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Nucleic Acids Research Advance Access originally published online on February 5, 2008
Nucleic Acids Research 2008 36(6):1783-1791; doi:10.1093/nar/gkm1171
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Nucleic Acids Research, 2008, Vol. 36, No. 6 1783-1791
© 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

Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes

Tomohiro Miyoshi and Toshio Uchiumi*

Department of Biology, Faculty of Science, Niigata University, Niigata 950-2181, Japan

*To whom correspondence should be addressed. Tel: +81 25 262 7792; Fax: +81 25 262 7792; Email: uchiumi{at}bio.sc.niigata-u.ac.jp

Received October 21, 2007. Revised December 19, 2007. Accepted December 20, 2007.

The factor-binding center within the Escherichia coli ribosome is comprised of two discrete domains of 23S rRNA: the GTPase-associated region (GAR) in domain II and the sarcin–ricin loop in domain VI. These two regions appear to collaborate in the factor-dependent events that occur during protein synthesis. Current X-ray crystallography of the ribosome shows an interaction between C1049 in the GAR and G2751 in domain VI. We have confirmed this interaction by site-directed mutagenesis and chemical probing. Disruption of this base pair affected not only the chemical modification of some bases in domains II and VI and in helix H89 of domain V, but also ribosome function dependent on both EF-G and EF-Tu. Mutant ribosomes carrying the C1049 to G substitution, which show enhancement of chemical modification at G2751, were used to probe the interactions between the regions around 1049 and 2751. Binding of EF-G-GDP-fusidic acid, but not EF-G-GMP-PNP, to the ribosome protected G2751 from modification. The G2751 protection was also observed after tRNA binding to the ribosomal P and E sites. The results suggest that the interactions between the bases around 1049 and 2751 alter during different stages of the translation process.


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