Thermodynamic control of \u22121 programmed ribosomal frameshifting

Lars V Bock,Frank Peske,Natalia Korniy,Marina V Rodnina,Neva Caliskan,Helmut Grubmüller

doi:10.1038/s41467-019-12648-x

Abstract

mRNA contexts containing a ‘slippery’ sequence and a downstream secondary structure element stall the progression of the ribosome along the mRNA and induce its movement into the −1 reading frame. In this study we build a thermodynamic model based on Bayesian statistics to explain how −1 programmed ribosome frameshifting can work. As training sets for the model, we measured frameshifting efficiencies on 64 dnaX mRNA sequence variants in vitro and also used 21 published in vivo efficiencies. With the obtained free-energy difference between mRNA-tRNA base pairs in the 0 and −1 frames, the frameshifting efficiency of a given sequence can be reproduced and predicted from the tRNA−mRNA base pairing in the two frames. Our results further explain how modifications in the tRNA anticodon modulate frameshifting and show how the ribosome tunes the strength of the base-pair interactions.

Highlights

MRNA contexts containing a ‘slippery’ sequence and a downstream secondary structure element stall the progression of the ribosome along the mRNA and induce its movement into the −1 reading frame
Frameshifting is facilitated by mRNA elements that slow down the ribosome progression along the mRNA, such as secondary structures downstream of the slippery site. −1PRF is common in viruses and is found in bacteria and eukaryotes[12,13,14], where it is employed to increase the coding capacity of the genome, define stoichiometry of translation products or to regulate the lifetime of the mRNA
We generated all possible mutant variants that encoded for combinations of either Lys or Phe codons in the 0-frame (Fig. 1, Supplementary Fig. 1a, and Supplementary Table 1). 70S ribosomes programmed with dnaX mRNA and carrying the initiator f[3H]Met-tRNAfMet in the P site were mixed with aminoacyl-tRNAs that are required to translate the mRNA up to the frameshifting site and elongation factors EF-Tu and EF-G

Summary

Introduction

MRNA contexts containing a ‘slippery’ sequence and a downstream secondary structure element stall the progression of the ribosome along the mRNA and induce its movement into the −1 reading frame. Spontaneous ribosome slippage is a rare event that occurs, on average, once in 104–105 codons[5,6] This low spontaneous frameshifting increases dramatically on particular mRNAs that contain sequences for programmed ribosomal frameshifting (PRF). Frameshifting can occur when the delivery of aminoacyl-tRNA to the A site is delayed, e.g., due to the lack of a particular amino acid[20,21,23,24] In this case, a tRNA bound to the P site can slip from the 0-frame to the −1-frame independently of the mRNA secondary structure elements[20,21]. The modified nucleotide mnm5s2U (S) at the first anticodon position (U34 in the tRNA sequence) is important for the wobble base pairing at the third codon position[27]. The interpretation of mutational data and understanding the frameshifting efficiencies at other slippery sequences is hampered by the lack of a conceptual model for −1PRF that could quantitatively predict frameshifting efficiencies for various tRNAs and slippery sequences

Methods

Results

Conclusion