The mechanism by which tmRNA rescues stalled ribosomes
Not all translation reactions end in the synthesis of a full-length protein. In bacteria, ribosomes stall at the 3′ end of mRNA transcripts lacking stop codons, as they cannot efficiently employ release factors for termination and recycling. Some non-stop
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David Healey, Mickey Miller, Christopher Woolstenhulme, Allen Buskirk
1. Introduction Not all translation reactions end in the synthesis of a full-length protein. In bacteria, ribosomes stall at the 3’ end of mRNA transcripts lacking stop codons, as they cannot efficiently employ release factors for termination and recycling. Some non-stop mRNAs arise from defects in transcription. RNA polymerase occasionally terminates transcription prematurely; this can occur either as a result of pausing at specific sequences or encountering a tightly-bound protein on the DNA (Abo et al., 2000). Another likely source is the regular process of mRNA degradation. mRNAs are turned over quickly in bacteria, with an average half-life of about six or seven minutes (Bernstein et al., 2002; Selinger et al., 2003). Bacterial mRNAs are degraded by endonucleases and by processive 3’ to 5’ exonucleases (Condon, 2007). An exonuclease that collides with a translating ribosome leaves it stalled on the truncated transcript. Ribosome stalling constitutes a serious threat to the integrity of bacterial cells: roughly 1 in 250 of all translation reactions result in an irreversible arrest (Moore and Sauer, 2005). If these arrested ribosomes were not released, the majority of ribosomes would become inoperative within a single generation. A translational quality control system in bacteria rescues stalled ribosomes with a small stable RNA known as tmRNA. This remarkable molecule possesses both transfer and messenger RNA activity: aminoacylated with alanine, tmRNA enters stalled ribosomes and adds Ala to the nascent peptide chain (Figure 1). Leaving the broken mRNA, the ribosome resumes translation on the tmRNA template, adding a short tag to the growing polypeptide and terminating translation at a stop codon. The stalled ribosome is recycled and the 11 amino acid tag marks the aborted nascent polypeptide for destruction by cellular proteases (KeiM. V. Rodnina et al. (eds.), Ribosomes © Springer-Verlag/Wien 2011
Fig. 1 Model of trans-translation. Alanyl-tmRNA (green) and its protein partner SmpB (purple) are delivered to stalled ribosomes by EF-Tu (orange). The nascent polypeptide is transferred to tmRNA. Translocation of tmRNA∙SmpB to the P site releases the truncated mRNA and positions the tmRNA ORF (dark blue) in the ribosomal A site. Translation resumes on the tmRNA ORF, directing the addition of an additional ten-residue tag to the nascent polypeptide, after which termination occurs at a stop codon. This process recycles stalled ribosomes, allowing the subunits to dissociate, and tags the nascent peptide for degradation by proteases.
ler et al., 1996). Because the ribosome switches templates during protein synthesis, this process is called trans-translation (Figure 1). tmRNA and its protein partner, small protein B (SmpB), are found in all fully-sequenced eubacterial genomes (Moore and Sauer, 2007). tmRNA is essential for viability or pathogenicity in some species of bacteria (Huang et al., 2000; Hutchison et al., 1999), and loss of the tmRNA
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