TY - JOUR
T1 - Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms
AU - Leamy, Kathleen A.
AU - Yennawar, Neela H.
AU - Bevilacqua, Philip C.
N1 - Funding Information:
The authors thank Dr. Richard Gillian and Dr. Jesse Hopkins for help with small-angle X-ray scattering experiments. Experiments conducted at the Cornell High Energy Synchrotron Source (CHESS) were supported by NSF Grant DMR-0936384, using the Macromolecular Diffraction at CHESS (MacCHESS) facility, which is supported by Grant GM-103485 from the National Institutes of Health, through its National Institute of General Medical Sciences. The authors thank Elizabeth Jolley, Raghav Poudyal, Laura Ritchey, Jacob Sieg, and Ryota Yamagami for helpful comments on and discussions about the manuscript.
Funding Information:
*Address: 104 Chemistry Building, Pennsylvania State University, University Park, PA 16802. E-mail: pcb5@psu. edu. Phone: 814-863-3812. ORCID Philip C. Bevilacqua: 0000-0001-8074-3434 Funding This work was supported by National Institutes of Health Grant R01-GM110237 (P.C.B.). Notes The authors declare no competing financial interest.
Publisher Copyright:
Copyright © 2018 American Chemical Society.
PY - 2018/5/22
Y1 - 2018/5/22
N2 - A 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.
AB - A 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.
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U2 - 10.1021/acs.biochem.8b00345
DO - 10.1021/acs.biochem.8b00345
M3 - Article
C2 - 29733204
AN - SCOPUS:85047548414
VL - 57
SP - 2994
EP - 3002
JO - Biochemistry
JF - Biochemistry
SN - 0006-2960
IS - 20
ER -