RegulonDB RegulonDB 11.1: Operon Form
   

fliAZ-tcyJ operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: tcyJ
Synonym(s): fliY
Gene(s): tcyJ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Chonoles Imlay KR., et al., 2015
[2] Zaslaver A., et al., 2006
Promoter
Name: tcyJp
+1: 2000410
Distance from start of the gene: 25
Sequence: aagaataagatgtagcggagttgtttttgtgtttacaaacaatggctctacactgcaaacAgacataacaacattcggggt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [1] Chonoles Imlay KR., et al., 2015
[3] Salgado H, et al., 2012
[2] Zaslaver A., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: acgcgtaaatAAAAAAGGCGCTAGTGAAAGCGCCCTTTTTTgtcattatgc
Reference(s): [5] Mytelka DS., et al., 1996
TF binding sites (TFBSs)
[CysB,+] 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
nd CysB activator tcyJp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA GcvB tcyJ repressor 2000397 2000410 AUGUUGUUAUGUCU MRNA-DEGRADATION [EXP-IEP], [EXP-NUC-ACID-BINDING] [4]


Transcription unit          
Name: fliAZY
Synonym(s): fliA
Gene(s): tcyJ, fliZ, fliA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on gene expression analysis, Typas A, Stella S, Johnson RC, Hengge R,2007determined that fliA (flagellum-specific σ factor) is under positive control of ArcA. However, they did not mention which of the two promoters of fliA is controlled by ArcA. ArcB does not seem to be involved in this process and perhaps ArcA is regulated by another histidine kinase.
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 fliA 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: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [5] Mytelka DS., et al., 1996
Promoter
Name: fliAp2
+1: 2001808
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 19
Sequence: acccactaatcgtccgattaaaaaccctgcagaaacggataatcatgccgataactcataTaacgcagggctgtttatcgt
                                -35                   -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Huerta AM., et al., 2003
[7] Ide N., et al., 1999
[8] Liu X., et al., 1996
[5] Mytelka DS., et al., 1996
[9] Park K., et al., 2001
Terminator(s)
Type: rho-independent
Sequence: acgcgtaaatAAAAAAGGCGCTAGTGAAAGCGCCCTTTTTTgtcattatgc
Reference(s): [5] Mytelka DS., et al., 1996
TF binding sites (TFBSs)
[NsrR,-] 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 NsrR repressor fliAp2 2001808 2001819 -5.0 taatcatgccGATAACTCATATaacgcagggc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
remote NsrR repressor fliAp2 2002021 2002032 -218.0 cctacaagttGAATTGCAATTTattgaatttg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]


Transcription unit          
Name: fliAZY
Synonym(s): fliA
Gene(s): tcyJ, fliZ, fliA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on gene expression analysis, Kato Y, Sugiura M, Mizuno T, Aiba H,2007determined that fliA (flagellum-specific σ factor) is under positive control of ArcA. However, they did not mention which of the two promoters of fliA is controlled by ArcA. ArcB does not seem to be involved in this process and perhaps ArcA is regulated by another histidine kinase.
fliAZY expression is enhanced by AtoSC in the presence of acetoacetate Theodorou MC, Theodorou EC, Kyriakidis DA,2012.
RpoS (σ38) indirectly inhibits the transcription of the flagellar sigma factor FliA (σ28), in the exponential growth phase through CsgD, which is RpoS promoter dependent Dudin O,2014
tynA, feaB, and fliA promoters are strongly repressed when the nsrR start codon from the wild-type GUG is changed to AUG Chhabra S,2015
Based on glucose system and gene expression analyses, it was determined that CRP activates fliA expression, while on the other hand IHF represses fliA expression Amores GR,2017
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 fliA 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: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [11] Bertin P., et al., 1994
[5] Mytelka DS., et al., 1996
Promoter
Name: fliAp1
+1: 2001819
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 30
Sequence: cccctcatttcacccactaatcgtccgattaaaaaccctgcagaaacggataatcatgccGataactcatataacgcaggg
                                 -35                  -10   +1                   
Note(s): The activity of the fliAp1 promoter is dependent on FlhDC, but it has been observed that flhDC expression is not a guarantee that fliAp is activated. Rather, spontaneous on-off switching occurs in the promoter Kim JM, Garcia-Alcala M, Balleza E, Cluzel P,2020.
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [11] Bertin P., et al., 1994
[12] Brandi A., et al., 2016
[6] Huerta AM., et al., 2003
[13] Liu X., et al., 1994
[8] Liu X., et al., 1996
[5] Mytelka DS., et al., 1996
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: acgcgtaaatAAAAAAGGCGCTAGTGAAAGCGCCCTTTTTTgtcattatgc
Reference(s): [5] Mytelka DS., et al., 1996
TF binding sites (TFBSs)
[CsgD,-] 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 CsgD repressor fliAp1 2001823 2001837 -10.5 aaaccctgcaGAAACGGATAATCATgccgataact nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [17]
[FlhDC,+] 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 FlhDC activator fliAp1 2001849 2001865 -38.0 tcatttcaccCACTAATCGTCCGATTAaaaaccctgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [13], [15], [16]
proximal FlhDC activator fliAp1 2001878 2001894 -67.0 gaatttacctGTAACCCCCAAATAACCcctcatttca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [13], [15], [16]
[H-NS,+] 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
nd H-NS activator fliAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP] W [11]
[IHF,-] 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
remote IHF repressor fliAp1 2001998 2002014 -186.5 atttattgaaTTTGCACATTTTTGTAGgccggataag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IMP-SITE-MUTATION] W [14]
remote IHF repressor fliAp1 2002014 2002030 -202.5 tacaagttgaATTGCAATTTATTGAATttgcacattt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IMP-SITE-MUTATION] W [14]
[MatA,-] 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
nd MatA repressor fliAp1 nd nd nd nd nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [18]
[NsrR,-] 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 NsrR repressor fliAp1 2001808 2001819 7.0 taatcatgccGATAACTCATATaacgcagggc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [10]
remote NsrR repressor fliAp1 2002021 2002032 -207.0 cctacaagttGAATTGCAATTTattgaatttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
[SutR,-] 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
nd SutR repressor fliAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [19]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.3 2001910 2001935 caacgtgcttCCCCGCCACCGGCGGGGTTTTTTTCtgcctggaat
  anti-terminator -9.0 2001929 2001970 cgccgcatccGGCAACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGCcaccggcggg
  anti-anti-terminator -22.7 2001959 2002005 atttgcacatTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACATAAAgcgcaatttg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

 [EXP-NUC-ACID-BINDING] Nucleic acid binding evidence

 [COMP-AINF] Inferred computationally without human oversight

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IMP] Inferred from mutant phenotype

 [COMP-HINF] Inferred by a human based on computational evidence


Reference(s)    

 [1] Chonoles Imlay KR., Korshunov S., Imlay JA., 2015, Physiological Roles and Adverse Effects of the Two Cystine Importers of Escherichia coli., J Bacteriol 197(23):3629-44

 [2] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Lalaouna D., Eyraud A., Devinck A., Prevost K., Masse E., 2019, GcvB small RNA uses two distinct seed regions to regulate an extensive targetome., Mol Microbiol 111(2):473-486

 [5] Mytelka DS., Chamberlin MJ., 1996, Escherichia coli fliAZY operon., J Bacteriol 178(1):24-34

 [6] 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

 [7] 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

 [8] Liu X., Matsumura P., 1996, Differential regulation of multiple overlapping promoters in flagellar class II operons in Escherichia coli., Mol Microbiol 21(3):613-20

 [9] 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

 [10] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [11] Bertin P., Terao E., Lee EH., Lejeune P., Colson C., Danchin A., Collatz E., 1994, The H-NS protein is involved in the biogenesis of flagella in Escherichia coli., J Bacteriol 176(17):5537-40

 [12] 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

 [13] Liu X., Matsumura P., 1994, The FlhD/FlhC complex, a transcriptional activator of the Escherichia coli flagellar class II operons., J Bacteriol 176(23):7345-51

 [14] Amores GR., de Las Heras A., Sanches-Medeiros A., Elfick A., Silva-Rocha R., 2017, Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli., Sci Rep 7(1):16768

 [15] Lee YY., Barker CS., Matsumura P., Belas R., 2011, Refining the Binding of the Escherichia coli Flagellar Master Regulator, FlhD4C2, on a Base-Specific Level., J Bacteriol 193(16):4057-68

 [16] 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

 [17] Dudin O., Geiselmann J., Ogasawara H., Ishihama A., Lacour S., 2014, Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation., J Bacteriol 196(3):707-15

 [18] 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

 [19] Yamamoto K., Nakano M., Ishihama A., 2015, Regulatory role of transcription factor SutR (YdcN) in sulfur utilization in Escherichia coli., Microbiology 161(Pt 1):99-111

RegulonDB