Promoter and regulon analysis of nitrogen assimilation factor, σ54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis
Open Access
- 4 December 2009
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 38 (4) , 1273-1283
- https://doi.org/10.1093/nar/gkp1123
Abstract
Bacteria core RNA polymerase (RNAP) must associate with a σ factor to recognize promoter sequences. Promoters recognized by the σ54 (or σN) 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 σ54, the nitrogen assimilation σ factor, and estimate that there are 70 σ54 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 σ54 promoter carried by insB-5 in the upstream of flhDC operon. The involvement of σ54 in flagellar biosynthesis in sequenced E. coli strain MG1655 indicates a fluid gene regulation phenomenon carried by some mobile elements in bacteria genome.Keywords
This publication has 75 references indexed in Scilit:
- Sigma factors inPseudomonas aeruginosaFEMS Microbiology Reviews, 2008
- Adaptation in bacterial flagellar and motility systems: from regulon members to ‘foraging’-like behavior in E. coliNucleic Acids Research, 2007
- The σ54 regulon (sigmulon) of Pseudomonas putidaEnvironmental Microbiology, 2003
- Mechanism of Action of the Escherichia coli Phage Shock Protein PspA in Repression of the AAA Family Transcription Factor PspFJournal of Molecular Biology, 2002
- Transcription of the ibpB Heat-Shock Gene Is under Control of ς32- and ς54-Promoters, a Third Regulon of Heat-Shock ResponseBiochemical and Biophysical Research Communications, 2001
- Two novel flagellar components and H-NS are involved in the motor function of Escherichia coliJournal of Molecular Biology, 2000
- The Complete Genome Sequence of Escherichia coli K-12Science, 1997
- Sigma factor and sporulation genes inClostridiumFEMS Microbiology Reviews, 1995
- Specific binding of the transcription factor sigma-54 to promoter DNANature, 1992
- Sequence logos: a new way to display consensus sequencesNucleic Acids Research, 1990