Arginine Methylation Regulates Ribosome CAR Function.

Kristen Scopino,Michael P Weir,Carol Dalgarno,Clara Nachmanoff,Daniel Krizanc,Kelly M Thayer

doi:10.3390/ijms22031335

Kristen Scopino, Michael P Weir + Show 4 more

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https://doi.org/10.3390/ijms22031335

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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 cation-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.

Highlights

Many of these control points are modulated by post-translational modifications such as: through stress-signaled phosphorylation of the alpha-subunit of EIF2 which blocks translation initiation [1,2]; stress-induced inhibitory phosphorylation of EEF2 leading to inhibition of translation elongation [3]; stress-regulated halting of translation through K63 polyubiquitination of ribosome proteins at multiple mainly solvent-exposed sites [4,5]; and stress-mediated modulation of tRNA modifications including nucleotides of the anticodon loop which are important in translation fidelity, frameshifting, and translation efficiency [6,7,8]
Molecular dynamics (MD) studies have provided important insights into ribosome function [22,23]. This has included the use of ribosome subsystems to characterize important steps in recognition of the correct tRNA through interactions of 16S/18S A1492, A1493 and G530 (E. coli numbering) with the minor groove of the codon-anticodon base pairs in the A-site decoding center [22,24,25]
We used a subsystem of the yeast ribosome with 495 residues—183 rRNA nucleotides and 312 ribosomal protein amino acids—and applied a restraining force on an “onion shell” of residues around the surface of the subsystem in order to maintain the topologies and structures of the different translocation stages of the yeast ribosome identified in cryo-EM studies [12]

Summary

Introduction

Protein translation is regulated under different cellular conditions by multiple mechanisms including control of translation initiation, elongation, termination, and ribosome biogenesis. Many of these control points are modulated by post-translational modifications such as: through stress-signaled phosphorylation of the alpha-subunit of EIF2 which blocks translation initiation [1,2]; stress-induced inhibitory phosphorylation of EEF2 leading to inhibition of translation elongation [3]; stress-regulated halting of translation through K63 polyubiquitination of ribosome proteins at multiple mainly solvent-exposed sites [4,5]; and stress-mediated modulation of tRNA modifications including nucleotides of the anticodon loop which are important in translation fidelity, frameshifting, and translation efficiency [6,7,8].

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