Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.

In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize DNA sequences specifically. To help the RNAP recognize DNA sequences with high affinity, specialized proteins called transcription factors bind to particular regions of DNA to initiate transcription. In bacteria, the sigma factor helps the RNAP recognize the promoter sequence and secures its binding at the transcription start site. Bacteria contain a variety of sigma factors that associate with different promoter sequences. Such different sigma factors bind to the cellular pool of RNAPs to express different genes, depending on the cellular requirement.

Other prokaryotic transcription factors allow the cell to turn transcription of certain genes on or off in response to changes in environmental or cellular conditions. Depending on the number of genes targeted, these transcription factors can control gene expression locally or globally. Some transcription factors use their signal-sensing domains to sense the change and modulate the transcription rate by controlling RNAP binding on the template DNA. Thus, even with a single RNAP enzyme, bacteria can use different transcription factors to control which gene to express and when.