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Name: | flhDC | ||||||||||
Synonym(s): | OP00183 | ||||||||||
Gene(s): | flhC, flhD Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The transcription of the flhDC operon is repressed in acidic phospholipid-deficient cells, but the gadW, metE, and yeaB genes in multicopy suppress this repression through the reduction of overexpression of RpoS caused by the same mutation in the gene producing acidic phospholipid Uchiyama J, Nobue Y, Zhao H, Matsuzaki H, Nagahama H, Matsuoka S, Matsumoto K, Hara H,2010 The mechanism for this is not known. Under motility-inducing environmental growth conditions, a motile element (IS5) is inserted into the upstream region of the flhDC operon. This event appears to enhance the expression of the operon, because motility and biofilm formation are increased Wang X, Wood TK,2011CITS: [28100305]|. IS5 insertion disrupts the H-NS binding site, thus preventing transcriptional repression of the operon Wang X, Wood TK,2011 Three novel cis-acting IS elements upstream of flhDC (IS5, located at -166 and -315, IS1, inserted at -303, and a trans-acting missense mutation in lrhA) were found that enhanced motility by relieving transcriptional repression of flhDC Lee C, Park C,2013 Both effects act in parallel, suggesting their apparently independent regulation of flagellar expression Lee C, Park C,2013 Several insertion sequence (IS) elements upstream of the promoter for flhDC stimulate motility independently of orientation and have a long-range effect Fahrner KA, Berg HC,2015 fllhDC expression is enhanced by AtoSC in the presence of acetoacetate Theodorou MC, Theodorou EC, Kyriakidis DA,2012. Under NlpE outer membrane lipoprotein overexpression, the transcription of the flhC gene is decreased Raivio TL,2013 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 flhDC 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. Based on mutations analysis, it was shown that OmpR and RcsB abolish temporal and spatial changes in expression of flhDC Samanta P, Clark ER, Knutson K, Horne SM, Prüß BM,2013 Single nucleotide changes in the -10 element and the spacer of the flhDC promoter, and also in the cAMP-CRP-binding region, increase motility Fahrner KA, Berg HC,2015 Several mutations in the flhDC promoter allow motility in H-NS mutant strains Fahrner KA, Berg HC,2015 YjjQ represses transcription of the flhDC operon independently from the previously characterized RcsA-RcsB repressor, even though the two DNA-binding motifs contain overlapping sequences Wiebe H,2015 flhDC requires a specific transcription rate to maintain optimal flagellum numbers Albanna A, Sim M, Hoskisson PA, Gillespie C, Rao CV, Aldridge PD,2018 The impact of a two-component signal transduction system (2CSTS) was reviewed with regard to EnvZ/OmpT, RscCDB, CheAYB, and QueCB. Studies of the effects of changes in signaling on the expression of motility and biofilm genes revealed the involvement of the flhDC operon in the induction of changes in motility in the early phases of biofilm development and the swim-or-stick switch that allows bacteria to transit from reversible to irreversible attachment Prüß BM,2017. Orthologous flhDC from E. coli can functionally complement flhDC in S. Enterica, and flhCEC is not functionally identical to flhCST Albanna A, Sim M, Hoskisson PA, Gillespie C, Rao CV, Aldridge PD,2018 The phenotypic differences between species arise from adaptations during evolution to expand or modify cellular function with respect to movement within specific environmental niches Albanna A, Sim M, Hoskisson PA, Gillespie C, Rao CV, Aldridge PD,2018 The mRNA that contains the flhD gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019. |
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Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined | ||||||||||
Reference(s): |
[1] Bertin P., et al., 1994 [2] Lehti TA., et al., 2012 [3] Shin S., et al., 1995 |
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Promoter | |||||||||||
Name: | flhDp | ||||||||||
+1: | 1978395 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 198 | ||||||||||
Sequence: |
tattgaaaatcgcagcccccctccgttgtatgtgcgtgtagtgacgagtacagttgcgtcGatttaggaaaaatcttagat -35 -10 +1 |
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Evidence: |
[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[4] Barker CS., et al., 2004 [5] Huerta AM., et al., 2003 [3] Shin S., et al., 1995 [6] Soutourina O., et al., 1999 [7] Wei BL., et al., 2001 |
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Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | ttaacgcgcgATTGGGGCAAAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTcaccgtatca | ||||||||||
Reference(s): |
[11] Feng CQ., et al., 2019 [12] Lesnik EA., et al., 2001 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | AcrR | repressor | flhDp | 1978422 | 1978432 | -31.5 | agcccccctcCGTTGTATGTGcgtgtagtga | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [16] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | CRP-cyclic-AMP | activator | flhDp | 1978456 | 1978477 | -71.5 | attgagtgttTTGTGTGATCTGCATCACGCATtattgaaaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [6], [14], [15] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | FliZ | repressor | flhDp | 1978370 | 1978399 | 12.0 | agtacagttgCGTCGATTTAGGAAAAATCTTAGATAAGTGtaaagaccca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [20] |
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 | Fur-Fe2+ | repressor | flhDp | 1978272 | 1978290 | 115.0 | caactattctAATGCTAATTATTTTTTACcggggcttcc | nd | [COMP-AINF-SIMILAR-TO-CONSENSUS] | nd | [21] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
nd | H-NS | activator | flhDp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [6] |
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 | HdfR | repressor | flhDp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [23] |
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 | IHF | repressor | flhDp | 1978481 | 1978493 | -92.0 | ccatttatgtTAAGTAATTGAGTgttttgtgtg | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS] | nd | [3] |
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 | LrhA | repressor | flhDp | 1978500 | 1978514 | -112.0 | tcaataagttGGAGTCATTACCCATttatgttaag | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [13] |
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 | flhDp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | OmpR-phosphorylated | repressor | flhDp | 1978368 | 1978387 | 18.5 | tcgatttaggAAAAATCTTAGATAAGTGTAaagacccatt | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS] | nd | nd |
remote | OmpR-phosphorylated | repressor | flhDp | 1978531 | 1978550 | -145.5 | caaagtcatcGGGCATTATCTGAACATAAAacactatcaa | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS] | nd | nd |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
nd | QseB-Phosphorylated | activator | flhDp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [22] |
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 | RcsAB | repressor | flhDp | 1978378 | 1978392 | 11.0 | ttgcgtcgatTTAGGAAAAATCTTAgataagtgta | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [18], [19] |
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 | YjjQ | repressor | flhDp | 1978378 | 1978392 | 11.0 | ttgcgtcgatTTAGGAAAAATCTTAgataagtgta | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] | W | [17] |
sRNA | TU Regulated | Function | Binding Sites | Regulatory Mechanism | Evidence (Confirmed, Strong, Weak) | Reference(s) | ||
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PosLeft | PosRight | Target sequence (mRNA) | ||||||
small regulatory RNA OmrB | flhDC | repressor | 1978206 | 1978251 | CCCAGAAUAACCAACUUUAUUUUUAUGCGGUUUCACCGCACCCCGU | nd | [EXP-IMP], [EXP-IMP-SITE-MUTATION] | [8] |
small regulatory RNA McaS | flhDC | activator | 1978274 | 1978283 | AAAAAAUAAU | TRANSLATION-BLOCKING | [EXP-IEP], [EXP-IMP] | [9] |
small regulatory RNA ArcZ | flhDC | repressor | 1978244 | 1978261 | CACCCCGUGAUGUCGCCG | nd | [EXP-IMP], [EXP-IMP-SITE-MUTATION] | [8] |
small regulatory RNA McaS | flhDC | activator | 1978249 | 1978258 | CGUGAUGUCG | nd | [EXP-IEP], [EXP-IMP-SITE-MUTATION] | [9] |
small regulatory RNA OxyS | flhDC | repressor | 1978200 | 1978219 | UUCCCACCCAGAAUAACCAA | nd | [EXP-IMP], [EXP-IMP-SITE-MUTATION] | [8] |
small regulatory RNA OmrA | flhDC | repressor | 1978206 | 1978251 | CCCAGAAUAACCAACUUUAUUUUUAUGCGGUUUCACCGCACCCCGU | nd | [EXP-IMP], [EXP-IMP-SITE-MUTATION] | [8], [10] |
Name: | flhDC | ||||||||||
Gene(s): | flhC, flhD Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The transcription of the flhDC operon is repressed in acidic phospholipid-deficient cells, but the gadW, metE, and yeaB genes in multicopy suppress this repression through the reduction of overexpression of RpoS caused by the same mutation in the gene producing acidic phospholipid Uchiyama J, Nobue Y, Zhao H, Matsuzaki H, Nagahama H, Matsuoka S, Matsumoto K, Hara H,2010 The mechanism for this is not known. Under motility-inducing environmental growth conditions, a motile element (IS5) is inserted into the upstream region of the flhDC operon. This event appears to enhance the expression of the operon, because motility and biofilm formation are increased Wang X, Wood TK,2011 IS5 insertion disrupts the H-NS binding site, thus preventing transcriptional repression of the operon Wang X, Wood TK,2011br>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 flhDC as well as other falgellar genes Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019. The mRNA that contains the flhD gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019. |
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Reference(s): |
[1] Bertin P., et al., 1994 [3] Shin S., et al., 1995 |
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Promoter | |||||||||||
Name: | flhDp2 | ||||||||||
+1: | 1978577 | ||||||||||
Sigma Factor: | Sigma54 Sigmulon | ||||||||||
Distance from start of the gene: | 380 | ||||||||||
Sequence: |
aacctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaaTcggtggagctgcatgacaaa -24 -12 +1 |
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Note(s): | This promoter was identified by microarray assays with a mutant σ54 strain and a σ54-overexpressing strain, and by σ54-related promoter element identification Zhao K,2010 We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999. |
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Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IEP] |
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Reference(s): |
[5] Huerta AM., et al., 2003 [24] Zhao K., et al., 2010 |
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Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | ttaacgcgcgATTGGGGCAAAAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGAATGTTGCGCCTcaccgtatca | ||||||||||
Reference(s): |
[11] Feng CQ., et al., 2019 [12] Lesnik EA., et al., 2001 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
nd | MatA | repressor | flhDp2 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2] |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Translational |
Strand: | reverse |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
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terminator | -8.4 | 1978230 | 1978246 | acatcacgggGTGCGGTGAAACCGCAtaaaaataaa |
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" |
Reference(s) |
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