Reevaluation of the promoter structure of the class 3 flagellar operons of Escherichia coli and Salmonella

Flagellar class 3 operons of Escherichia coli and Salmonella are transcribed by RNA polymerase containing σ²⁸. The consensus sequence of the σ²⁸-dependent promoters was believed to be TAAA N₁₅ GCCGATAA. In this study, we found that the E. coli genome contains a large number of sequences homologous to this consensus. However, we showed that they do not always exert a σ²⁸-dependent promoter activity. We compare more carefully the sequences of the class 3 flagellar promoters and propose a revised structure of the σ²⁸-dependent promoters as TAAAGTTT N₁₁ GCCGATAA.