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Nucleic Acids Research Advance Access originally published online on May 2, 2008
Nucleic Acids Research 2008 36(11):3539-3551; doi:10.1093/nar/gkn224
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Nucleic Acids Research, 2008, Vol. 36, No. 11 3539-3551
© 2008 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

Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments

Takeshi Yokoyama and Tsutomu Suzuki*

Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan

*To whom correspondence should be addressed. Tel: +81 3 5841 8752; Fax: +81 3 3816 0106; Email: ts{at}chembio.t.u-tokyo.ac.jp

Received February 20, 2008. Revised April 10, 2008. Accepted April 10, 2008.

Ribosomal RNAs (rRNAs), assisted by ribosomal proteins, form the basic structure of the ribosome, and play critical roles in protein synthesis. Compared to prokaryotic ribosomes, eukaryotic ribosomes contain elongated rRNAs with several expansion segments and larger numbers of ribosomal proteins. To investigate architectural evolution and functional capability of rRNAs, we employed a Tn5 transposon system to develop a systematic genetic insertion of an RNA segment 31 nt in length into Escherichia coli rRNAs. From the plasmid library harboring a single rRNA operon containing random insertions, we isolated surviving clones bearing rRNAs with functional insertions that enabled rescue of the E. coli strain ({Delta}7rrn) in which all chromosomal rRNA operons were depleted. We identified 51 sites with functional insertions, 16 sites in 16S rRNA and 35 sites in 23S rRNA, revealing the architecture of E. coli rRNAs to be substantially flexible. Most of the insertion sites show clear tendency to coincide with the regions of the expansion segments found in eukaryotic rRNAs, implying that eukaryotic rRNAs evolved from prokaryotic rRNAs suffering genetic insertions and selections.


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