In order to recognize their promoters, bacterial RNA polymerase enzymes require a specialized subunit called the sigma factor (σ), which directly contacts the promoter sequence (Figure 9-2.1). The complex formed by the sigma subunit with the remaining polymerase core subunits constitutes the bacterial holoenzyme. Bacteria contain a variety of sigma factors that specifically recognize different promoter sequences. It is therefore the sigma factor that determines which genes are transcribed.

All cells have a primary sigma factor, which directs transcription from the promoters of essential housekeeping genes, and a variable number of alternative sigma factors whose levels or activities are increased in response to specific signals or stress conditions. Bacterial species differ significantly in the number of sigma factors they express, reflecting the different environmental conditions to which they must respond. E. coli, a symbiotic bacterium leading a relatively sheltered life in the gut of other organisms, has only seven sigma factors. In contrast, the genome of the soil organism B. subtilis encodes 17 sigma factors and S. coelicolor, which is also free-living, has 65. The large number of sigma factors makes possible a broader array of genetic programs, thus allowing these organisms to meet changing conditions and undergo major morphological changes upon starvation.

Bacterial promoters are generally composed of two elements: one conserved sequence centered at -35 nucleotides and a second conserved sequence centered at -10 nucleotides from the start of the transcript, which is typically a purine nucleotide (A or G) (Figure 9-2.2). The terms -35 and -10 refer to the typical location of these sequences, although the number of base pairs separating them can vary among different promoters. As we shall see, variations in both promoter element spacing and sequence allow for differential regulation of genes by influencing the relative binding of different classes of sigma factors as well as the rates of promoter opening and transcription initiation. Many highly expressed genes have similar promoter sequences, with a consensus sequence of TTGACA at the -35 position and TATAAT at the -10 position (Figure 9-2.2). However, the -35 or the -10 sequence - or both - may diverge considerably from typical consensus sequences and few strictly match the consensus sequence. Some bacterial promoters contain sequences in addition to the -35 and -10 regions that can further modulate RNA polymerase binding and initiation. At some promoters lacking a conserved -35 sequence, initiation depends on recognition of an extended -10 region consisting of an additional two bases located upstream of the -10 region. Some bacterial genes that are transcribed at a high rate contain an additional AT-rich sequence called the UP element upstream of the -35 region and which promotes tighter binding of RNA polymerase to DNA through contacts made with the α subunit.

The sigma subunit contains a poorly structured region at the N-terminus, followed by three distinct structured domains (domains 2—4), that correspond roughly to the four main regions of amino acid conservation found in sequence comparisons of diverse sigma factors (Figure 9-2.2). Within the holoenzyme, the three structured domains of sigma are positioned to recognize the promoter sequence (Figure 9-2.3). Domain 2 binds to the -10 region and is implicated in melting of the DNA to form the open complex, while the immediately adjacent domain 3 recognizes the two bases comprising the extended -10 region. Domain 4 recognizes the -35 region and is bound to a flexible flap of the β subunit that may allow movement of domain 4 to accommodate variably spaced -35 and -10 elements. The N-terminal unstructured region of sigma, termed region 1.1, inhibits DNA binding by the free sigma subunit and accelerates the rate of open complex formation at certain promoters.

While the amounts of the core subunits of RNA polymerase remain relatively constant under different growth conditions, the levels and activities of many sigma factors can vary significantly in response to environmental or developmental signals, thereby enabling the cell to alter its pattern of gene expression to meet changing needs. This regulation of sigma factor activity can be accomplished in a variety of ways. Some sigma factors are synthesized as pro-sigma factors carrying inhibitory domains that must be cleaved off before the sigma factor can associate with the core RNA polymerase enzyme. The activities of other sigma factors are controlled by anti-sigma factor proteins that bind to specific sigma factors and prevent their interaction with the RNA polymerase core enzymes. The activities of anti-sigma factors, in turn, can be regulated by controlling their levels of expression in the cell or by sequestering them through interactions with other cellular proteins (called anti-anti sigma factors). As one example, the anti-sigma factor FlgM forms a complex with σ^F (also called σ²⁸), which directs transcription of genes required for completing the assembly of flagella in the bacterium S. typhimurium. During late stages of flagellar synthesis, FlgM is exported from the cell through the incomplete flagellar apparatus, releasing σ^F (σ²⁸) to activate transcription of the genes necessary for final assembly of the flagella (Figure 9-2.4).

-10: promoter sequence located 10 nucleotides upstream of the start of transcription and comprising half of the sequence directing bacterial RNA polymerase to bind and initiate transcription, also called the Pribnow box.

-35: promoter sequence located 35 nucleotides upstream of the start of transcription and comprising half of the sequence directing bacterial RNA polymerase to bind and initiate transcription.

alternative sigma factor: sigma factor that recognizes promoters of specialized sets of genes and is expressed or activated in specific conditions when it associates with the core RNA polymerase enabling the specialized genes to be expressed.

anti-sigma factor: protein that binds a sigma factor and prevents it from binding to the core RNA polymerase enzyme.

extended -10 region: additional bases upstream of some -10 sequences that are bound by the σ₃ domain.

primary sigma factor: sigma factor that is present in all normal growth conditions and associates with the core RNA polymerase to bind the promoters of many highly expressed genes. Each bacterial species has only one primary sigma factor.

sigma factor: RNA polymerase subunit required for promoter recognition.

UP element: AT-rich sequence located just upstream of the -35 sequence and bound by the α subunit of RNA polymerase.