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Mechanisms of ribosome rescue in bacteria

Key Points

  • Bacterial ribosomes that are stalled at the end of an mRNA that lack a stop codon cannot be released by the translation termination factors peptide chain release factor 1 (RF1) and RF2. Ribosomes in these non-stop translation complexes must be rescued to maintain the protein synthesis capacity of the cell.

  • The primary pathway used by bacteria to rescue ribosomes stalled in non-stop complexes is trans-translation, which results in release of the ribosome and degradation of the nascent polypeptide and the mRNA.

  • Some bacteria have the alternative ribosome-rescue factor A (ArfA) or ArfB pathways as a backup for trans-translation. ArfA recruits RF2 to rescue ribosomes, and ArfB functions directly to hydrolyse the peptidyl-tRNA and rescue the ribosome.

  • Ribosomes stalled in the middle of an mRNA can be targeted for rescue if the mRNA is cleaved to produce a non-stop complex, or they can resume elongation. Ribosomes stalled as part of a regulatory programme for gene expression are protected from rescue mechanisms.

  • The broadly conserved translation elongation factor EF-P promotes translation through polyproline sequences and reduces the number of ribosomes that must be rescued.

Abstract

Ribosomes that stall during translation need to be rescued to ensure that the protein synthesis capacity of the cell is maintained. Stalling arises when ribosomes become trapped at the 3′ end of an mRNA, which occurs when a codon is unavailable, as this leads to the arrest of elongation or termination. In addition, various factors can induce ribosome stalling in the middle of an mRNA, including the presence of specific amino acid sequence motifs in the nascent polypeptide. Almost all bacteria use a mechanism known as trans-translation to rescue stalled ribosomes, and some species also have other rescue mechanisms that are mediated either by the alternative ribosome-rescue factor A (ArfA) or ArfB. In this Review, I summarize the recent studies that have demonstrated the conditions that trigger ribosome stalling, the pathways that bacteria use to rescue stalled ribosomes and the physiological effects of these processes.

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Figure 1: Triggers for translation stalling and ribosome rescue.
Figure 2: Ribosome rescue by trans-translation.
Figure 3: ArfA and ArfB: alternative pathways for ribosome rescue.
Figure 4: Elongation factor P promotes translation elongation.

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Acknowledgements

K.C.K. was supported by grant GM68720 from the National Institutes of Health.

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Glossary

Cognate aminoacyl-tRNA

A charged tRNA containing an anticodon that corresponds to a particular codon.

Splicing

The process of removing introns from a pre-mRNA transcript followed by the joining of exons to form a mature mRNA.

Polyadenylation

The addition of multiple adenosine residues to the 3′ end of an mRNA.

Frameshifting

A change in the reading frame of the ribosome during translation that alters the order in which the triplet nucleotides of the mRNA are recognized as codons.

Ribosome profiling

This technique (also known as ribo-seq) identifies ribosome footprints on mRNA using deep sequencing. Increased occupancy at one site on the mRNA compared with the footprints at other sites on the same mRNA is indicative of ribosome stalling.

Pseudoknots

RNA secondary structures that are formed by two stem-loop structures, in which the loop of one stem-loop forms half of the stem in the other stem-loop.

Transpeptidation

In the context of translation, the transfer of the nascent polypeptide from the tRNA in the P-site to the aminoacyl-tRNA in the A-site, which results in extension of the polypeptide by one amino acid.

A-site finger

The structure formed by helix 38 of 23S rRNA, which interacts with the A-site tRNA and forms a bridge between the large and small subunits of the ribosome.

Persister cells

Dormant or slow-growing populations of bacterial cells that are refractory to antibiotics.

Anti-Shine–Dalgarno element

The conserved sequence at the 3′ end of 16S rRNA that is complementary to the Shine–Dalgarno element found in the 5′ untranslated region of many mRNAs in Escherichia coli. This element is used for the positioning of the mRNA on the 30S subunit, and it has also been implicated in translation pausing.

Peptide exit tunnel

The tunnel in the 50S ribosomal subunit that is used for transfer of the nascent polypeptide from the peptidyl-transferase centre to the exterior of the ribosome.

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Keiler, K. Mechanisms of ribosome rescue in bacteria. Nat Rev Microbiol 13, 285–297 (2015). https://doi.org/10.1038/nrmicro3438

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