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Journal of Bacteriology, July 2009, p. 4513-4521, Vol. 191, No. 14
0021-9193/09/$08.00+0     doi:10.1128/JB.00193-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Analysis of DNA Binding by a Eubacterial Zinc Finger Transcription Factor{triangledown}

Victor J. McAlister{dagger} and Gail E. Christie*

Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298-0678

Received 12 February 2009/ Accepted 5 May 2009

The Serratia marcescens NucC protein is structurally and functionally homologous to the P2 Ogr family of eubacterial zinc finger transcription factors required for late gene expression in P2- and P4-related bacteriophages. These activators exhibit site-specific binding to a conserved DNA sequence, TGT-N3-R-N4-Y-N3-aCA, that is located upstream of NucC-dependent S. marcescens promoters and the late promoters of P2-related phages. In this report we describe the interactions of NucC with the P2 FETUD late operon promoter PF. NucC is shown to bind PF as a tetramer and to make 12 symmetrical contacts to the DNA phosphodiester backbone. The backbone contacts are centered on the TGT-N3-R-N4-Y-N3-aCA motif. Major groove base contacts can be seen at most positions within the ~24-bp binding site. Minor groove contacts map to adjacent positions in the downstream half of the binding site, which corresponds to the area in which the DNA also appears to be bent by NucC binding. NucC binding provides a new example of protein-DNA interaction that is strikingly different from the DNA binding demonstrated for eukaryotic zinc-finger transcription factors.

* Corresponding author. Mailing address: Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, P.O. Box 980678, Richmond, VA 23298-0678. Phone: (804) 828-9093. Fax: (804) 828-9946. E-mail: christie{at}vcu.edu

{triangledown} Published ahead of print on 15 May 2009.

{dagger} Present address: National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, Maryland.

Journal of Bacteriology, July 2009, p. 4513-4521, Vol. 191, No. 14
0021-9193/09/$08.00+0     doi:10.1128/JB.00193-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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