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Nucleic Acids Research Advance Access originally published online on July 25, 2007
Nucleic Acids Research 2007 35(15):5108-5119; doi:10.1093/nar/gkm546
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Nucleic Acids Research, 2007, Vol. 35, No. 15 5108-5119
© 2007 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

Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine

Ekaterini C. Kouvela, George V. Gerbanas, Maria A. Xaplanteri, Alexandros D. Petropoulos, George P. Dinos and Dimitrios L. Kalpaxis*

Laboratory of Biochemistry, School of Medicine, University of Patras, GR-26500 Patras, Greece

*To whom correspondence should be addressed. Tel: +302610 996124; Fax: +302610969167; Email: dimkal{at}med.upatras.gr

Received April 12, 2007. Revised June 11, 2007. Accepted July 4, 2007.

5S rRNA is an integral component of the large ribosomal subunit in virtually all living organisms. Polyamine binding to 5S rRNA was investigated by cross-linking of N1-azidobenzamidino (ABA)-spermine to naked 5S rRNA or 50S ribosomal subunits and whole ribosomes from Escherichia coli cells. ABA-spermine cross-linking sites were kinetically measured and their positions in 5S rRNA were localized by primer extension analysis. Helices III and V, and loops A, C, D and E in naked 5S rRNA were found to be preferred polyamine binding sites. When 50S ribosomal subunits or poly(U)-programmed 70S ribosomes bearing tRNAPhe at the E-site and AcPhe-tRNA at the P-site were targeted, the susceptibility of 5S rRNA to ABA-spermine was greatly reduced. Regardless of 5S rRNA assembly status, binding of spermine induced significant changes in the 5S rRNA conformation; loop A adopted an apparent ‘loosening’ of its structure, while loops C, D, E and helices III and V achieved a more compact folding. Poly(U)-programmed 70S ribosomes possessing 5S rRNA cross-linked with spermine were more efficient than control ribosomes in tRNA binding, peptidyl transferase activity and translocation. Our results support the notion that 5S rRNA serves as a signal transducer between regions of 23S rRNA responsible for principal ribosomal functions.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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