Escherichia coli σ38 promoters use two UP elements instead of a −35 element: resolution of a paradox and discovery that σ38 transcribes ribosomal promoters

1AbstractInE. coli, one RNA polymerase (RNAP) transcribes all RNA species, and different regulons are transcribed by employing different sigma (σ) factors. RNAP containingσ38(σS) activates genes responding to stress conditions such as stationary phase. The structure ofσ38promoters has been controversial for more than two decades. To construct a model ofσ38promoters using information theory, we aligned proven transcriptional start sites to maximize the sequence information, in bits, and identified a −10 element similar toσ70promoters. We could not align any −35 sequence logo; instead we found two patterns upstream of the −35 region. These patterns have dyad symmetry sequences and correspond to the location of UP elements in ribosomal RNA (rRNA) promoters. Additionally the UP element dyad symmetry suggests that the two polymeraseαsubunits, which bind to the UPs, should have two-fold dyad axis of symmetry on the polymerase and this is indeed observed in an X-ray crystal structure. Curiously theαCTDs should compete for overlapping UP elements.In vitroexperiments confirm thatσ38recognizes therrnBP1 promoter, requires a −10, UP elements and no −35. This clarifies the long-standing paradox of howσ38promoters differ from those ofσ70.