The −35 sequence location and the Fis–sigma factor interface determine σS selectivity of the proP (P2) promoter in Escherichia coli

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Abstract

Summary

The P2 promoter of proP, encoding a transporter for proline and glycine betaine in Escherichia coli, is a unique paradigm, where master regulators of different growth stages, Fis and σS (RpoS), collaborate to achieve promoter activation. It is also the only case described where Fis functions as class II transcriptional activator (centred at −41). Here we show that the degenerate −35 sequence, and the location of the Fis binding site, which forces a suboptimal 16 bp spacing between the −35 and −10 elements, allow only σS but not σ70 to function at proP (P2). Moreover, the interface between Fis and σS seems better suited to σS, due to a single residue difference between σS and σ70. Nevertheless, Fis can activate RNA polymerase containing σ70 at a proP (P2) promoter variant, in which a typical σ70−35 recognition sequence has been introduced at a 17 bp distance from the −10 hexamer. In summary, we elucidate the rules that govern sigma factor selectivity in the presence of a class II activator, provide new insight into transcriptional activation by Fis from this position, and clarify, why the proP (P2) promoter is precisely activated during a short time window of the growth cycle, when Fis and σS are both present.

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