity in vitro and both molecules are necessary for gene regulation in bacterial cells. Stacked effector recognition appears to be a hallmark of the largest subgroup of preQ1 riboswitches, including those from pathogens such as Neisseria gonorrhoeae. We postulate that binding to stacked effectors arose in the RNA World to closely position two substrates for RNA-mediated catalysis. These findings expand known effector recognition capabilities of riboswitches and have implications for antimicrobial development.

Highlights

Riboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs
PreQ1-I riboswitches are the founding group of bacterial gene regulators that control the cellular concentration of queuosine (Q)[9] (Fig. 1a)—a hypermodified 7-deazapurine nucleobase required for translational fidelity in mammals and bacteria[10,11,12]
Using isothermal titration calorimetry (ITC) with inhouse software that models two interdependent binding sites, we demonstrated that two preQ1 effectors bind with positive cooperativity

Summary

Introduction

Riboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs. We report the 2.60-Å resolution co-crystal structure of a class I type I preQ1-sensing riboswitch that reveals two effectors stacked atop one another in a single binding pocket. These effectors bind with positive cooperativity in vitro and both molecules are necessary for gene regulation in bacterial cells. 1234567890():,; Riboswitches are found primarily in the 5′ leader sequences of bacterial mRNAs where they regulate the expression of genes by recognizing a cognate effector[1,2,3] PreQ1-III (type II) sequences prefer adenosine before the cytidine specificity base, preQ1-II sequences prefer uracil followed by CUA in the 3′-expression platform[9,27]

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