113.12 In most prokaryotic promoters, the actual sequence is not TATAAT. The sequences shown are found in five E. coli promoters, including those of genes for tryptophan biosynthesis (trp), tyrosine tRNA (tRNATyr), lactose metabolism (lac), a recombination protein (recA), and arabinose metabolism (araB, A, D). These sequences are on the nontemplate strand and read 5': 3', left to right.

The sigma factor associates with the core enzyme (iFigure 13.13a) to form a holoenzyme, which binds to the —35 and —10 consensus sequences in the DNA promoter (iFigure 13.13b). Although it binds only the nucleotides of consensus sequences, the enzyme extends from —50 to +20 when bound to the promoter. The holoenzyme initially binds weakly to the promoter but then undergoes a change in structure that allows it to bind more tightly and unwind the double-stranded DNA (IFigure 13.13c). Unwinding begins within the — 10 consensus sequence and extends downstream for about 17 nucleotides, including the start site.

Some bacterial promoters contain a third consensus sequence that also takes part in the initiation of transcription. Called the upstream element, this sequence contains a number of A - T pairs and is found at about —40 to —60. The alpha subunit of the RNA polymerase interacts directly with this upstream element, greatly enhancing the rate of transcription in those bacterial promoters that possess it. A number of other proteins may bind to sequences in and near the promoter; some stimulate the rate of transcription and others repress it; we will consider the proteins that regulate gene expression in Chapter 16.

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