Nucleic Acids Research, 2003, Vol. 31, No. 2 551-555
© 2003 Oxford University Press
Mutational analysis of the Chlamydia trachomatis dnaK promoter defines the optimal –35 promoter element
1 Department of Microbiology and Molecular Genetics and 2 Department of Medicine, College of Medicine, University of California, Irvine, CA 92697-4025, USA
*To whom correspondence should be addressed at B240, Med Sci I, Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697-4025, USA. Tel: +1 949 824 3397; Fax: +1 949 824 8598; Email: mingt{at}uci.edu
A long-standing question in the biology of the intracellular bacterium, Chlamydia, has been the structure of the promoter recognized by its RNA polymerase. The ‘RNA polymerase sigma subunit paradox’ refers to the difficulty reconciling the conservation between the RNA polymerases of Chlamydia and Escherichia coli, especially at the level of the promoter-recognition sigma subunit, with the general lack of homology between chlamydial promoters and the E.coli 
70 consensus promoter. While the –10 promoter element appears to be conserved between Chlamydia and E.coli, the structure of the chlamydial –35 promoter element has not been defined. We have investigated the structure of the –35 element of the Chlamydia trachomatis dnaK promoter by measuring the effects of single base pair substitutions on in vitro promoter activity. Most substitutions produced large decreases in promoter activity, which allowed us to define the optimal –35 sequence in the context of the dnaK promoter. We found that the optimal chlamydial –35 promoter sequence is identical to the E.coli 70 consensus –35 promoter element (TTGACA). These results indicate that the optimal promoter specificities of the major form of chlamydial RNA polymerase and E.coli 70 RNA polymerase are in fact highly conserved. A further implication of our results is that many chlamydial promoters have a suboptimal promoter structure. We hypothesize that these chlamydial promoters are intrinsically weak promoters that can be regulated during the chlamydial developmental cycle by additional transcription factors.
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