A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation

Shomyseh Sanjabi; Kevin J. Williams; Simona Saccani; Liang Zhou; Alexander Hoffmann; Gourisankar Ghosh; Steve Gerondakis; Gioacchino Natoli; Stephen T. Smale

doi:10.1101/gad.1329805

A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation

¹Howard Hughes Medical Institute, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095-1662, USA; ²Institute for Research in Biomedicine, CH6500 Bellinzona, Switzerland; ³Department of Biology, California Institute of Technology, Pasadena, California 91125, USA; ⁴Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 93093-0375; ⁵The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia

Abstract

The NF-κB family members p65 (RelA) and c-Rel recognize similar DNA sequences, yet the phenotypes of mutant mice suggest that these proteins regulate distinct sets of genes. Here we demonstrate that 46 unique residues within an 86-residue segment of the Rel homology region (RHR) of c-Rel are responsible for the c-Rel requirement for Il12b gene induction by lipopolysaccharide in bone marrow-derived macrophages. These same residues were responsible for the c-Rel requirement for Il12a induction in dendritic cells, and in both instances, no evidence of c-Rel-specific coactivator interactions was found. Although the residues of c-Rel and p65 that contact specific bases and the DNA backbone within nuclear factor-κB (NF-κB) recognition sequences are identical, homodimers of c-Rel and of a chimeric p65 protein containing the critical c-Rel residues bound with high affinity to a broader range of NF-κB recognition sequences than did wild-type p65 homodimers. These results demonstrate that the unique functions of closely related transcription factor family members can be dictated by differences in the range of DNA sequences recognized at high affinity, despite having similar binding site consensus sequences and DNA contact residues.

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Footnotes

Supplemental material is available at http://www.genesdev.org.
Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/gad.1329805.
↵6 These authors contributed equally to this work.
↵7 Present address: Section of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
↵8 Present address: Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
↵9 Present address: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0375, USA.
↵10 Corresponding author. E-MAIL smale{at}mednet.ucla.edu; FAX (310) 206-8623.
- Accepted July 19, 2005.
- Received May 3, 2005.
Cold Spring Harbor Laboratory Press