RegulonDB RegulonDB 10.6.3: Operon Form
   

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




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


Transcription unit          
Name: fliC
Gene(s): fliC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Lehti TA., et al., 2012
Promoter
Name: fliCp
+1: 2003676
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 70
Sequence: aaaaatggctgtttttgaaaaaaattctaaaggttgttttacgacagacgataacagggtTgacggcgattgagccgacgg
                            -10                -35          +1                   
Note(s): The sequence of this promoter has been defined, by computational analyses, from the consensus sequence of the σ28F) promoters TAAAGTTT in the -35 box and GCCGATAA in the -10 box Park K,2001. Helmann JD,1987. Ide N,1999
Thus, 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 -12 to -10 positions 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.
Kundu et al. showed in 1997 that transcription of fliC is highly dependent on alternative factor σF and can be transcribed by RNA polymerase σ28 in vitro Kundu TK,1997
Evidence: [FP]
[HIPP]
Reference(s): [2] Chilcott GS., et al., 2000
[3] Clarke MB., et al., 2005
[4] Helmann JD., et al., 1987
[5] Ide N., et al., 1999
[6] Kundu TK., et al., 1997
[7] Park K., et al., 2001
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadE activator fliCp nd nd nd nd nd [GEA] [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS activator fliCp nd nd nd nd nd [GEA] [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd MatA1 repressor fliCp nd nd nd nd nd [BPP] [1]
Note(s): 1MatA-fliCp regulatory interaction was identified in Escherichia coli strain IHE 3034 Lehti TA,2012
MatA binds weakly to fliCp Lehti TA,20123MatA-fliCp regulatory interaction was identified in Escherichia coli strain IHE 3034 Lehti TA,2012
MatA binds weakly to fliCp Lehti TA,2012




Reference(s)    

 [1] Lehti TA., Bauchart P., Dobrindt U., Korhonen TK., Westerlund-Wikstrom B., 2012, The fimbriae activator MatA switches off motility in Escherichia coli by repression of the flagellar master operon flhDC., Microbiology 158(Pt 6):1444-55

 [2] Chilcott GS., Hughes KT., 2000, Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli., Microbiol Mol Biol Rev 64(4):694-708

 [3] Clarke MB., Sperandio V., 2005, Transcriptional regulation of flhDC by QseBC and sigma (FliA) in enterohaemorrhagic Escherichia coli., Mol Microbiol 57(6):1734-49

 [4] Helmann JD., Chamberlin MJ., 1987, DNA sequence analysis suggests that expression of flagellar and chemotaxis genes in Escherichia coli and Salmonella typhimurium is controlled by an alternative sigma factor., Proc Natl Acad Sci U S A 84(18):6422-4

 [5] Ide N., Ikebe T., Kutsukake K., 1999, Reevaluation of the promoter structure of the class 3 flagellar operons of Escherichia coli and Salmonella., Genes Genet Syst 74(3):113-6

 [6] Kundu TK., Kusano S., Ishihama A., 1997, Promoter selectivity of Escherichia coli RNA polymerase sigmaF holoenzyme involved in transcription of flagellar and chemotaxis genes., J Bacteriol 179(13):4264-9

 [7] 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

 [8] Landini P., Zehnder AJ., 2002, The global regulatory hns gene negatively affects adhesion to solid surfaces by anaerobically grown Escherichia coli by modulating expression of flagellar genes and lipopolysaccharide production., J Bacteriol 184(6):1522-9

 [9] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72


RegulonDB