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Orientational control of fimE expression in Escherichia coli

Phase‐variable expression of type 1 fimbriae is, in part, controlled by site‐specific DNA inversion of the fim switch in Escherichia coli. Of the two fim recombinases (FimB and FimE) that catalyse the inversion reaction, FimE exhibits a strong bias for phase switching from the ON to the OFF orientation. The specificity associated with fimE is the result of two different mechanisms: (i) FimE exhibits a preference for the invertible element in the ON orientation as substrate for recombination; (ii) the invertible element in the OFF orientation acts in cis to inhibit recombinase activity (orientational control). We show here that the invertible element negatively regulates fimE, even though expression of a fimE–lacZYA transcriptional fusion is unaffected by orientational control. The fimE transcript extends into the invertible region and hence switch ON‐specific and switch OFF‐specific mRNA contain different sequences. Furthermore, we show that orientational control is suppressed by the insertion of a structured RNA (tRNAGly) between fimE and the fim switch, indicating that the switch OFF‐specific mRNA is inactivated by 3′ to 5′ degradation. Analysis of the fim switch reveals that it contains two inhibitory elements that exert orientational control independently.