The tmRNA ribosome-rescue system

Abstract

The bacterial tmRNA quality control system monitors protein synthesis and recycles stalled translation complexes in a process termed "ribosome rescue." During rescue, tmRNA acts first as a transfer RNA to bind stalled ribosomes, then as a messenger RNA to add the ssrA peptide tag to the C-terminus of the nascent polypeptide chain. The ssrA peptide targets tagged peptides for proteolysis, ensuring rapid degradation of potentially deleterious truncated polypeptides. Ribosome rescue also facilitates turnover of the damaged messages responsible for translational arrest. Thus, tmRNA increases the fidelity of gene expression by promoting the synthesis of full-length proteins. In addition to serving as a global quality control system, tmRNA also plays important roles in bacterial development, pathogenesis, and environmental stress responses. This review focuses on the mechanism of tmRNA-mediated ribosome rescue and the role of tmRNA in bacterial physiology.

Figure 1. The trans-translation model of tmRNA activity

Translation of non-stop mRNA leads to ribosome arrest. tmRNA•SmpB binds the A site of stalled ribosomes and accepts the nascent chain. The non-stop mRNA is released and preferentially degraded by RNase R. Translation then resumes using the open reading frame found within tmRNA. After synthesis of the ssrA peptide, release factors (RF) terminate translation and the ribosome is recycled into large and small subunits. The ssrA-tagged chain is degraded by a number of proteases.

Figure 2. Structure of tmRNA and SmpB

The secondary structure of E. coli tmRNA is shown, highlighting the tRNA-like domain (TLD) and the ssrA open reading frame (Nameki et al., 1999a). Pseudoknot (PK) structures are shown schematically to simplify the image. The wild-type ssrA peptide is shown in one-letter code, as are the modified ssrA(DD) and ssrA(His₆) peptide tags. The inset shows the crystal structure of SmpB bound to the tmRNA TLD (1P6V) (Gutmann et al., 2003).

Figure 3. tmRNA regulates the synthesis of ArfA

The arfA transcript coding sequence contains a hairpin structure, which is cleaved by RNase III to generate non-stop mRNA. Ribosomes stalled at the 3′-end of the truncated arfA message have at least two fates. tmRNA-mediated rescue results in tagging of the ArfA nascent chain, thereby maintaining ArfA at low levels in the cell. When tmRNA activity is limiting or absent, the incomplete ArfA nascent chain is released from the ribosome. ArfA chain release may require pre-existing cytosolic ArfA in collaboration with an unknown factor.

Figure 4. Premature transcription termination and tmRNA activity

Potential mechanisms of premature transcription termination in bacteria. Collisions between RNA polymerase (RNAP) and DNA replication forks, DNA-bound transcription factors, or covalently cross-linked proteins are predicted to generate stalled transcription complexes. Antibiotics (e.g. streptolydigin) and adventitious Rho activity can also promote premature transcription termination. Termination within coding sequences generates non-stop mRNA, which ultimately leads to tmRNA-mediated ribosome rescue.