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J. Bacteriol. doi:10.1128/JB.01014-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Selective promoter recognition by chlamydial ²⁸ holoenzyme

Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA 02118; Department of Statistics, Harvard University, Cambridge, MA 02138, USA; Department of Molecular Sciences, University of Tennessee, Memphis, TN 38163; Department of Biology, University of Utah, Salt Lake City, UT 84112

^* To whom correspondence should be addressed. Email: lshen{at}bu.edu,

	Abstract

The transcription factor confers the promoter recognition specificity of RNA polymerase (RNAP) in eubacteria. Chlamydia trachomatis has three known factors, ⁶⁶, ⁵⁴ and ²⁸. We developed two methods to facilitate the characterization of promoter sequences recognized by chlamydial ²⁸ (Ct²⁸). One involved arabinose-induced expression of plasmid-encoded Ct²⁸ in a strain of Escherichia coli defective in the ²⁸ structural gene, fliA. The second was analysis of transcription in vitro with a hybrid holoenzyme reconstituted with E. coli RNAP core and the recombinant Ct²⁸. These approaches were used to investigate the interactions of Ct²⁸ with the Ct²⁸-dependent hctB promoter and selected E. coli ²⁸ (Ec²⁸)-dependent promoters, in parallel, compared with the promoter recognition properties of Ec²⁸. Our results indicate that RNAP containing Ct²⁸ has at least three characteristics: 1) it is capable of recognizing some but not all Ec²⁸-dependent promoters; 2) it can distinguish different promoter structures, preferentially activating promoters with upstream AT-rich sequences; and 3) it possesses a greater flexibility than Ec²⁸ in recognizing variants of spacing length separating the -35 and -10 elements of the core promoter.

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