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Nucleic Acids Research Advance Access published online on March 1, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn063
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© 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

Evolution of acceptor stem tRNA recognition by class II prolyl-tRNA synthetase

Songon An1, George Barany1 and Karin Musier-Forsyth2,*

1Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 and 2Department of Chemistry and Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA

To whom correspondence should be addressed. Tel: +1 614 292 2021; Fax: +1 614 688 5402; Email: musier{at}chemistry.ohio-state.edu

Received January 2, 2008. Revised January 29, 2008. Accepted January 31, 2008.

Aminoacyl-tRNA synthetases (AARS) are an essential family of enzymes that catalyze the attachment of amino acids to specific tRNAs during translation. Previously, we showed that base-specific recognition of the tRNAPro acceptor stem is critical for recognition by Escherichia coli prolyl-tRNA synthetase (ProRS), but not for human ProRS. To further delineate species-specific differences in acceptor stem recognition, atomic group mutagenesis was used to probe the role of sugar–phosphate backbone interactions in recognition of human tRNAPro. Incorporation of site-specific 2'-deoxynucleotides, as well as phosphorothioate and methylphosphonate modifications within the tRNA acceptor stem revealed an extensive network of interactions with specific functional groups proximal to the first base pair and the discriminator base. Backbone functional groups located at the base of the acceptor stem, especially the 2'-hydroxyl of A66, are also critical for aminoacylation catalytic efficiency by human ProRS. Therefore, in contrast to the bacterial system, backbone-specific interactions contribute significantly more to tRNA recognition by the human enzyme than base-specific interactions. Taken together with previous studies, these data show that ProRS-tRNA acceptor stem interactions have co-adapted through evolution from a mechanism involving ‘direct readout’ of nucleotide bases to one relying primarily on backbone-specific ‘indirect readout’.

Present address: Songon An, Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA


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