Differential regulation of multiple overlapping promoters in flagellar class II operons in Escherichia coli

The Escherichia coli flagellar operons are divided into three categories: classes I, II and III, Expression of class II depends on expression of class I, One of the class II gene products, the FliA protein, is an alternative sigma factor (sigma(28)) required for transcription of the class III operons, In this study, we have characterized, in vitro, a role of sigma(28) in the regulation of the class II operons, Among the three class II operons examined, the fliA and fliL operons, but not the flhB operon, could be transcribed by both sigma(70) RNA polymerase holoenzyme with FlhD/C (E sigma(70)-FlhD/C) and sigma(28) RNA polymerase holoenzyme (E sigma(28)), The flhB operon could only be transcribed by E sigma(70)-FlhD/C under the conditions used. Both the fliA and fliL operons contained two overlapping promoters oriented in tandem, The transcription of fliA directed by E sigma(28) could outcompete that by E sigma(70)-FlhD/C, indicating a positive autoregulation, However, E sigma(28) could not displace E sigma(70)-FlhD/C bound to the fliL promoter. The sigma(28)-mediated positive regulation of the class II operons involved a mechanism in which sigma(28) competed with sigma(70) for core RNA polymerase. In addition, recruitment of core RNA polymerase from the sigma(70) -10 site to the sigma(28) -10 was facilitated by formation of E sigma(70)-FlhD/C pre-initiation complex, Taken together, the three class II promoters investigated are different in terms of their regulation by sigma(28), We propose that class II operons may be further divided into different subcategories.