Nucleic Acids Research · 2007 · 49 citations · 49 references
Life SciencesBiochemistryMolecular BiologyProtein TranslationRna ProcessingStructural BiologyProtein SynthesisRibosome StructureTranslation In EukaryotesTranslation In ProkaryotesTranslation RegulationTranslational RegulationAnticodon PairingCodon-anticodon InteractionsCodon-anticodon PairingMessenger Rna StructureRibosome-associated Protein-rna InteractionsRibosome-associated Rna-binding ProteinsRibosome-nascent Chain InteractionsTrna Binding Sites
To add a tag-peptide for degradation to the nascent polypeptide in a stalled ribosome, an unusual translation called trans-translation is facilitated by transfer-messenger RNA (tmRNA) having an upper half of the tRNA structure and the sequence encoding the tag-peptide except the first alanine. During this event, tmRNA enters the vacant A-site of the stalled ribosome without a codon-anticodon interaction, but with a protein factor SmpB. Here, we studied the sites and modes of binding of SmpB to the ribosome by directed hydroxyl radical probing from Fe(II) tethered to SmpB variants. It revealed two SmpB-binding sites, A-site and P-site, on the ribosome. Each SmpB can be superimposed on the lower half of tRNA behaving in translation. The sites of cleavages from Fe(II) tethered to the C-terminal residues of A-site SmpB are aligned along the mRNA path towards the downstream tunnel, while those of P-site SmpB are found almost exclusively around the region of the codon-anticodon interaction in the P-site. We propose a new model of trans-translation in that the C-terminal tail of SmpB initially recognizes the decoding region and the mRNA path free of mRNA by mimicking mRNA.
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