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Journal of Bacteriology, October 2008, p. 6817-6828, Vol. 190, No. 20
0021-9193/08/$08.00+0     doi:10.1128/JB.00719-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

The Use of Chromatin Immunoprecipitation to Define PpsR Binding Activity in Rhodobacter sphaeroides 2.4.1 ^,

Patrice Bruscella, Jesus M. Eraso, Jung Hyeob Roh, and Samuel Kaplan^*

Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030

Received 21 May 2008/ Accepted 30 July 2008

The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA (RegBA) two-component system, and the transcriptional repressor/antirepressor PpsR/AppA. Of the three regulators, PpsR appears to have the narrowest range of physiological effects, which are limited to effects on the structural and pigment biosynthetic activities involved in photosynthetic membrane function. Although a PrrA^– mutant is unable to grow under photosynthetic conditions, when a ppsR mutation was present, photosynthetic growth occurred. An examination of the double mutant under anaerobic-dark-dimethyl sulfoxide conditions using microarray analysis revealed the existence of an "extended" PpsR regulon and new physiological roles. To characterize the PpsR regulon and to better ascertain the significance of degeneracy within the PpsR binding sequence in vivo, we adapted the chromatin immunoprecipitation technique to R. sphaeroides. We demonstrated that in vivo there was direct and significant binding by PpsR to newly identified genes involved in microaerobic respiration and periplasmic stress resistance, as well as to photosynthesis genes. The new members of the PpsR regulon are located outside the photosynthesis gene cluster and have degenerate PpsR binding sequences. The possible interaction under physiologic conditions with degenerate binding sequences in the presence of other biologically relevant molecules is discussed with respect to its importance in physiological processes and to the existence of complex phenotypes associated with regulatory mutants. This study further defines the DNA structure necessary for PpsR binding in situ.

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* Corresponding author. Mailing address: Department of Microbiology and Molecular Genetics, 6431 Fannin St., Houston, TX 77030. Phone: (713) 500-5502. Fax: (713) 500-5499. E-mail: Samuel.Kaplan{at}uth.tmc.edu

Published ahead of print on 8 August 2008.

Supplemental material for this article may be found at http://jb.asm.org/.

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Journal of Bacteriology, October 2008, p. 6817-6828, Vol. 190, No. 20
0021-9193/08/$08.00+0     doi:10.1128/JB.00719-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

This article has been cited by other articles:

• Eraso, J. M., Kaplan, S. (2009). Regulation of Gene Expression by PrrA in Rhodobacter sphaeroides 2.4.1: Role of Polyamines and DNA Topology. J. Bacteriol. 191: 4341-4352 [Abstract] [Full Text]  
• Eraso, J. M., Kaplan, S. (2009). Half-Site DNA Sequence and Spacing Length Contributions to PrrA Binding to PrrA Site 2 of RSP3361 in Rhodobacter sphaeroides 2.4.1. J. Bacteriol. 191: 4353-4364 [Abstract] [Full Text]