Escherichia coli σ38 promoters use two UP elements instead of a -35 element: resolution of a paradoxand discovery that σ38 transcribes ribosomal promoters

1In E. coli, one RNA polymerase (RNAP) transcribes all RNA species, and different regulons are transcribed by employing different sigma ({sigma}) factors. RNAP containing{sigma} 38 ({sigma}S) activates genes responding to stress conditions such as stationary phase. The structure of{sigma} 38 promoters has been controversial for more than two decades. To construct a model of{sigma} 38 promoters using information theory, we aligned proven transcriptional start sites to maximize the sequence information, in bits, and identified a -10 element similar to{sigma} 70 promoters. 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 polymerase subunits, 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 the CTDs should compete for overlapping UP elements. In vitro experiments confirm that{sigma} 38 recognizes the rrnB P1 promoter, requires a -10, UP elements and no -35. This clarifies the long-standing paradox of how{sigma} 38 promoters differ from those of{sigma} 70.