A possible universal role for mRNA secondary structure in bacterial translation revealed using a synthetic operon

Yonatan Chemla,Tamir Tuller,Lital Alfonta,Mogens Høgh Jensen,Michael Peeri,Jerry Eichler,Mathias Luidor Heltberg

doi:10.1038/s41467-020-18577-4

Abstract

In bacteria, translation re-initiation is crucial for synthesizing proteins encoded by genes that are organized into operons. The mechanisms regulating translation re-initiation remain, however, poorly understood. We now describe the ribosome termination structure (RTS), a conserved and stable mRNA secondary structure localized immediately downstream of stop codons, and provide experimental evidence for its role in governing re-initiation efficiency in a synthetic Escherichia coli operon. We further report that RTSs are abundant, being associated with 18%–65% of genes in 128 analyzed bacterial genomes representing all phyla, and are selectively depleted when translation re-initiation is advantageous yet selectively enriched so as to insulate translation when re-initiation is deleterious. Our results support a potentially universal role for the RTS in controlling translation termination-insulation and re-initiation across bacteria.

Highlights

In bacteria, translation re-initiation is crucial for synthesizing proteins encoded by genes that are organized into operons
In bacteria, where a single mRNA transcript can contain several genes clustered into an operon, translation initiation must account for the space between genes
This distance is too small to simultaneously accommodate one ribosome terminating on the stop codon of the proximal gene and a second ribosome initiating de novo translation on the start codon of the distal gene[3]

Summary

Introduction

Translation re-initiation is crucial for synthesizing proteins encoded by genes that are organized into operons. When monocistronic mRNA encoding a single gene is translated, spatial considerations that could interfere with ribosome binding are largely irrelevant. The intergenic distance between most of the neighboring cistrons is shorter than 25–30 nucleotides[2,3] This distance is too small to simultaneously accommodate one ribosome terminating on the stop codon of the proximal gene and a second ribosome initiating de novo translation on the start codon of the distal gene[3]. Using Escherichia coli transformed with a synthetic operon as a model system, we discover a stable mRNA secondary structure found near the stop codon, termed the ribosome termination structure (RTS), that controls the efficiency of translation reinitiation. These results illustrate the inverse correlation between expression levels of the distal gene-encoded

Methods

Results

Conclusion