the bacterial promoter and sigma factor

Bacteria keep things lean, and their way of marking where transcription starts is a model of economy. Two short, recognizable patches of DNA, plus a single detachable subunit that lets the polymerase read them — that's the whole start system. Once you see how it works, the bacterial promoter is the clearest illustration of how a protein reads a specific DNA address.

A typical bacterial promoter has two conserved sequence boxes upstream of the transcription start. The -10 box (the Pribnow box, often close to TATAAT) sits about ten bases before the start; the -35 box (often near TTGACA) sits about thirty-five bases before. The bacterial core RNA polymerase cannot recognize these on its own — it needs a sigma factor, a protein subunit that joins the core to form the holoenzyme and acts as the reading head. The sigma factor's job is to recognize the -10 and -35 boxes, position the enzyme correctly, help melt open the DNA at the -10 region, and then drop off once transcription is underway, so the core can elongate alone. Because the spacing and exact sequence of the boxes vary, some promoters bind tightly (strong) and others loosely (weak).

The clever part is that bacteria carry several different sigma factors, each tuned to a different family of promoters. The everyday housekeeping sigma drives normal genes, but under heat shock, starvation, or other stress the cell switches in an alternative sigma factor that redirects the same core polymerase to a whole new set of genes. Swapping sigma factors is therefore a fast, sweeping way to reprogram which genes are transcribed — a single protein change that flips a large bank of switches at once.