In E. coli, there are alternative σ-factors in addition to the major “housekeeping”
σ-factor, σ70.

Transcription of genes by RNA polymerases
containing σ54 is regulated solely by activators whose
binding sites in DNA, referred to as , are generally
located 80–160 bp from the transcription start site.

Electron microscopy studies have shown that phosphorylated
NtrC bound at enhancers and σ54-polymerase bound
at the promoter interact directly, forming a in the
DNA between the binding sites (Figure 9-5). As discussed
later in this chapter, this activation mechanism resembles
the predominant mechanism of transcriptional activation
in .

The best-characterized σ54-activator—the protein

The operator is where the binds.

The is where RNA-Polymerase binds.

Gene expression in both prokaryotes and eukaryotes is regulated
primarily by mechanisms that control gene .

The first step in the initiation of transcription in E. coli
is the binding of a -factor complexed with an
to a .

are proteins that bind to sequences that
overlap or lie adjacent to promoters. Binding of a to
an operator inhibits transcription initiation or elongation.

Genes transcribed by σ54-RNA polymerase are regulated
by activators that bind to enhancers located about 100
base pairs from the start site. When the activator
and σ54-RNA polymerase interact, the DNA between their
binding sites forms a

In , one protein acts as
a sensor, monitoring the level of nutrients or other components
in the environment. Under appropriate conditions, the γ-phosphate of an ATP is transferred first to a in the sensor protein and then to an in a second protein,
the response regulator. The phosphorylated response regulator
then performs a specific function in response to the stimulus,
such as binding to DNA regulatory sequences, thereby stimulating
or repressing transcription of specific genes

Transcription in bacteria can also be regulated by control
of in the region.
This control can be exerted by ribosome binding to the
nascent mRNA, as in the case of the E. coli trp operon (see
Figure 9-7), or by riboswitches, RNA sequences that bind
small molecules, as for the B. subtilis xpt-pbuX operon (see
Figure 9-8), to determine whether a stem-loop followed by
a string of uracils forms, causing the bacterial RNA polymerase
to pause and terminate transcription.