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J. Biol. Chem., Vol. 279, Issue 35, 36708-36714, August 27, 2004

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Phosphorylation-independent Dimer-Dimer Interactions by the Enhancer-binding Activator NtrC of Escherichia coli

A THIRD FUNCTION FOR THE C-TERMINAL DOMAIN^*

Xiaofeng F. Yang, Youngran Ji¶, Barbara L. Schneider, and Larry Reitzer||

From the Molecular and Cell Biology Department, University of Texas at Dallas, Richardson, Texas 75083-0688

The response regulator NtrC transcriptionally activates genes of the nitrogen-regulated (Ntr) response. Phosphorylation of its N-terminal receiver domain stimulates an essential oligomerization of the central domain. Deletion of the central domain reduces, but does not eliminate, intermolecular interactions as assessed by cooperative binding to DNA. To analyze the structural determinants and function of this central domain-independent as well as phosphorylation-independent oligomerization, we randomly mutagenized DNA coding for an NtrC without its central domain and isolated strains containing NtrC with defective phosphorylation-independent cooperative binding. The alterations were primarily localized to helix B of the C-terminal domain. Site-specific mutagenesis that altered surface residues of helix B confirmed this localization. The purified NtrC variants, with or without the central domain, were specifically defective in phosphorylation-independent cooperative DNA binding and had little defect, if any, on other functions, such as non-cooperative DNA binding. We propose that this region forms an oligomerization interface. Full-length NtrC variants did not efficiently repress the glnA-ntrBC operon when NtrC was not phosphorylated, which suggests that phosphorylation-independent cooperative binding sets the basal level for glutamine synthetase and the regulators of the Ntr response. The NtrC variants in these cells generally, but not always, supported wild-type growth in nitrogen-limited media and wild-type activation of a variety of Ntr genes. We discuss the differences and similarities between the NtrC C-terminal domain and the homologous Fis, which is also capable of intermolecular interactions.

Received for publication, May 10, 2004 , and in revised form, June 10, 2004.

^* The work was supported by Grants MCB-0323931 from the National Science Foundation and GM47965 from the National Institutes of Health. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Current address: Dept. of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9048.

^¶ Current address: Dept. of Surgery, Stanford University, Stanford, CA 94305-5492.

^|| To whom correspondence should be addressed. Tel.: 972-883-2502; Fax: 972-883-2409; E-mail: reitzer{at}utdallas.edu.

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