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Updated: Jun 18, 2026

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues
Published on: February 19, 2019
Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli
Kai Zhao1, Mingzhu Liu, Richard R Burgess
1McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA.
Abstract:
Bacteria core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Promoters recognized by the sigma(54) (or sigma(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 sigma(54), the nitrogen assimilation sigma factor, and estimate that there are 70 sigma(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 sigma(54) promoter carried by insB-5 in the upstream of flhDC operon. The involvement of sigma(54) in flagellar biosynthesis in sequenced E. coli strain MG1655 indicates a fluid gene regulation phenomenon carried by some mobile elements in bacteria genome.
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