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Nucleic Acids Research Advance Access published online on May 5, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp296
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© 2009 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

Contribution of ribosomal residues to P-site tRNA binding

Shinichiro Shoji1,2, Nimo M. Abdi1,2, Ralf Bundschuh2,3,4 and Kurt Fredrick1,2,5,*

1Department of Microbiology, 2Center for RNA Biology, 3Department of Physics, 4Department of Biochemistry and 5Ohio State Biochemistry Program, The Ohio State University, 484 W., 12th Ave, Columbus, OH 43210, USA

*To whom correspondence should be addressed. Tel: +1 614 292 6679; Fax: +1 614 292 8120; Email: fredrick.5{at}osu.edu

Received March 18, 2009. Revised April 14, 2009. Accepted April 15, 2009.

Structural studies have revealed multiple contacts between the ribosomal P site and tRNA, but how these contacts contribute to P-tRNA binding remains unclear. In this study, the effects of ribosomal mutations on the dissociation rate (koff) of various tRNAs from the P site were measured. Mutation of the 30S P site destabilized tRNAs to various degrees, depending on the mutation and the species of tRNA. These data support the idea that ribosome-tRNA interactions are idiosyncratically tuned to ensure stable binding of all tRNA species. Unlike deacylated elongator tRNAs, N-acetyl-aminoacyl-tRNAs and tRNAfMet dissociated from the P site at a similar low rate, even in the presence of various P-site mutations. These data provide evidence for a stability threshold for P-tRNA binding and suggest that ribosome-tRNAfMet interactions are uniquely tuned for tight binding. The effects of 16S rRNA mutation G1338U were suppressed by 50S E-site mutation C2394A, suggesting that G1338 is particularly important for stabilizing tRNA in the P/E site. Finally, mutation C2394A or the presence of an N-acetyl-aminoacyl group slowed the association rate (kon) of tRNA dramatically, suggesting that deacylated tRNA binds the P site of the ribosome via the E site.


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