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


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.

SUBMITTER: Knappenberger AJ 

PROVIDER: S-EPMC6031431 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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

Knappenberger Andrew John AJ   Reiss Caroline Wetherington CW   Strobel Scott A SA  

eLife 20180607


Two classes of riboswitches related to the <i>ykkC</i> 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  ...[more]

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