RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: fliFGHIJK
Gene(s): fliF, fliG, fliH, fliI, fliJ, fliK   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 fliGHIJ 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: fliFp1
+1: 2013146
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 83
Sequence: acaaaaaaacgggtttattggcggatagaaaaaaacgaaagcacaaataatgggagcgtcAatttttcgagtttgctgacc
                         -35                  -10           +1                   
Note(s): The activity of the fliFp promoter is dependent on FlhDC, but it has been observed that flhDC expression is not a guarantee that fliFp is activated. A better correlation for expression of flhDC and fliFp activity is observed when YdiV, the anti-FlhDC protein, is deleted Kim JM, Garcia-Alcala M, Balleza E, Cluzel P,2020.
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, present a distance of 6 nucleotides between the transcriptional start site and the -10 box.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
[2] 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 fliFp1 2013054 2013068 -85.5 aagcctaccaGTAAGTCAATAAGACaaaggcgcta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
proximal CsgD repressor fliFp1 2013069 2013083 -70.5 tcaataagacAAAGGCGCTAAATAGcaacaaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[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 fliFp1 2013068 2013086 -69.5 gtcaataagaCAAAGGCGCTAAATAGCAAcaaaaaaacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [2], [4]
proximal FlhDC activator fliFp1 2013097 2013113 -41.0 caaaaaaacgGGTTTATTGGCGGATAGaaaaaaacga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [2], [4]
[PdeL,-] 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 PdeL repressor fliFp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


Transcription unit       
Name: fliFGHIJK
Gene(s): fliF, fliG, fliH, fliI, fliJ, fliK   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 fliGHIJ 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.
Reference(s): [5] Al Mamun AA., et al., 1997
Promoter
Name: fliFp2
+1: 2013205
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 24
Sequence: caatttttcgagtttgctgacccgggagtgagtcttgttccactttgccaataacgccgtCcataatcagccacgaggtgc
                          -35                  -10          +1                   
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 Muller V,1992. Therefore, 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 positions -12 to -10 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.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
Reference(s): [1] Huerta AM., et al., 2003
[6] Muller V., et al., 1992


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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


Reference(s)    

 [1] 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

 [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] 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

 [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] Al Mamun AA., Tominaga A., Enomoto M., 1997, Cloning and characterization of the region III flagellar operons of the four Shigella subgroups: genetic defects that cause loss of flagella of Shigella boydii and Shigella sonnei., J Bacteriol 179(14):4493-500

 [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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