Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis

Nucleic Acids Res. 2010 Mar;38(4):1273-83. doi: 10.1093/nar/gkp1123. Epub 2009 Dec 6.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • Binding Sites
  • Consensus Sequence
  • Escherichia coli K12 / genetics*
  • Escherichia coli K12 / metabolism
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Flagella / metabolism*
  • Gene Deletion
  • Gene Expression Regulation, Bacterial
  • Genes, Bacterial
  • Promoter Regions, Genetic*
  • RNA Polymerase Sigma 54 / genetics
  • RNA Polymerase Sigma 54 / metabolism*
  • Regulon*
  • Sequence Analysis, DNA


  • Escherichia coli Proteins
  • rpoN protein, E coli
  • RNA Polymerase Sigma 54