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

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-angstrom resolution co-crystal structure of a class I type I preQ(1)-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 preQ(1) 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. Riboswitches contain an aptamer domain that recognizes a metabolite and an expression platform that regulates gene expression. Here the authors report the crystal structure of a preQ(1)-sensing riboswitch from Carnobacterium antarcticus that shows two metabolites in a single binding pocket.

Automated summary

Riboswitches are non-coding RNAs that regulate gene expression in bacteria by recognizing specific cellular effectors. This study reveals the crystal structure of a preQ(1)-sensing riboswitch, showing two effectors stacked in a single binding pocket. The recognition of stacked effectors expands the effector recognition capabilities of riboswitches and has implications for antimicrobial development.