Poster abstracts

Poster number 80 submitted by Blake Sweeney

The role of non Watson Crick base pairs in recurrent 3D motifs in the small subunit of extremophilic ribosomes

Blake A. Sweeney (Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403), Emil F. Khisamutdinov (Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, OH 43403), Anton Alenko (Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, OH 43403), Dr. Craig L. Zirbel (Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403), Dr. Neocles B. Leontis (Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, OH 43403)

Abstract:
Temperature is one of the most important environmental variables to which living organisms adapt. At the molecular level, organisms adapt to different environments by changing the sequences of their macromolecules as well as the compositions of their membranes. At high temperature, macromolecules must resist thermal denaturation, while at low temperatures, they must retain flexibility for reversible binding and catalytic action. An essential component found in all cells is the ribosome. Leveraging atomic-resolution X-ray structures of diverse ribosomes and curated sequence alignments that include psychrophiles, mesophiles, thermophiles and hyperthermophiles, we are studying how ribosomal RNAs (rRNA) evolve to adapt to different environments. Previous work has focused on sequence changes of Watson-Crick paired bases in response to extreme heat, but little work has examined cold adaptation or the roles of non-WC base pairs. The non-WC base pairs comprise about 33% all base pairs in 16S and 23S rRNA and are essential components of RNA 3D motifs, modular structural units that correspond to hairpin, internal and junction loops in secondary structures. Non-WC pairs are also critical components of RNA tertiary and quaternary interactions that stabilize 3D architectures and inter-molecular complexes. We have assembled sequence alignments of bacterial 16S rRNAs, organized by optimal growth temperature, and used them to examine sequence variations at positions that form non-Watson-Crick basepairs. We observe systematic sequence variations at many non-WC paired sites. We examined in detail the sequence variations in the Sarcin/Ricin motif, a highly structured and widespread, recurrent 3D motif. Based on these observations, we designed RNA oligonucleotides containing this motif that correspond to sequence variants found in organisms that grow at different temperature. We measured their thermodynamic properties using UV-melting and isothermal titration calorimetry techniques to elucidate principles of thermal adaptation in recurrent 3D motifs.

Keywords: Temperature adaptation, Motifs