RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: fliDST
Gene(s): fliD, fliS, fliT   Genome Browser M3D Gene expression COLOMBOS
Note(s): In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid downregulated the expression of fliDS as well as other flagellar genes Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Kawagishi I., et al., 1992
[2] Stafford GP., et al., 2005
[3] Yokoseki T., et al., 1995
Promoter
Name: fliDp2
+1: 2003817
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 55
Sequence: ttttctctgccccttattcccgctattaaaaaaaacaattaaacgtaaactttgcgcaatTcagaccgataaccccggtat
                         -35                  -10           +1                   
Evidence: [HIPP]
[ICWHO]
[IDA]
[IHBCE]
Reference(s): [4] Brandi A., et al., 2016
[5] Huerta AM., et al., 2003
[1] Kawagishi I., et al., 1992
[2] Stafford GP., et al., 2005
Terminator(s)
Type: rho-independent
Sequence: cgaataatccGATTACGGCTACGCTTCTAATGTTCCCCTTGAATGGAGTCGAAGAATGCGTAATCccacgctgtt
Reference(s): [1] Kawagishi I., et al., 1992
TF binding sites (TFBSs)
[FlhDC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FlhDC activator fliDp2 2003740 2003756 -69.0 cattttttgtTAGTCGCCGAAATACTCttttctctgc nd [APIORCISFBSCS] [2]
proximal FlhDC activator fliDp2 2003768 2003784 -41.0 tttctctgccCCTTATTCCCGCTATTAaaaaaaacaa nd [APIORCISFBSCS] [2]


Transcription unit       
Name: fliDST
Gene(s): fliD, fliS, fliT   Genome Browser M3D Gene expression COLOMBOS
Note(s): In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid downregulated the expression of fliDS as well as other flagellar genes Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
Promoter
Name: fliDp1
+1: Unknown
Sigma Factor: Sigma28 Sigmulon
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. Helmann JD,1987. Ide N,1999. Ko M,2000
Kundu et al. (1997) showed that the transcription of fliD is highly dependent on alternative factor σF and can be transcribed by RNA polymerase σ28 in vitro Kundu TK,1997
Evidence: [APIORCISFBSCS]
[HIPP]
[RPF]
Reference(s): [6] Chilcott GS., et al., 2000
[7] Helmann JD., et al., 1987
[8] Ide N., et al., 1999
[9] Ko M., et al., 2000
[10] Kundu TK., et al., 1997
[11] Park K., et al., 2001


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IDA] Inferred from direct assay

 [IHBCE] Inferred by a human based on computational evidence

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [RPF] RNA polymerase footprinting


Reference(s)    

 [1] Kawagishi I., Muller V., Williams AW., Irikura VM., Macnab RM., 1992, Subdivision of flagellar region III of the Escherichia coli and Salmonella typhimurium chromosomes and identification of two additional flagellar genes., J Gen Microbiol 138 ( Pt 6):1051-65

 [2] Stafford GP., Ogi T., Hughes C., 2005, Binding and transcriptional activation of non-flagellar genes by the Escherichia coli flagellar master regulator FlhD2C2., Microbiology 151(Pt 6):1779-88

 [3] Yokoseki T., Kutsukake K., Ohnishi K., Iino T., 1995, Functional analysis of the flagellar genes in the fliD operon of Salmonella typhimurium., Microbiology 141 ( Pt 7):1715-22

 [4] Brandi A., Giangrossi M., Giuliodori AM., Falconi M., 2016, An Interplay among FIS, H-NS, and Guanosine Tetraphosphate Modulates Transcription of the Escherichia coli cspA Gene under Physiological Growth Conditions., Front Mol Biosci 3:19

 [5] 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

 [6] 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

 [7] 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

 [8] 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

 [9] Ko M., Park C., 2000, Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli., J Mol Biol 303(3):371-82

 [10] 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

 [11] 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

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