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Nucleic Acids Research Advance Access originally published online on October 24, 2007
Nucleic Acids Research 2007 35(21):7248-7255; doi:10.1093/nar/gkm677
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Nucleic Acids Research, 2007, Vol. 35, No. 21 7248-7255
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Interaction of SmpB with ribosome from directed hydroxyl radical probing

Daisuke Kurita1,2, Rumi Sasaki1, Akira Muto1,2,3 and Hyouta Himeno1,2,3,*

1Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, 2The United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8551 and 3RNA Research Center, Hirosaki University, Hirosaki 036-8561, Japan

*To whom correspondence should be addressed. Tel: +81 172 39 3592; Fax: +81 172 39 3593; Email: himeno{at}cc.hirosaki-u.ac.jp

Received May 12, 2007. Revised August 17, 2007. Accepted August 17, 2007.

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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