Kwon, J. (2022). Probing putative mRNA/CAR interactions through ribosome profiling. Retrieved from https://doi.org/10.14418/wes01.2.360
The ribosome is an important macromolecular machine as it is responsible for the production of proteins. Recent MD simulations discovered a highly conserved region of the ribosome called the CAR interaction surface (consisting of 16S/18S rRNA C1054, A1196, and R146 of yeast ribosomal protein Rps3), and interactions between the CAR surface and mRNA has been observed. Specifically, the CAR surface hydrogen bonds with the +1 codon which is a codon downstream of the A-site codon. Hence, it has been postulated that the CAR-mRNA interactions may serve as a regulatory mechanism which modulates protein translation rates. However, whether the CAR-mRNA interaction surface can modulate translation rates has yet to be shown. Here we show in our model organism, S. cerevisiae, that there is a possibility that the CAR-mRNA interaction surface is regulating the translation rates under stress conditions. We analyzed pre-existing ribosome profiling datasets and extracted the codon identities of the +1 codons under stressed and unstressed conditions and discovered that the relative ribosome densities of +1 codons change in a direction that suggests the CAR/+1 codon interactions may increase under stress. Our results demonstrate that the CAR-mRNA interaction surface may explain the changes in relative ribosome densities of the +1 codons under stress and suggests that the CAR-mRNA interaction surface may be induced to regulate translation rates. We expect the results of the thesis to be a starting point for a more sophisticated model of the CAR-mRNA interaction surface as additional functional assays can be performed to determine the CAR-mRNA interaction surface’s functions.