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Nucleic Acids Research Advance Access originally published online on February 3, 2009
Nucleic Acids Research 2009 37(6):1886-1896; doi:10.1093/nar/gkp036
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Nucleic Acids Research, 2009, Vol. 37, No. 6 1886-1896
© 2009 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

A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly

Deepti L. Bellur1 and Sarah A. Woodson2,*

1Program in Cell, Molecular and Developmental Biology and Biophysics and 2T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218-2685, USA

*To whom correspondence should be addressed. Tel: +1 410 516 2015; Fax: +1 410 516 2118; Email: swoodson{at}jhu.edu

Received November 24, 2008. Revised January 2, 2009. Accepted January 8, 2009.

Primary ribosomal protein S4 is essential for 30S ribosome biogenesis in eubacteria, because it nucleates subunit assembly and helps coordinate assembly with the synthesis of its rRNA and protein components. S4 binds a five-helix junction (5WJ) that bridges the 5' and 3' ends of the 16S 5' domain. To delineate which nucleotides contribute to S4 recognition, sequential deletions of the 16S 5' domain were tested in competitive S4-binding assays based on electrophoretic mobility shifts. S4 binds the minimal 5WJ RNA containing just the five-helix junction as well or better than with affinity comparable to or better than the 5' domain or native 16S rRNA. Internal deletions and point mutations demonstrated that helices 3, 4, 16 and residues at the helix junctions are necessary for S4 binding, while the conserved helix 18 pseudoknot is dispensable. Hydroxyl radical footprinting and chemical base modification showed that S4 makes the same interactions with minimal rRNA substrates as with the native 16S rRNA, but the minimal substrates are more pre-organized for binding S4. Together, these results suggest that favorable interactions with S4 offset the energetic penalty for folding the 16S rRNA.

Present address: Deepti L. Bellur, Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E. 58th St., Chicago, IL 60637, USA


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