posted on 2020-03-06, 21:43authored byBoris Fürtig, Eva Marie Oberhauser, Heidi Zetzsche, Dean-Paulos Klötzner, Alexander Heckel, Harald Schwalbe
The
adenine-sensing riboswitch from the Gram-negative bacterium Vibrio vulnificus is an RNA-based gene regulatory element
that acts in response to both its cognate low-molecular weight ligand
and temperature. The combined sensitivity to environmental temperature
and ligand concentration is maintained by an equilibrium of three
distinct conformations involving two ligand-free states and one ligand-bound
state. The key structural element that undergoes refolding in the
ligand-free states comprises a 35-nucleotide temperature response
module. Here, we present the structural characterization of this temperature
response module. We employ high-resolution NMR spectroscopy and photocaged
RNAs as molecular probes to decipher the kinetic and thermodynamic
framework of the secondary structure transition in the apo state of
the riboswitch. We propose a model for the transition state adopted
during the thermal refolding of the temperature response module that
connects two mutually exclusive long-lived and stable conformational
states. This transition state is characterized by a comparatively
low free activation enthalpy. A pseudoknot conformation in the transition
state, as commonly seen in RNA refolding, is therefore unlikely. More
likely, the transition state of the adenine-sensing riboswitch temperature
response module features a linear conformation.