Thus far we have described a promoter as a specific DNA sequence located upstream of a transcription initiation site. The promoter binds RNA polymerase so that the enzyme can then catalyze the synthesis of RNA from a gene-encoding region of DNA. The promoter also orients the polymerase so that it transcribes the correct one of the two DNA strands. Not all promoters are identical, but they all have similar sequences by which they are recognized by the RNA polymerase and other proteins. Prokaryotic promoters generally have two sites for these recognition sequences, which begin 10 and 35 base pairs upstream of the transcription start site (the –10 element and the –35 element). Different classes of promoters have different recognition sequences at these two sites. The largest class consists of promoters for “housekeeping genes,” which are all the genes that are normally expressed in actively growing cells. In these genes, the –10 element is 5′-TATAAT-3′, and the –35 element is 5′-TTGACAT-3′ (N stands for any nucleotide):

Other classes of genes have different recognition sequences at their –10 and –35 sites. Why do DNA recognition sequences differ in different classes of promoters? After all, aren’t they all binding the same protein, RNA polymerase? The answer lies in the fact that these DNA sequences bind not just RNA polymerase but other proteins as well. And it is those other proteins that enhance RNA polymerase binding at certain promoters, thereby giving the system a degree of specificity.

Sigma factors are the proteins in prokaryotic cells that bind to RNA polymerase and direct it to specific classes of promoters. The RNA polymerase must be bound to a sigma factor before it can recognize a promoter and begin transcription. For example, the sigma-70 factor is active most of the time and binds to the recognition sequences of housekeeping genes; other sigma factors are activated only under specific conditions. When E. coli cells experience conditions such as DNA damage or osmotic stress, the sigma-38 factor is activated, and it directs RNA polymerase to the promoters of various genes that are expressed under stress conditions. E. coli has seven sigma factors; this number varies in other prokaryotes.

Regulation of proteins directing RNA polymerase to certain promoters is not unusual. In fact, you’ll see in the next section that it is also common in eukaryotes.