Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA

Abstract
Data availability
Article and author information
Metrics

Abstract

Two classes of riboswitches related to the ykkC guanidine-I riboswitch bind phosphoribosyl pyrophosphate (PRPP) and guanosine tetraphosphate (ppGpp). Here we report the co-crystal structure of the PRPP aptamer and its ligand. We also report the structure of the G96A point mutant that prefers ppGpp over PRPP with a dramatic 40,000-fold switch in specificity. The ends of the aptamer form a helix that is not present in the guanidine aptamer and is involved in the expression platform. In the mutant, the base of ppGpp replaces G96 in three-dimensional space. This disrupts the S-turn, which is a primary structural feature of the ykkC RNA motif. These dramatic differences in ligand specificity are achieved with minimal mutations. ykkC aptamers are therefore a prime example of an RNA fold with a rugged fitness landscape. The ease with which the ykkC aptamer acquires new specificity represents a striking case of evolvability in RNA.

Data availability

Diffraction data and coordinates have been deposited under the accession codes 6CK4 and 6CK5.

The following data sets were generated

The following previously published data sets were used

(2018) Structure of a guanidine-I riboswitch from S. acidophilus
5T83.

https://www.rcsb.org/structure/5T83

Article and author information

Author details

Andrew John Knappenberger

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2659-4305
Caroline Wetherington Reiss

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States

Competing interests
The authors declare that no competing interests exist.
Scott A Strobel

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States

For correspondence
scott.strobel@yale.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8402-4226

Funding

National Institutes of Health (GM022778)

Scott A Strobel

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.