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OmpR DNA-binding transcriptional dual regulator

Synonyms: OmpR-Phosphorylated, OmpR
Summary:
The response regulator OmpR, for "Outer membrane protein Regulator," [7] belongs to the two-component system EnvZ/OmpR [35] EnvZ is an osmosensor histidine kinase and is known to be a transmembrane protein composed of three domains: an external sensory domain (amino terminal), a cytoplasmic transmitter domain (carboxyl terminal), and a transmembrane hydrophobic central domain [36] The sensor domain responds to changes in extracellular osmolarity. EnvZ and OmpR comprise a signal transduction system where the signal generated by the periplasmic receptor affects through a protein-protein interaction the EnvZ cytoplasmic component, which is transmitted via autophosphorylation of histidine kinase to the response regulator OmpR [18] OmpR is localized preferentially at the nucleoid edges and close to the cell membrane under low-salt and acidic conditions [] Phosphorylated OmpR controls the transcriptional expression of several genes and operons whose products are involved in adaptation to changes in osmolarity, such as major outer membrane porins [19, 35, 37, 38], and it negatively regulates the expression of flagella [16] promotes biofilm formation [12] increases curli gene expression [10] increases expression of several drug exporter genes [39] and confers increased beta-lactam resistance [40] among other effects [9, 17, 34, 41] When the genes csgD or ompR are overexpressed, the curli number is increased, with higher levels found in cells overexpressing the csgD gene, and there is not an additive effect on the curli number or structure in a strain overexpressing both the csgD and ompR genes.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
OmpR Non-Functional   Apo [BPP] [1]
OmpR-Phosphorylated Functional Covalent Holo [APPHINH], [BPP], [GEA], [HIFS], [IMP], [IPI] [1], [2], [3], [4], [5], [6], [7], [8]
Evolutionary Family: OmpR
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, 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 (4)
activator (4)
repressor (4)
Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily) (4)
antisense RNA (4)
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Regulated operon(s) bdm-sra, bolA, csgDEFG, dtpA, ecnAB, fadL, flhDC, micF, nmpC, ompC, ompF, omrA, omrB, pgaABCD
First gene in the operon(s) bolA, csgD, dtpA, ecnB, fadL, flhD, micF, nmpC, ompC, ompF, omrA, omrB, pgaA, sra
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
BasR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA
CRP,CpxR,EnvY,Fur,IHF,OmpR,PhoB,RstA
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[OmpR,-](7)
[OmpR,+](7)
[OmpR,+-](1)


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-Phosphorylated repressor bolAp1 Sigma38, Sigma70 -47.5 -85.5 bolA
aggacgaaacCTAAATATTTGTTGTTAAGCtgcaatggaa
454377 454396 [BPP], [HIBSCS] [9]
  OmpR-Phosphorylated activator csgDp1 Sigma38, Sigma70 -49.5 -197.5 csgD, csgE, csgF, csgG
tcaagtgttaAACATGTAACTAAATGTAACtcgttatatt
1103384 1103403 [BPP], [GEA], [HIBSCS] [10], [11], [12]
  OmpR-Phosphorylated repressor ecnBp Sigma38 18.5 -26.5 ecnB
tttgctatagGCAAACATAAATAACATTACctaaaaggaa
4376517 4376536 [HIBSCS] [13]
  OmpR-Phosphorylated repressor fadLp Sigma38 -149.5 -250.5 fadL
gataagtgacCGAAATCACACTTAAAAATGatctaaaaca
2461046 2461065 [HIBSCS], [SM] [14], [15]
  OmpR-Phosphorylated repressor fadLp Sigma38 -60.5 -161.5 fadL
atcgcgtttcTTAGATCATATTTGAAAAAAgatagaaaca
2461135 2461154 [GEA], [HIBSCS] [15]
  OmpR-Phosphorylated repressor fadLp Sigma38 69.5 -32.5 fadL
gttacagcacGTAACATAGTTTGTATAAAAataaatcatt
2461264 2461283 [GEA], [HIBSCS] [15]
  OmpR-Phosphorylated repressor fadLp Sigma38 119.5 17.5 fadL
tcatgagccaGAAAACCCTGTTTACAAAGTctgctctcgc
2461314 2461333 [GEA], [HIBSCS] [15]
  OmpR-Phosphorylated repressor flhDp Sigma70 -145.5 -343.5 flhD, flhC
ttgatagtgtTTTATGTTCAGATAATGCCCgatgactttg
1978531 1978550 [HIBSCS] [16]
  OmpR-Phosphorylated repressor flhDp Sigma70 18.5 -180.5 flhD, flhC
aatgggtcttTACACTTATCTAAGATTTTTcctaaatcga
1978368 1978387 [HIBSCS] [16]
  OmpR-Phosphorylated activator micFp Sigma70 -206.5 -206.5 micF
atccaacacgAATATGATACTAAAACTTTTaagatgtttc
2312868 2312887 [BPP], [GEA], [HIBSCS], [SM] [4], [17], [18], [19]
  OmpR-Phosphorylated activator micFp Sigma70 -186.5 -186.5 micF
taaaacttttAAGATGTTTCATTTATCGCTatagatgttt
2312888 2312907 [BPP], [GEA], [HIBSCS], [SM] [1], [4], [17], [19]
  OmpR-Phosphorylated activator micFp Sigma70 -165.5 -165.5 micF
tttatcgctaTAGATGTTTCAAAATGTAAAtgcaagggaa
2312909 2312928 [BPP], [GEA], [HIBSCS], [SM] [1], [4], [17], [19]
  OmpR-Phosphorylated repressor nmpCp nd -45.5 -90.5 nmpC
tgattatttcAAGATGTAAGTTTTGGTTTCtcgtttgatt
576906 576925 [HIBSCS], [SM] [20]
  OmpR-Phosphorylated activator ompCp1 Sigma70 -88.5 -169.5 ompC
ttcccttgcaTTTACATTTTGAAACATCTAtagcgataaa
2312909 2312928 [BPP], [GEA], [HIBSCS], [SM] [1], [4], [17], [19], [21]
  OmpR-Phosphorylated activator ompCp1 Sigma70 -67.5 -148.5 ompC
aaacatctatAGCGATAAATGAAACATCTTaaaagtttta
2312888 2312907 [BPP], [GEA], [HIBSCS], [SM] [1], [4], [17], [19], [21]
  OmpR-Phosphorylated activator ompCp1 Sigma70 -47.5 -128.5 ompC
gaaacatcttAAAAGTTTTAGTATCATATTcgtgttggat
2312868 2312887 [BPP], [GEA], [HIBSCS], [SM] [4], [17], [18], [19], [21]
  OmpR-Phosphorylated repressor ompFp Sigma38, Sigma70 -370.5 -480.5 ompF
cgtaaatgttGCAATGTAATATTCCGTAACaggatgatcg
987453 987472 [BPP], [GEA] [19], [21], [22], [23], [24]
  OmpR-Phosphorylated activator ompFp Sigma38, Sigma70 -90.5 -200.5 ompF
aaaaagaaaaAATATGTAACCAAAAGTAAAatttaaggaa
987173 987192 [BPP], [GEA], [HIBSCS], [SM] [1], [4], [18], [19], [25], [26], [27], [28]
  OmpR-Phosphorylated dual ompFp Sigma38, Sigma70 -70.5 -180.5 ompF
aaagataaagATTTGGTTTCAAAAAGAAAAaatatgtaac
987153 987172 [BCE], [BPP], [GEA], [HIBSCS], [SM] [1], [4], [18], [19], [21], [25], [26], [27], [28], [29], [30]
  OmpR-Phosphorylated dual ompFp Sigma38, Sigma70 -50.5 -160.5 ompF
cgctaccgtgAAAGTGCTACAAAGATAAAGatttggtttc
987133 987152 [AIBSCS], [BPP], [GEA], [SM] [1], [4], [18], [19], [22], [23], [24], [25], [26], [27], [28], [29]
  OmpR-Phosphorylated activator omrAp nd -70.5 -70.5 omrA
ggaatgaaggGAAATGCAACGAGGTGTGTAaattgtcggt
2976250 2976269 [GEA], [HIBSCS] [31]
  OmpR-Phosphorylated activator omrBp nd -71.5 -71.5 omrB
agcgtttcgcAAAGTGTAACCAAAGGTTTGcaatctcttt
2976447 2976466 [GEA], [HIBSCS] [31]
  OmpR-Phosphorylated repressor pgaAp nd -31.5 -265.5 pgaA, pgaB, pgaC, pgaD
aattaggattAAAATAATTAAATCAGTAAAttccgatgca
1092545 1092564 [BPP], [GEA], [HIBSCS] [32]
  OmpR-Phosphorylated repressor srap Sigma38 nd 1555963.0 sra nd nd [GEA] [33]
  OmpR-Phosphorylated activator tppBp Sigma70 -45.5 -143.5 dtpA
tcagttatatGTAACAGATTATTACAAAGGacttgtctga
1712616 1712635 [BPP], [GEA] [34]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  OmpR activator acrR gene 31.0 485730 485740 nd nd
  OmpR activator acrR gene 41.0 485720 485730 nd nd
  OmpR activator tolC gene 239.0 3177876 3177886 nd nd
  OmpR activator tolC gene 249.0 3177866 3177876 nd nd
Other High-throughput regulatory interactions with weak evidence


Alignment and PSSM for OmpR TFBSs    

Aligned TFBS of OmpR   
  Sequence
  GCAGCTTAACAACAAATAT
  AACGAGAAACCAAAACTTA
  AAAGTGCTACAAAGATAAA
  TTTTTGAAACCAAATCTTT
  AATATGTAACCAAAAGTAA
  ATCCTGTTACGGAATATTA
  AACATGTAACTAAATGTAA
  TATATGTAACAGATTATTA
  TACACTTATCTAAGATTTT
  TATCTGAACATAAAACACT
  AATATGATACTAAAACTTT
  TAAATGAAACATCTTAAAA
  TAGATGTTTCAAAATGTAA
  TGACCGAAATCACACTTAA
  TATCTTTTTTCAAATATGA
  AGCACGTAACATAGTTTGT
  ACTTTGTAAACAGGGTTTT
  GAAATGCAACGAGGTGTGT
  AAAGTGTAACCAAAGGTTT
  TATAGGCAAACATAAATAA

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

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

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

 [GEA] Gene expression analysis

 [HIFS] Human inference of function from sequence

 [IMP] Inferred from mutant phenotype

 [IPI] Inferred from physical interaction

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [BCE] Binding of cellular extracts

 [AIBSCS] Automated inference based on similarity to consensus sequences



Reference(s)    

 [1] 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

 [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] 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

 [6] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [12] 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

 [13] 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

 [14] 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

 [15] 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

 [16] 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

 [17] 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

 [18] 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

 [19] 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

 [20] 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

 [21] 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

 [22] 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

 [23] 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

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

 [25] 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

 [26] 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

 [27] 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

 [28] 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

 [29] 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

 [30] 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

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

 [32] 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

 [33] 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

 [34] 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

 [35] Cai SJ., Inouye M., 2002, EnvZ-OmpR interaction and osmoregulation in Escherichia coli., J Biol Chem 277(27):24155-61

 [36] Forst S., Delgado J., Inouye M., 1989, Phosphorylation of OmpR by the osmosensor EnvZ modulates expression of the ompF and ompC genes in Escherichia coli., Proc Natl Acad Sci U S A 86(16):6052-6

 [37] 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

 [38] Mizuno T., Mizushima S., 1987, Isolation and characterization of deletion mutants of ompR and envZ, regulatory genes for expression of the outer membrane proteins OmpC and OmpF in Escherichia coli., J Biochem (Tokyo) 101(2):387-96

 [39] Hirakawa H., Nishino K., Hirata T., Yamaguchi A., 2003, Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli., J Bacteriol 185(6):1851-6

 [40] Hirakawa H., Nishino K., Yamada J., Hirata T., Yamaguchi A., 2003, Beta-lactam resistance modulated by the overexpression of response regulators of two-component signal transduction systems in Escherichia coli., J Antimicrob Chemother 52(4):576-82

 [41] Guillier M., Gottesman S., 2008, The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator., Nucleic Acids Res 36(21):6781-94



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