RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: fliLMNOPQR
Gene(s): fliL, fliM, fliN, fliO, fliP, fliQ, fliR   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 fliLMOPQR 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: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Malakooti J., et al., 1994
[2] Raha M., et al., 1994
Promoter
Name: fliLp1
+1: 2019584
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 34
Sequence: agcaccgtaatccgcgtcttttccccgctttgttgcgctcaagacgcaggataattagccGataagcagtagcgacacagg
                             -35                  -10       +1                   
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Brandi A., et al., 2016
[4] Huerta AM., et al., 2003
[5] Liu X., et al., 1994
[6] Liu X., et al., 1996
TF binding sites (TFBSs)
[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 fliLp1 2019511 2019527 -65.0 tattttcgccTAACGTCAGAGGTAGCAccgtaatccg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [7]
proximal FlhDC activator fliLp1 2019539 2019555 -37.0 cgtaatccgcGTCTTTTCCCCGCTTTGttgcgctcaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [6], [7]


Transcription unit       
Name: fliLMNOPQR
Gene(s): fliL, fliM, fliN, fliO, fliP, fliQ, fliR   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 fliLMOPQR 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: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Malakooti J., et al., 1994
[2] Raha M., et al., 1994
Promoter
Name: fliLp2
+1: 2019595
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 23
Sequence: ccgcgtcttttccccgctttgttgcgctcaagacgcaggataattagccgataagcagtaGcgacacaggaagaccgcaac
                            -35                -10          +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [8] Arnosti DN., et al., 1989
[9] Chilcott GS., et al., 2000
[10] Helmann JD., et al., 1987
[4] Huerta AM., et al., 2003
[11] Ide N., et al., 1999
[6] Liu X., et al., 1996


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA] Inferred from direct assay

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

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

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

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

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

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


Reference(s)    

 [1] Malakooti J., Ely B., Matsumura P., 1994, Molecular characterization, nucleotide sequence, and expression of the fliO, fliP, fliQ, and fliR genes of Escherichia coli., J Bacteriol 176(1):189-97

 [2] Raha M., Sockett H., Macnab RM., 1994, Characterization of the fliL gene in the flagellar regulon of Escherichia coli and Salmonella typhimurium., J Bacteriol 176(8):2308-11

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] Arnosti DN., Chamberlin MJ., 1989, Secondary sigma factor controls transcription of flagellar and chemotaxis genes in Escherichia coli., Proc Natl Acad Sci U S A 86(3):830-4

 [9] 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

 [10] 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

 [11] 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

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