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Mar 29, 2024;

RNA folding kinetics control riboswitch sensitivity in vivo.

David Z Bushhouse, Jiayu Fu, Julius B Lucks
Author Information
  1. David Z Bushhouse: Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA. ORCID
  2. Jiayu Fu: Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA. ORCID
  3. Julius B Lucks: Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA. ORCID
PMID: 38585885 DOI: 10.1101/2024.03.29.587317

Abstract

Riboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity is controlled is critical to understanding how highly conserved aptamer domains are deployed in a variety of contexts with different sensitivity demands. Here we uncover new roles by which RNA folding dynamics control riboswitch sensitivity in cells. By investigating the ZTP riboswitch, we identify multiple mechanistic routes of altering expression platform sequence and structure to slow RNA folding, all of which enhance riboswitch sensitivity. Applying these methods to riboswitches with diverse aptamer architectures that regulate transcription and translation with ON and OFF logic demonstrates the generality of our findings, indicating that any riboswitch that operates in a kinetic regime can be sensitized by slowing expression platform folding. Comparison of the most sensitized versions of these switches to equilibrium aptamer:ligand dissociation constants suggests a limit to the sensitivities achievable by kinetic RNA switches. Our results add to the growing suite of knowledge and approaches that can be used to rationally program cotranscriptional RNA folding for biotechnology applications, and suggest general RNA folding principles for understanding dynamic RNA systems in other areas of biology.

Keywords

RNA dynamics RNA folding Riboswitches Strand Displacement

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Grants

  1. R01 GM130901/NIGMS NIH HHS
  2. T32 GM008382/NIGMS NIH HHS
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