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Archaea
Volume 2012 (2012), Article ID 260909, 11 pages
http://dx.doi.org/10.1155/2012/260909
Research Article

tRNA-Derived Fragments Target the Ribosome and Function as Regulatory Non-Coding RNA in Haloferax volcanii

1Department of Chemistry and Biochemistry, University of Bern, Freiestraße 3, 3012 Bern, Switzerland
2Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
3Division of Genomics and RNomics, Innsbruck Biocenter, Innsbruck Medical University , Innrain 80/82, 6020 Innsbruck, Austria
4Laboratory of Computational Genomics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-712 Poznan, Poland

Received 14 September 2012; Revised 16 November 2012; Accepted 28 November 2012

Academic Editor: Anita Marchfelder

Copyright © 2012 Jennifer Gebetsberger et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Nonprotein coding RNA (ncRNA) molecules have been recognized recently as major contributors to regulatory networks in controlling gene expression in a highly efficient manner. These RNAs either originate from their individual transcription units or are processing products from longer precursor RNAs. For example, tRNA-derived fragments (tRFs) have been identified in all domains of life and represent a growing, yet functionally poorly understood, class of ncRNA candidates. Here we present evidence that tRFs from the halophilic archaeon Haloferax volcanii directly bind to ribosomes. In the presented genomic screen of the ribosome-associated RNome, a 26-residue-long fragment originating from the 5′ part of valine tRNA was by far the most abundant tRF. The Val-tRF is processed in a stress-dependent manner and was found to primarily target the small ribosomal subunit in vitro and in vivo. As a consequence of ribosome binding, Val-tRF reduces protein synthesis by interfering with peptidyl transferase activity. Therefore this tRF functions as ribosome-bound small ncRNA capable of regulating gene expression in H. volcanii under environmental stress conditions probably by fine tuning the rate of protein production.