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

1 Abstract

In E. coli, one RNA polymerase (RNAP) transcribes all RNA species, and different regulons are transcribed by employing different sigma (σ) factors. RNAP containing σ³⁸ (σ^S) activates genes responding to stress conditions such as stationary phase. The structure of σ³⁸ promoters has been controversial for more than two decades. To construct a model of σ³⁸ promoters using information theory, we aligned proven transcriptional start sites to maximize the sequence information, in bits, and identified a −10 element similar to σ⁷⁰ 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 α 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 αCTDs should compete for overlapping UP elements. In vitro experiments confirm that σ³⁸ recognizes the rrnB P1 promoter, requires a −10, UP elements and no −35. This clarifies the long-standing paradox of how σ³⁸ promoters differ from those of σ⁷⁰.