The CAR–mRNA Interaction Surface Is a Zipper Extension of the Ribosome A Site

Carol Dalgarno,Michael P Weir,Kristen Scopino,Mitsu Raval,Clara Nachmanoff,Kelly M Thayer,Eric D Sakkas,Daniel Krizanc

doi:10.3390/ijms23031417

Abstract

The ribosome CAR interaction surface behaves as an extension of the decoding center A site and has H-bond interactions with the +1 codon, which is next in line to enter the A site. Through molecular dynamic simulations, we investigated the codon sequence specificity of this CAR–mRNA interaction and discovered a strong preference for GCN codons, suggesting that there may be a sequence-dependent layer of translational regulation dependent on the CAR interaction surface. Dissection of the CAR–mRNA interaction through nucleotide substitution experiments showed that the first nucleotide of the +1 codon dominates over the second nucleotide position, consistent with an energetically favorable zipper-like activity that emanates from the A site through the CAR–mRNA interface. Moreover, the CAR/+1 codon interaction is affected by the identity of nucleotide 3 of +1 GCN codons, which influences the stacking of G and C. Clustering analysis suggests that the A-site decoding center adopts different neighborhood substates that depend on the identity of the +1 codon.

Highlights

Protein translation is controlled by multiple mechanisms, providing overlapping layers of regulation that operate at the levels of translation initiation, elongation, and termination
We propose that energetically favorable interactions between CAR and the +1 codon are highly sequence specific, implying that CAR regulation of translation depends on the codon content of open reading frames (ORFs)
We investigated the effects of changing the second nucleotide of +1 codons and showed that the CAR/+1 codon interaction is strongest with GCU codons [19]

Summary

Introduction

Protein translation is controlled by multiple mechanisms, providing overlapping layers of regulation that operate at the levels of translation initiation, elongation, and termination. In recent years, increasing evidence has emerged suggesting that alternative versions of ribosomes with different translation properties are made under different cellular conditions, such as stress [13,14,15,16]. Alternative versions of ribosomes arise through several mechanisms: They may lack or have different isoforms of ribosomal proteins or they can have differentially regulated residue modifications in their ribosomal proteins or rRNAs. Alternative versions of ribosomes arise through several mechanisms: They may lack or have different isoforms of ribosomal proteins or they can have differentially regulated residue modifications in their ribosomal proteins or rRNAs Integrating these observations with our structural understanding of ribosome function presents an exciting challenge

Methods

Results

Conclusion