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J. Biol. Chem., Vol. 281, Issue 15, 10561-10566, April 14, 2006

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Genetic Analysis of the Structure and Function of Transfer Messenger RNA Pseudoknot 1^*

From the Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602

tmRNA rescues stalled ribosomes in eubacteria by forcing the ribosome to abandon its mRNA template and resume translation with tmRNA itself as a template. Pseudoknot 1 (pk1), immediately upstream of this coding region in tmRNA, is a structural element that is considered essential for tmRNA function based on the analysis of pk1 mutants in vitro. pk1 binds near the ribosomal decoding site and may make base-specific contacts with tmRNA ligands. To study pk1 structure and function in vivo, we have developed a genetic selection that ties the life of Escherichia coli cells to tmRNA activity. Mutation of pk1 at 20% per base and selection for tmRNA activity yielded sequences that retain the same pseudoknot fold. In contrast, selection of active mutants from 10⁶ completely random sequences identified hairpin structures that functionally replace pk1. Rational design of a hairpin with increased stability using an unrelated sequence yielded a tmRNA mutant with nearly wild-type activity. We conclude that the role of pk1 in tmRNA function is purely structural and that it can be replaced with a variety of hairpin structures. Our results demonstrate that in the study of functional RNAs, the inactivity of a mutant designed to destroy a given structure should not be interpreted as proof that the structure is necessary for RNA function. Such mutations may only destabilize a global fold that could be formed equally well by an entirely different, stable structure.

Received for publication, January 6, 2006 , and in revised form, February 14, 2006.

^* This work was supported by funds from Brigham Young University. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ To whom correspondence should be addressed: C203 BNSN, Dept. of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602. Tel.: 801-422-1967; Fax: 801-422-0153; E-mail: buskirk{at}chem.byu.edu.

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				I. K. Wower, C. Zwieb, and J. Wower Escherichia coli tmRNA lacking pseudoknot 1 tags truncated proteins in vivo and in vitro RNA, January 1, 2009; 15(1): 128 - 137. [Abstract] [Full Text] [PDF]