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 ß factor (ß28) required for transcription of the class III operons. In this study, we have characterized, in vitro, a role of ß28 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 ß70 RNA polymerase holoenzyme with FlhD/C (Eß70-FlhD/C) and ß28 RNA polymerase holoenzyme (Eß28). The flhB operon could only be transcribed by Eß70-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 Eß28 could outcompete that by Eß70-FlhD/C, indicating a positive autoregulation. However, Eß28 could not displace Eß70-FlhD/C bound to the fliL promoter. The c28-mediated positive regulation of the class II operons involved a mechanism in which ß28 competed with ß70 for core RNA polymerase. In addition, recruitment of core RNA polymerase from the ß70 -10 site to the ß28 -10 was facilitated by formation of Eß70-FlhD/C pre-initiation complex. Taken together, the three class II promoters investigated are different in terms of their regulation by ß28. We propose that class II operons may be further divided into different subcategories.