Functional evidence for D- and T-loop interactions in tmRNA

Barends, Sharief; Björk, Karl; Gultyaev, Alexander P.; de Smit, Maarten H.; Pleij, Cornelis W.A.; Kraal, Barend

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Volume 514, Issue 1 , Pages 78-83, 6 March 2002

Functional evidence for D- and T-loop interactions in tmRNA

Edited by Lev Kisselev

Sharief Barends
- Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
Karl Björk
- Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
Alexander P. Gultyaev
- Group Theoretical Biology and Phylogenetics, Institute of Evolutionary and Ecological Sciences, Leiden University, Kaiserstraat 63, 2311 GP Leiden, The Netherlands
Maarten H. de Smit
- Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
Cornelis W.A. Pleij
- Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
Barend Kraal
- Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
- Corresponding author. Fax: (31)-71-5274340

Received 1 November 2001; accepted 5 November 2001.

Abstract

During bacterial protein synthesis, stalled ribosomes can be rescued by tmRNA, a molecule with both tRNA and mRNA features. The tRNA region of tmRNA has sequence similarity with tRNA^Ala and also has a clover-leaf structure folded similarly as in canonical tRNAs. Here we propose the L-shape of tmRNA to be stabilized by two tertiary interactions between its D- and T-loop on the basis of phylogenetic and experimental evidence. Mutational analysis clearly demonstrates a tertiary interaction between G₁₃ and U₃₄₂. Strikingly, this in evolution conserved interaction is not primarily important for tmRNA alanylation and for binding to elongation factor Tu, but especially for a proper functioning of SmpB.

Keywords: tmRNA, Ala-tRNA synthetase, Elongation factor Tu, SmpB, tRNA folding, trans-Translation