Abstract
RNA polymerases initiate transcription at DNA sequences called promoters. In bacteria, the best conserved promoter feature is the AT-rich -10 element; a sequence essential for DNA unwinding. Further elements, and gene regulatory proteins, are needed to recruit RNA polymerase to the -10 sequence. Hence, -10 elements cannot function in isolation. Many horizontally acquired genes also have a high AT-content. Consequently, sequences that resemble the -10 element occur frequently. As a result, foreign genes are predisposed to spurious transcription. However, it is not clear how RNA polymerase initially recognizes such sequences. Here, we identify a non-canonical promoter element that plays a key role. The sequence, itself a short AT-tract, resides 5 base pairs upstream of otherwise cryptic -10 elements. The AT-tract alters DNA conformation and enhances contacts between the DNA backbone and RNA polymerase.
Highlights
All living organisms transcribe their genomes using the enzyme RNA polymerase [1]
Fragments were fused to lacZ in plasmid pRW50 and used to transform E. coli strain JCB387
Structural analysis provides a rationale for this observation; base specific interactions between 70 and the -10 hexamer only occur after DNA unwinding [5]
Summary
All living organisms transcribe their genomes using the enzyme RNA polymerase [1]. The process initiates at defined DNA sequences called promoters [1]. In Escherichia coli, a multisubunit core RNA polymerase (␣2’) binds one of seven dissociable factors to recognise promoter DNA [2]. The housekeeping 70 factor is best studied and targets two promoter regions; the -10 (5 -TATAAT-3 ) and -35 elements (5 -TTGACA-3 ) [2]. The -10 sequence facilitates promoter DNA unwinding and is usually indispensable [3]. The -35 element aids initial RNA polymerase recruitment and can be replaced by transcription factors fulfilling the same role [3]. Core promoter elements are ineffective [4].
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