Beyond ribosome rescue: tmRNA and co-translational processes

Abstract

tmRNA is a unique bi-functional RNA that acts as both a tRNA and an mRNA to enter stalled ribosomes and direct the addition of a peptide tag to the C terminus of nascent polypeptides. Despite a reasonably clear understanding of tmRNA activity, the reason for its absolute conservation throughout the eubacteria is unknown. Although tmRNA plays many physiological roles in different bacterial systems, recent studies suggest a general role for trans-translation in monitoring protein folding and perhaps other co-translational processes. This review will focus on these new hypotheses and the data that support them.

Figure 1

The trans-translation model of tmRNA activity. The tmRNA•SmpB complex is recruited with EF-Tu (not shown) to the A site of substrate ribosomes. Acting like a tRNA, tmRNA accepts the nascent polypeptide in a normal transpeptidation reaction. The tmRNA open reading frame (ORF) replaces the mRNA in the decoding center, and the mRNA is released and degraded. Translation resumes using the tmRNA ORF as a template. After synthesis of the tmRNA-encoded peptide, the tagged protein is released for degradation by cellular proteases, and ribosomal subunits are recycled for further rounds of translation.

Figure 2

Postulated tmRNA-independent ribosome release mechanisms. Two pathways are proposed to explain release of ribosomes from nonstop messages in E. coli cells lacking tmRNA. The peptidyl-tRNA could be hydrolyzed in the P site, resulting in a canonical post-termination complex that can be recycled by RRF and EF-G (left). Instead of standard release factors that require a stop codon, this pathway could use an intrinsic peptidyl-tRNA hydrolysis activity recently observed in E. coli ribosomes, or hydrolysis may be stimulated by the alternative release factors PrfH and YaeJ, which are proposed to catalyze stop-codon independent nascent peptide release. Ribosomes will also dissociate from the 3' end of truncated messages in E. coli (right). The dissociated monosomes may be processed by the intrinsic peptidyl-tRNA hydrolase activity or alternative release factors to produce a vacant ribosome, which is then recycled by the IF-1/IF-3 pathway.

Figure 3

Co-translational protein folding and tmRNA activity. Translation typically results in a properly folded protein, either through correct folding during synthesis or refolding in conjuction with ribosome-associated chaperones such as DnaJ/K. Disruption of DnaK leads to increased trans-translation activity, particularly during the synthesis of large, multidomain proteins. We propose that misfolded nascent chains may induce translational pausing, allowing tmRNA to tag the defective protein for degradation after release from the ribosome.

Figure 4

Hypothetical role for tmRNA in the release of jammed protein translocators. Inhibition of protein synthesis during co-translational protein secretion leads to FtsH-dependent proteolysis of the SecY and SecE components of the translocator [61] (left). tmRNA may help to protect the translocator from degradation by relieving some translational arrests.