Arginine Methylation Regulates Ribosome CAR Function

Abstract

The ribosome CAR interaction surface is hypothesized to provide a layer of translation regulation through hydrogen-bonding to the +1 mRNA codon that is next to enter the ribosome A site during translocation. The CAR surface consists of three residues, 16S/18S rRNA C1054, A1196 (E. coli 16S numbering), and R146 of yeast ribosomal protein Rps3. R146 can be methylated by the Sfm1 methyltransferase which is downregulated in stressed cells. Through molecular dynamics analysis, we show here that methylation of R146 compromises the integrity of CAR by reducing the pi stacking of the R146 guanidinium group with A1196, leading to reduced CAR hydrogen-bonding with the +1 codon. We propose that ribosomes assembled under stressed conditions have unmethylated R146, resulting in elevated CAR/+1 codon interactions, which tunes translation levels in response to the altered cellular context.

Codon Dependency Of Ribosome Car Function

“…At +1 codon nt2, GCU had high hydrogen bonding to R146 while GGU, GAU, and GUU had decreased hydrogen bonding. (Scopino et al, 2021). Thus, the change in hydrogen bond levels between N1 and N2 was due to the inclusion of the rRNA modifications, not the difference in residues included in the subsystem.…”

“…MD simulations provides an ideal model system for the development of a novel approach to conformational analysis because only one perturbation is made to the system and the impact of the methylation of R146 is well characterized. mR146 disrupts the integrity of the CAR surface and decreases hydrogen bonding between the +1 codon and CAR (Scopino et al, 2021).…”

“…Restrained residues are shown as Van der Waals spheres while unrestrained residues are shown as licorice (tRNA and CAR residues), cartoon (mRNA), or wire (all other unrestrained residues). Adapted fromScopino et al 2021.…”