Promoter and regulon analysis of nitrogen assimilation factor, σ(54), reveal alternative strategy for E. coli MG1655 flagellar biosynthesis

Bacteria core RNA polymerase (RNAP) must associate with a σ factor to recognize promoter sequences. Promoters recognized by the σ(54) (or σ(N)) associated RNA polymerase are unique in having conserved positions around −24 and −12 nucleotides upstream from the transcriptional start site. Using DNA microarrays representing the entire Escherichia coli genome and promoter validation approaches, we identify 40 in vivo targets of σ(54), the nitrogen assimilation σ factor, and estimate that there are 70 σ(54) promoters in total. Immunoprecipitation assays have been performed to further evaluate the efficiency of our approaches. In addition, promoter consensus binding search and primer extension assay helped us to identify a new σ(54) promoter carried by insB-5 in the upstream of flhDC operon. The involvement of σ(54) in flagellar biosynthesis in sequenced E. coli strain MG1655 indicates a fluid gene regulation phenomenon carried by some mobile elements in bacteria genome.