In E. coli, about half the genes are clustered into operons, each of which encodes enzymes involved in a particular metabolic pathway or proteins that interact to form one multisubunit protein complex. For instance, the trp operon discussed in Chapter 5 encodes five polypeptides needed in the biosynthesis of tryptophan (see Figure 5-13). Similarly, the lac operon encodes three proteins required for the metabolism of lactose, a sugar present in milk. Because a bacterial operon is transcribed from one start site into a single mRNA, all the genes within an operon are coordinately regulated; that is, they are all activated or repressed at the same time to the same extent.

The transcription of operons, as well as that of isolated genes, is controlled by interplay between RNA polymerase and specific repressor and activator proteins. In order to initiate transcription, E. coli RNA polymerase must associate with one of a small number of σ (sigma) factors. The most common one in eubacterial cells is σ⁷⁰. This σ-factor binds to both RNA polymerase and promoter DNA sequences, bringing the RNA polymerase enzyme to the promoter. It recognizes and binds to both a six-base-pair sequence centered at about 10 bp and a seven-base-pair sequence centered at about 35 bp upstream from the +1 transcription start. Consequently, the −10 sequence and the −35 sequence together constitute a promoter for E. coli RNA polymerase associated with σ⁷⁰ (see Figure 5-10b). Although the promoter sequences contacted by σ⁷⁰ are located at −35 and −10, E. coli RNA polymerase binds to the promoter-region DNA from roughly −50 to +20 through interactions with DNA that do not depend on the sequence. The σ-factor also assists the RNA polymerase in separating the DNA strands at the transcription start site and in inserting the coding strand into the active site of the polymerase so that transcription starts at +1 (see Figure 5-11, step 2). The optimal σ⁷⁰-RNA polymerase promoter sequence, determined as the “consensus sequence” of multiple strong promoters, is

−35 region −10 region

TTGACAT——15–17 bp——TATAAT

This consensus sequence shows the most commonly occurring base at each of the positions in the −35 and −10 regions. The size of the font indicates the importance of the base at that position, as determined by the influence of mutations of these bases on the frequency of transcription initiation (i.e., the number of times per minute that RNA polymerases initiate transcription). The sequence shows the strand of DNA that has the same 5′→3′ orientation as the transcribed RNA (i.e., the nontemplate strand). However, the σ⁷⁰-RNA polymerase initially binds to double-stranded DNA. After the polymerase transcribes a few tens of base pairs, σ⁷⁰ is released. Thus σ⁷⁰ acts as an initiation factor that is required for transcription initiation, but not for RNA strand elongation once initiation has taken place.