RegulonDB RegulonDB 11.1: Operon Form
   

flxA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: flxA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: flxA
Gene(s): flxA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Ide N., et al., 1997
Promoter
Name: flxAp
+1: 1646388
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 17
Sequence: aacaattaatgacacaagaaatacgattaaagatttttttgtgcatgccgatagtgctttTttaaaaggagaaatctatgt
                            -35                -10          +1                   
Note(s): The sequence of this promoter has been defined, by computational analyses, from the consensus sequence of the σ28 (σF) promoters: TAAAGTTT in the -35 box and GCCGATAA in the -10 box Park K,2001. Therefore, we assigned a putative transcription start site for this promoter based on the observation that the majority of the σ28 promoters, determined experimentally, present an important -10 motif (5'-CGA-3') at the positions -12 to -10 and a distance of 6 nucleotides between the transcription start site and the -10 box Yu HH, Di Russo EG, Rounds MA, Tan M,2006. Yu HH,2006. Park K,2001.
Ide et al. showed in 1997 that transcription of flxA is highly dependent on alternative factor σF Ide N,1997. The transcription expression level was examined in a fliA mutant background.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [2] Huerta AM., et al., 2003
[1] Ide N., et al., 1997
[3] Park K., et al., 2001
[4] Zhao K., et al., 2007
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator flxAp 1646309 1646323 -72.0 agcccgcgagGAAAACAATCTGAACatcaaacaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] Ide N., Kutsukake K., 1997, Identification of a novel Escherichia coli gene whose expression is dependent on the flagellum-specific sigma factor, FliA, but dispensable for motility development., Gene 199(1-2):19-23

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] Park K., Choi S., Ko M., Park C., 2001, Novel sigmaF-dependent genes of Escherichia coli found using a specified promoter consensus., FEMS Microbiol Lett 202(2):243-50

 [4] Zhao K., Liu M., Burgess RR., 2007, Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli., Nucleic Acids Res 35(13):4441-52

 [5] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

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