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Nucleic Acids Research Advance Access published online on June 10, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp452
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© 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

RNA-binding specificity of E. coli NusA

Stefan Prasch1,*, Marcel Jurk1, Robert S. Washburn2, Max E. Gottesman2, Birgitta M. Wöhrl1 and Paul Rösch1

1Lehrstuhl für Struktur und Chemie der Biopolymere & Research Center for Bio-Macromolecules, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany and 2Department of Microbiology and Institute of Cancer Research, Columbia University Medical Center, New York, NY 10032, USA

*To whom correspondence should be addressed. Tel: +49 921 55 3862; Fax: +49 921 553544; Email: stefan.prasch{at}uni-bayreuth.de

Received March 18, 2009. Revised May 12, 2009. Accepted May 13, 2009.

The RNA sequences boxA, boxB and boxC constitute the nut regions of phage {lambda}. They nucleate the formation of a termination-resistant RNA polymerase complex on the {lambda} chromosome. The complex includes E. coli proteins NusA, NusB, NusG and NusE, and the {lambda} N protein. A complex that includes the Nus proteins and other factors forms at the rrn leader. Whereas RNA-binding by NusB and NusE has been described in quantitative terms, the interaction of NusA with these RNA sequences is less defined. Isotropic as well as anisotropic fluorescence equilibrium titrations show that NusA binds only the nut spacer sequence between boxA and boxB. Thus, nutR boxA5-spacer, nutR boxA16-spacer and nutR boxA69-spacer retain NusA binding, whereas a spacer mutation eliminates complex formation. The affinity of NusA for nutL is 50% higher than for nutR. In contrast, rrn boxA, which includes an additional U residue, binds NusA in the absence of spacer. The Kd values obtained for rrn boxA and rrn boxA-spacer are 19-fold and 8-fold lower, respectively, than those for nutR boxA-spacer. These differences may explain why {lambda} requires an additional protein, {lambda} N, to suppress termination. Knowledge of the different affinities now describes the assembly of the anti-termination complex in quantitative terms.


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B. M. Burmann, X. Luo, P. Rosch, M. C. Wahl, and M. E. Gottesman
Fine tuning of the E. coli NusB:NusE complex affinity to BoxA RNA is required for processive antitermination
Nucleic Acids Res., October 23, 2009; (2009) gkp736v1.
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