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Nucleic Acids Research Advance Access published online on September 8, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl629
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© 2006 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

Sequence-specific recognition of colicin E5, a tRNA-targeting ribonuclease

Tetsuhiro Ogawa, Sakura Inoue, Shunsuke Yajima1, Makoto Hidaka and Haruhiko Masaki

Department of Biotechnology, The University of Tokyo Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan 1 Department of Bioscience, Tokyo University of Agriculture Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan

*To whom correspondence should be addressed. Tel: +81 3 5841 3080; Fax: +81 3 5841 8016; Email: hmasaki{at}mcb.bt.a.u-tokyo.ac.jp

Received May 15, 2006. Revised August 7, 2006. Accepted August 10, 2006.

Colicin E5 is a novel Escherichia coli ribonuclease that specifically cleaves the anticodons of tRNATyr, tRNAHis, tRNAAsn and tRNAAsp. Since this activity is confined to its 115 amino acid long C-terminal domain (CRD), the recognition mechanism of E5-CRD is of great interest. The four tRNA substrates share the unique sequence UQU within their anticodon loops, and are cleaved between Q (modified base of G) and 3' U. Synthetic minihelix RNAs corresponding to the substrate tRNAs were completely susceptible to E5-CRD and were cleaved in the same manner as the authentic tRNAs. The specificity determinant for E5-CRD was YGUN at –1 to +3 of the ‘anticodon’. The YGU is absolutely required and the extent of susceptibility of minihelices depends on N (third letter of the anticodon) in the order A > C > G > U accounting for the order of susceptibility tRNATyr > tRNAAsp > tRNAHis, tRNAAsn. Contrastingly, we showed that GpUp is the minimal substrate strictly retaining specificity to E5-CRD. The effect of contiguous nucleotides is inconsistent between the loop and linear RNAs, suggesting that nucleotide extension on each side of GpUp introduces a structural constraint, which is reduced by a specific loop structure formation that includes a 5' pyrimidine and 3' A.


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