bi8b00345_si_001.pdf (1.64 MB)
Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms
journal contribution
posted on 2018-05-07, 13:23 authored by Kathleen
A. Leamy, Neela H. Yennawar, Philip C. BevilacquaA diverse set of
organisms has adapted to live under extreme conditions.
The molecular origin of the stability is unclear, however. It is not
known whether the adaptation of functional RNAs, which have intricate
tertiary structures, arises from strengthening of tertiary or secondary
structure. Herein we evaluate effects of sequence changes on the thermostability
of tRNAphe using experimental and computational approaches.
To separate out effects of secondary and tertiary structure on thermostability,
we modify base pairing strength in the acceptor stem, which does not
participate in tertiary structure. In dilute solution conditions,
strengthening secondary structure leads to non-two-state thermal denaturation
curves and has small effects on thermostability, or the temperature
at which tertiary structure and function are lost. In contrast, under
cellular conditions with crowding and Mg2+-chelated amino
acids, where two-state cooperative unfolding is maintained, strengthening
secondary structure enhances thermostability. Investigation of stabilities
of each tRNA stem across 44 organisms with a range of optimal growing
temperatures revealed that organisms that grow in warmer environments
have more stable stems. We also used Shannon entropies to identify
positions of higher and lower information content, or sequence conservation,
in tRNAphe and found that secondary structures have modest
information content allowing them to drive thermal adaptation, while
tertiary structures have maximal information content hindering them
from participating in thermal adaptation. Base-paired regions with
no tertiary structure and modest information content thus offer a
facile evolutionary route to enhancing the thermostability of functional
RNA by the simple molecular rules of base pairing.