Organisms live in many extreme environments. Many studies on environmental adaptation have focused on temperature, particularly adaptations to high temperature. However, most of the planet is permanently cold.
Cold adaptation requires a variety of changes to the ribosome, protein structure and lipid content. Previous work has extensively examined protein and lipid adaptations, but little work has considered changes to the ribosome. We are interested in examining the ribosome since it is a large well structured RNA molecule that is critical to cell function. We aim to explore changes in interactions in ribosomes adapted to cold conditions. Previous work has examined the changes in Watson-Crick base pairing and only focused on 2D structure and found decreased hydrogen bonds with decreasing temperature. We focus our work on 3D structure and non-Watson-Crick base pairing. We expect to find changes which decrease the overall hydrogen bonding.
In order to address this issue we have assembled a dataset of optimal growth temperatures of bacterial type strains. We then annotated a sequence alignment with temperatures and aligned it to a high quality 3D structure. Using annotations of base pairs and the correspondences between the alignment and positions in this structure we determined sequence variations of base pairs.
Using our method we were able to reproduce known changes in the Watson-Crick base pairing. We also found that there are statistically significant changes in non-Watson-Crick base pairing that appear to decrease hydrogen bonding. However, these changes are small and they may not be biologically meaningful. In addition, not all individual base pairs show this pattern. This highlights the importance of considering structure in this analysis.