RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: fliE
Gene(s): fliE   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 fliE 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: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Reference(s): [1] Stafford GP., et al., 2005
Promoter
Name: fliEp1
+1: 2013036
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 22
Sequence: cgtttttttgttgctatttagcgcctttgtcttattgacttactggtaggctttgctaccAgaaattatccgggagacgag
                               -35                  -10     +1                   
Note(s): We assigned a putative transcriptional start site to this promoter based on the observation that the majority of the promoters, whose transcriptional start sites were determined experimentally, are present at a distance of 6 nucleotides between the transcriptional start site and the -10 box.
In a cell-free expression system, FlhDC slightly activated fliE expression while σ28 did not show an effect on fliE expression Maddalena LL, Niederholtmeyer H, Turtola M, Swank ZN, Belogurov GA, Maerkl SJ,2016
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
Reference(s): [2] Brandi A., et al., 2016
[3] Huerta AM., et al., 2003
[1] Stafford GP., et al., 2005
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 fliEp1 2013054 2013068 -24.5 tagcgcctttGTCTTATTGACTTACtggtaggctt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [5]
proximal CsgD repressor fliEp1 2013069 2013083 -39.5 ttttttgttgCTATTTAGCGCCTTTgtcttattga nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [5]
[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 fliEp1 2013068 2013086 -40.5 cgtttttttgTTGCTATTTAGCGCCTTTGtcttattgac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [4]
proximal FlhDC activator fliEp1 2013097 2013113 -69.0 tcgtttttttCTATCCGCCAATAAACCcgtttttttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [4]


Transcription unit          
Name: fliE
Gene(s): fliE   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 flgBCDEFGHIJ 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: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [6] Muller V., et al., 1992
Promoter
Name: fliEp2
+1: 2013093
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 79
Sequence: gaaaaattgacgctcccattatttgtgctttcgtttttttctatccgccaataaacccgtTtttttgttgctatttagcgc
                              -35                     -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
Reference(s): [3] Huerta AM., et al., 2003
[6] Muller V., et al., 1992
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
remote CsgD repressor fliEp2 2013054 2013068 33.5 tagcgcctttGTCTTATTGACTTACtggtaggctt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [5]
proximal CsgD repressor fliEp2 2013069 2013083 18.5 ttttttgttgCTATTTAGCGCCTTTgtcttattga nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IDA] Inferred from direct assay

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

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

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence


Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [4] Yilmaz C., Rangarajan AA., Schnetz K., 2020, The transcription regulator and c-di-GMP phosphodiesterase PdeL represses motility in Escherichia coli., J Bacteriol

 [5] Ogasawara H., Yamamoto K., Ishihama A., 2011, Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis., J Bacteriol 193(10):2587-97

 [6] Muller V., Jones CJ., Kawagishi I., Aizawa S., Macnab RM., 1992, Characterization of the fliE genes of Escherichia coli and Salmonella typhimurium and identification of the FliE protein as a component of the flagellar hook-basal body complex., J Bacteriol 174(7):2298-304

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