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OmpR DNA-binding transcriptional dual regulator

Synonyms: OmpR-P, OmpR


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
OmpR Functional   Apo [BPP], [GEA], [IPI] [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15]
OmpR-P Functional Covalent Holo [APPHINH], [BPP], [GEA], [HIFS], [IMP], [IPI] [2], [3], [4], [12], [14], [16], [17], [18]
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: ompR
  Genome position: 3535865-3536584
  Length: 720 bp / 239 aa
Operon name: ompR-envZ
TU(s) encoding the TF:
Transcription unit        Promoter
ompR-envZ
ompRp1
ompR-envZ
ompRp2
ompR-envZ
ompRp3
ompR-envZ
ompRp4


Regulon       
Regulated gene(s) bolA, cadA, cadB, cadC, csgD, csgE, csgF, csgG, dtpA, ecnB, fadL, flhC, flhD, micF, nmpC, ompC, ompF, omrA, omrB, pgaA, pgaB, pgaC, pgaD, sra
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Transcription related (5)
activator (5)
repressor (4)
Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily) (4)
antisense RNA (4)
Read more >
Regulated operon(s) bdm-sra, bolA, cadBA, cadC, csgDEFG, dtpA, ecnAB, fadL, flhDC, micF, nmpC, ompC, ompF, omrA, omrB, pgaABCD
First gene in the operon(s) bolA, cadB, cadC, csgD, ecnB, fadL, flhD, micF, ompC, ompF, omrA, omrB, pgaA, sra, dtpA
Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
AcrR,H-NS,HU,IHF,Lrp,MarA,OmpR,Rob,SoxS
ArcA,CRP,FadR,OmpR,PhoP,ppGpp
ArcA,CadC,GadE-RcsB,GadX,H-NS,Lrp,OmpR
BasR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[OmpR,-](10)
[OmpR,+-](1)
[OmpR,+](7)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  OmpR-P repressor bolAp1 Sigma38, Sigma70 -47.5 -85.5 bolA
aggacgaaacCTAAATATTTGTTGTTAAGCtgcaatggaa
454377 454396 [APIORCISFBSCS], [BPP] [19]
  OmpR repressor cadBp Sigma70 nd nd cadB, cadA nd nd [BPP], [GEA] [20]
  OmpR repressor cadCp Sigma70 nd nd cadC nd nd [BPP], [GEA] [20]
  OmpR-P activator csgDp1 Sigma38, Sigma70 -49.5 -197.5 csgD, csgE, csgF, csgG
aatataacgaGTTACATTTAGTTACATGTTtaacacttga
1103384 1103403 [APIORCISFBSCS], [BPP], [GEA] [21], [22], [23]
  OmpR-P repressor ecnBp Sigma38 18.5 -26.5 ecnB
tttgctatagGCAAACATAAATAACATTACctaaaaggaa
4376517 4376536 [APIORCISFBSCS] [24]
  OmpR-P repressor fadLp Sigma38 -149.5 -250.5 fadL
gataagtgacCGAAATCACACTTAAAAATGatctaaaaca
2461046 2461065 [APIORCISFBSCS], [SM] [25], [26]
  OmpR-P repressor fadLp Sigma38 -60.5 -161.5 fadL
atcgcgtttcTTAGATCATATTTGAAAAAAgatagaaaca
2461135 2461154 [APIORCISFBSCS], [GEA] [26]
  OmpR-P repressor fadLp Sigma38 69.5 -32.5 fadL
gttacagcacGTAACATAGTTTGTATAAAAataaatcatt
2461264 2461283 [APIORCISFBSCS], [GEA] [26]
  OmpR-P repressor fadLp Sigma38 119.5 18.5 fadL
tcatgagccaGAAAACCCTGTTTACAAAGTctgctctcgc
2461314 2461333 [APIORCISFBSCS], [GEA] [26]
  OmpR-P repressor flhDp Sigma70 -145.5 -343.5 flhD, flhC
caaagtcatcGGGCATTATCTGAACATAAAacactatcaa
1978531 1978550 [APIORCISFBSCS] [27]
  OmpR-P repressor flhDp Sigma70 18.5 -180.5 flhD, flhC
tcgatttaggAAAAATCTTAGATAAGTGTAaagacccatt
1978368 1978387 [APIORCISFBSCS] [27]
  OmpR-P activator micFp Sigma38, Sigma70 -206.5 -206.5 micF
atccaacacgAATATGATACTAAAACTTTTaagatgtttc
2312868 2312887 [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [28], [29], [30]
  OmpR-P activator micFp Sigma38, Sigma70 -186.5 -186.5 micF
taaaacttttAAGATGTTTCATTTATCGCTatagatgttt
2312888 2312907 [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [12], [28], [30]
  OmpR-P activator micFp Sigma38, Sigma70 -165.5 -165.5 micF
tttatcgctaTAGATGTTTCAAAATGTAAAtgcaagggaa
2312909 2312928 [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [12], [28], [30]
  OmpR-P repressor nmpCp nd -45.5 nd nmpC
aatcaaacgaGAAACCAAAACTTACATCTTgaaataatca
576906 576925 [APIORCISFBSCS], [SM] [31]
  OmpR-P activator ompCp1 Sigma70 -88.5 -169.5 ompC
ttcccttgcaTTTACATTTTGAAACATCTAtagcgataaa
2312909 2312928 [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [12], [28], [30], [32]
  OmpR-P activator ompCp1 Sigma70 -67.5 -148.5 ompC
aaacatctatAGCGATAAATGAAACATCTTaaaagtttta
2312888 2312907 [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [12], [28], [30], [32]
  OmpR-P activator ompCp1 Sigma70 -47.5 -128.5 ompC
gaaacatcttAAAAGTTTTAGTATCATATTcgtgttggat
2312868 2312887 [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [28], [29], [30], [32]
  OmpR-P repressor ompFp Sigma38, Sigma70 -370.5 -480.5 ompF
cgatcatcctGTTACGGAATATTACATTGCaacatttacg
987453 987472 [BPP], [GEA] [30], [32], [33], [34], [35]
  OmpR-P activator ompFp Sigma38, Sigma70 -90.5 -200.5 ompF
ttccttaaatTTTACTTTTGGTTACATATTttttcttttt
987173 987192 [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [12], [29], [30], [36], [37], [38], [39]
  OmpR-P activator ompFp Sigma38, Sigma70 -70.5 -180.5 ompF
gttacatattTTTTCTTTTTGAAACCAAATctttatcttt
987153 987172 [APIORCISFBSCS], [BCE], [BPP], [GEA], [SM] [4], [12], [29], [30], [32], [36], [37], [38], [39], [40], [41]
  OmpR-P repressor ompFp Sigma38, Sigma70 -70.5 -180.5 ompF
gttacatattTTTTCTTTTTGAAACCAAATctttatcttt
987153 987172 [APIORCISFBSCS], [BCE], [BPP], [GEA], [SM] [4], [12], [29], [30], [32], [36], [37], [38], [39], [40], [41]
  OmpR-P activator ompFp Sigma38, Sigma70 -50.5 -160.5 ompF
gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg
987133 987152 [AIBSCS], [BPP], [GEA], [SM] [4], [12], [29], [30], [33], [34], [35], [36], [37], [38], [39], [40]
  OmpR-P repressor ompFp Sigma38, Sigma70 -50.5 -160.5 ompF
gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg
987133 987152 [AIBSCS], [BPP], [GEA], [SM] [4], [12], [29], [30], [33], [34], [35], [36], [37], [38], [39], [40]
  OmpR-P activator omrAp nd -70.5 -70.5 omrA
accgacaattTACACACCTCGTTGCATTTCccttcattcc
2976250 2976269 [APIORCISFBSCS], [GEA] [42]
  OmpR-P activator omrBp nd -71.5 -71.5 omrB
aaagagattgCAAACCTTTGGTTACACTTTgcgaaacgct
2976447 2976466 [APIORCISFBSCS], [GEA] [42]
  OmpR-P repressor pgaAp nd -31.5 -265.5 pgaA, pgaB, pgaC, pgaD
tgcatcggaaTTTACTGATTTAATTATTTTaatcctaatt
1092545 1092564 [APIORCISFBSCS], [BPP], [GEA] [43]
  OmpR-P repressor srap Sigma38 nd nd sra nd nd [GEA] [44]
  OmpR-P activator tppBp Sigma70 -45.5 -143.5 dtpA
tcagttatatGTAACAGATTATTACAAAGGacttgtctga
1712616 1712635 [BPP], [GEA] [45]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Growth Condition Evidence (Confirmed, Strong, Weak) References
  OmpR repressor speF-potE nd nd nd nd nd [BPP], [GEA] [20]


Alignment and PSSM for OmpR TFBSs    

Aligned TFBS of OmpR   
  Sequence
  AATATGTAACCAAAAGTAAAAT
  AACATGTAACTAAATGTAACTC
  AACGAGAAACCAAAACTTACAT
  AAAGTGTAACCAAAGGTTTGCA
  AATATGATACTAAAACTTTTAA
  TATATGTAACAGATTATTACAA
  TAGATGTTTCAAAATGTAAATG
  ATCCTGTTACGGAATATTACAT
  GAAATGCAACGAGGTGTGTAAA
  AAAGTGCTACAAAGATAAAGAT
  TATAGGCAAACATAAATAACAT
  ATTTGGTTTCAAAAAGAAAAAA
  AGCACGTAACATAGTTTGTATA
  TACACTTATCTAAGATTTTTCC
  TATCTTTTTTCAAATATGATCT
  TGACCGAAATCACACTTAAAAA
  GCAGCTTAACAACAAATATTTA
  TTAAAATAATTAAATCAGTAAA
  ACTTTGTAAACAGGGTTTTCTG
  GGGCATTATCTGAACATAAAAC
  TCTATAGCGATAAATGAAACAT

Position weight matrix (PWM). OmpR matrix-quality result   
A	10	12	6	11	3	2	3	14	15	3	6	17	16	15	8	6	4	10	13	8	13	9
C	0	3	5	4	4	0	3	1	0	15	7	0	2	0	2	3	0	0	0	7	3	3
G	3	3	2	4	2	15	1	0	1	0	2	3	2	5	2	7	0	4	0	2	0	2
T	8	3	8	2	12	4	14	6	5	3	6	1	1	1	9	5	17	7	8	4	5	7

Consensus   
;	consensus.strict             	aatatGtaaCcaaatgtaacaa
;	consensus.strict.rc          	TTGTTACATTTGGTTACATATT
;	consensus.IUPAC              	wayatGtaaCcaarwgtwwmaw
;	consensus.IUPAC.rc           	WTKWWACWYTTGGTTACATRTW
;	consensus.regexp             	[at]a[ct]atGtaaCcaa[ag][at]gt[at][at][ac]a[at]
;	consensus.regexp.rc          	[AT]T[GT][AT][AT]AC[AT][CT]TTGGTTACAT[AG]T[AT]

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IPI] Inferred from physical interaction

 [APPHINH] Assay of protein purified to homogeneity from its native host

 [HIFS] Human inference of function from sequence

 [IMP] Inferred from mutant phenotype

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [SM] Site mutation

 [BCE] Binding of cellular extracts

 [AIBSCS] Automated inference based on similarity to consensus sequences



Reference(s)    

 [1] Comeau DE., Ikenaka K., Tsung KL., Inouye M., 1985, Primary characterization of the protein products of the Escherichia coli ompB locus: structure and regulation of synthesis of the OmpR and EnvZ proteins., J Bacteriol 164(2):578-84

 [2] Forst S, Delgado J, Rampersaud A, Inouye M., 1990, In vivo phosphorylation of OmpR, the transcription activator of the ompF and ompC genes in Escherichia coli., J Bacteriol.

 [3] Huang KJ, Lan CY, Igo MM., 1997, Phosphorylation stimulates the cooperative DNA-binding properties of the transcription factor OmpR., Proc Natl Acad Sci U S A.

 [4] Mattison K., Oropeza R., Byers N., Kenney LJ., 2002, A phosphorylation site mutant of OmpR reveals different binding conformations at ompF and ompC., J Mol Biol 315(4):497-511

 [5] McBroom AJ., Johnson AP., Vemulapalli S., Kuehn MJ., 2006, Outer membrane vesicle production by Escherichia coli is independent of membrane instability., J Bacteriol 188(15):5385-92

 [6] Nara F., Matsuyama S., Mizuno T., Mizushima S., 1986, Molecular analysis of mutant ompR genes exhibiting different phenotypes as to osmoregulation of the ompF and ompC genes of Escherichia coli., Mol Gen Genet 202(2):194-9

 [7] Pao GM., Saier MH., 1995, Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution., J Mol Evol 40(2):136-54

 [8] Parkinson JS., 1993, Signal transduction schemes of bacteria., Cell 73(5):857-71

 [9] Parkinson JS., Kofoid EC., 1992, Communication modules in bacterial signaling proteins., Annu Rev Genet 26:71-112

 [10] Shuster Y., Steiner-Mordoch S., Alon Cudkowicz N., Schuldiner S., 2016, A Transporter Interactome Is Essential for the Acquisition of Antimicrobial Resistance to Antibiotics., PLoS One 11(4):e0152917

 [11] Stock JB., Stock AM., Mottonen JM., 1990, Signal transduction in bacteria., Nature 344(6265):395-400

 [12] Tsung K., Brissette RE., Inouye M., 1989, Identification of the DNA-binding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in vivo DNA footprinting., J Biol Chem 264(17):10104-9

 [13] Wurtzel ET., Chou MY., Inouye M., 1982, Osmoregulation of gene expression. I. DNA sequence of the ompR gene of the ompB operon of Escherichia coli and characterization of its gene product., J Biol Chem 257(22):13685-91

 [14] Yamamoto K., Hirao K., Oshima T., Aiba H., Utsumi R., Ishihama A., 2005, Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli., J Biol Chem 280(2):1448-56

 [15] Zhao Z., Eberhart LJ., Orfe LH., Lu SY., Besser TE., Call DR., 2015, Genome-Wide Screening Identifies Six Genes That Are Associated with Susceptibility to Escherichia coli Microcin PDI., Appl Environ Microbiol 81(20):6953-63

 [16] Nixon BT., Ronson CW., Ausubel FM., 1986, Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC., Proc Natl Acad Sci U S A 83(20):7850-4

 [17] Norioka S., Ramakrishnan G., Ikenaka K., Inouye M., 1986, Interaction of a transcriptional activator, OmpR, with reciprocally osmoregulated genes, ompF and ompC, of Escherichia coli., J Biol Chem 261(36):17113-9

 [18] Taylor RK., Hall MN., Enquist L., Silhavy TJ., 1981, Identification of OmpR: a positive regulatory protein controlling expression of the major outer membrane matrix porin proteins of Escherichia coli K-12., J Bacteriol 147(1):255-8

 [19] Yamamoto K., Nagura R., Tanabe H., Fujita N., Ishihama A., Utsumi R., 2000, Negative regulation of the bolA1p of Escherichia coli K-12 by the transcription factor OmpR for osmolarity response genes., FEMS Microbiol Lett 186(2):257-62

 [20] Chakraborty S., Winardhi RS., Morgan LK., Yan J., Kenney LJ., 2017, Non-canonical activation of OmpR drives acid and osmotic stress responses in single bacterial cells., Nat Commun 8(1):1587

 [21] Jubelin G., Vianney A., Beloin C., Ghigo JM., Lazzaroni JC., Lejeune P., Dorel C., 2005, CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli., J Bacteriol 187(6):2038-49

 [22] Ogasawara H., Yamada K., Kori A., Yamamoto K., Ishihama A., 2010, Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors., Microbiology 156(Pt 8):2470-83

 [23] Prigent-Combaret C., Brombacher E., Vidal O., Ambert A., Lejeune P., Landini P., Dorel C., 2001, Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene., J Bacteriol 183(24):7213-23

 [24] Bishop RE., Leskiw BK., Hodges RS., Kay CM., Weiner JH., 1998, The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death., J Mol Biol 280(4):583-96

 [25] Black PN., 1991, Primary sequence of the Escherichia coli fadL gene encoding an outer membrane protein required for long-chain fatty acid transport., J Bacteriol 173(2):435-42

 [26] Higashitani A., Nishimura Y., Hara H., Aiba H., Mizuno T., Horiuchi K., 1993, Osmoregulation of the fatty acid receptor gene fadL in Escherichia coli., Mol Gen Genet 240(3):339-47

 [27] Shin S., Park C., 1995, Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR., J Bacteriol 177(16):4696-702

 [28] Coyer J., Andersen J., Forst SA., Inouye M., Delihas N., 1990, micF RNA in ompB mutants of Escherichia coli: different pathways regulate micF RNA levels in response to osmolarity and temperature change., J Bacteriol 172(8):4143-50

 [29] Qin L., Yoshida T., Inouye M., 2001, The critical role of DNA in the equilibrium between OmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli., Proc Natl Acad Sci U S A 98(3):908-13

 [30] Yoshida T., Qin L., Egger LA., Inouye M., 2006, Transcription regulation of ompF and ompC by a single transcription factor, OmpR., J Biol Chem 281(25):17114-23

 [31] Coll JL., Heyde M., Portalier R., 1994, Expression of the nmpC gene of Escherichia coli K-12 is modulated by external pH. Identification of cis-acting regulatory sequences involved in this regulation., Mol Microbiol 12(1):83-93

 [32] Oshima T., Aiba H., Masuda Y., Kanaya S., Sugiura M., Wanner BL., Mori H., Mizuno T., 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12., Mol Microbiol 46(1):281-91

 [33] Huang KJ., Schieberl JL., Igo MM., 1994, A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene., J Bacteriol 176(5):1309-15

 [34] Rampersaud A., Harlocker SL., Inouye M., 1994, The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation., J Biol Chem 269(17):12559-66

 [35] Slauch JM., Silhavy TJ., 1991, cis-acting ompF mutations that result in OmpR-dependent constitutive expression., J Bacteriol 173(13):4039-48

 [36] Forst SA., Delgado J., Inouye M., 1989, DNA-binding properties of the transcription activator (OmpR) for the upstream sequences of ompF in Escherichia coli are altered by envZ mutations and medium osmolarity., J Bacteriol 171(6):2949-55

 [37] Lan CY., Igo MM., 1998, Differential expression of the OmpF and OmpC porin proteins in Escherichia coli K-12 depends upon the level of active OmpR., J Bacteriol 180(1):171-4

 [38] Rampersaud A., Norioka S., Inouye M., 1989, Characterization of OmpR binding sequences in the upstream region of the ompF promoter essential for transcriptional activation., J Biol Chem 264(31):18693-700

 [39] Sato M., Machida K., Arikado E., Saito H., Kakegawa T., Kobayashi H., 2000, Expression of outer membrane proteins in Escherichia coli growing at acid pH., Appl Environ Microbiol 66(3):943-7

 [40] Forst S., Kalve I., Durski W., 1995, Molecular analysis of OmpR binding sequences involved in the regulation of ompF in Escherichia coli., FEMS Microbiol Lett 131(2):147-51

 [41] Ramani N., Huang L., Freundlich M., 1992, In vitro interactions of integration host factor with the ompF promoter-regulatory region of Escherichia coli., Mol Gen Genet 231(2):248-55

 [42] Guillier M., Gottesman S., 2006, Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs., Mol Microbiol 59(1):231-47

 [43] Oropeza R., Salgado-Bravo R., Calva E., 2015, Deletion analysis of RcsC reveals a novel signalling pathway controlling poly-N-acetylglucosamine synthesis and biofilm formation in Escherichia coli., Microbiology 161(Pt 4):903-13

 [44] Izutsu K., Wada C., Komine Y., Sako T., Ueguchi C., Nakura S., Wada A., 2001, Escherichia coli ribosome-associated protein SRA, whose copy number increases during stationary phase., J Bacteriol 183(9):2765-73

 [45] Goh EB., Siino DF., Igo MM., 2004, The Escherichia coli tppB (ydgR) gene represents a new class of OmpR-regulated genes., J Bacteriol 186(12):4019-24



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