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NarL DNA-binding transcriptional dual regulator

Synonyms: NarL-phosphorylated, NarL
Summary:
NarL, "nitrate/nitrite response regulator NarL," is a transcriptional dual regulator of many anaerobic electron transport and fermentation-related genes in the response to the availability of high concentrations of nitrate or nitrite [45, 46]. NarL activates expression of 51 operons in response to nitrate, mostly genes needed for nitrate respiration. NarL represses 41 operons involved in alternative respiratory pathways, such as fumarate reduction or fermentation of simple sugars [47]. The response regulator NarL belongs to the LuxR/UhpA family [48, 49] and is part of the two-component system NarX-NarL. There is intensive cross-regulation with the paralogous two-component system NarQ-NarP [14, 50]. Each of the sensors, NarX and NarQ, is able to phosphorylate NarL and NarP, leading to the activation of both proteins. In the absence of nitrate and nitrite, NarX and NarQ stimulate the dephosphorylation of NarL-P and NarP-P [51, 52].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NarL Non-Functional   Apo [BPP], [IPI] [1]
NarL-phosphorylated Functional Covalent Holo [BPP], [IPI] [1]
Evolutionary Family: LuxR/UhpA
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: narL
  Genome position: 1275179-1275829
  Length: 651 bp / 216 aa
Operon name: narXL
TU(s) encoding the TF:
Transcription unit        Promoter
narXL
narXp


Regulon       
Regulated gene(s) adhE, aspA, caiF, ccmA, ccmB, ccmC, ccmD, ccmE, ccmF, ccmG, ccmH, citC, citD, citE, citF, citG, citX, cydC, cydD, cysG, dcuA, dcuB, dcuR, dcuS, dmsA, dmsB, dmsC, dmsD, dpiA, dpiB, fdhF, fdnG, fdnH, fdnI, focA, frdA, frdB, frdC, frdD, fumB, hcp, hcr, hyaA, hyaB, hyaC, hyaD, hyaE, hyaF, hybA, hybB, hybC, hybD, hybE, hybF, hybG, hybO, moeA, moeB, napA, napB, napC, napD, napF, napG, napH,
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Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
anaerobic respiration (60)
membrane (39)
electron donors (25)
aerobic respiration (22)
cytochromes (20)
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Regulated operon(s) abgABT-ogt, adhE, aspA-dcuA, caiF, citCDEFXG, cydDC, dcuB-fumB, dcuSR, dmsABC, dpiBA, fdhF, fdnGHI, focA-pflB, frdABCD, hcp-hcr-poxB-ltaE-ybjT, hyaABCDEF, hybOABCDEFG, moeAB, napFDAGHBC-ccmABCDEFGH, narGHJI, narK, nikABCDER, nirBDC-cysG, norVW, nrfABCDEFG, nuoABCEFGHIJKLMN, ompW, torCAD, ubiCA, ydeP, ydhYVWXUT, yeaR-yoaG, ynfEFGH-dmsD, ytfE
First gene in the operon(s) adhE, aspA, caiF, citC, cydD, dcuB, dcuS, dmsA, dpiB, fdhF, fdnG, focA, frdA, hcp, hyaA, hybO, moeA, napF, narG, narK, nikA, nirB, norV, nrfA, nuoA, ogt, ompW, torC, ubiC, ydeP, ydhY, yeaR, ynfE, ytfE
Simple and complex regulons AppY,ArcA,Fis,IscR,NarL,NarP,YdeO
ArcA,CRP,DpiA,FNR,NarL
ArcA,CRP,FNR,Fur,NarL,SoxS
ArcA,CRP,FNR,IHF,NarL
ArcA,FNR,IHF,NarL
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[NarL,+](13)
[NarL,-](30)


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
  NarL-phosphorylated repressor adhEp Sigma38 81.0 -212.0 adhE
acgtaatcagTACCCAGaagtgagtaa
1298330 1298336 [GEA], [APIORCISFBSCS] [2], [3]
  NarL-phosphorylated repressor adhEp Sigma38 90.0 -203.0 adhE
gtacccagaaGTGAGTAatcttgctta
1298321 1298327 [GEA], [APIORCISFBSCS] [2], [3]
  NarL-phosphorylated repressor adhEp1 Sigma70 81.0 -212.0 adhE
acgtaatcagTACCCAGaagtgagtaa
1298330 1298336 [GEA], [APIORCISFBSCS] [2], [3]
  NarL-phosphorylated repressor adhEp1 Sigma70 90.0 -203.0 adhE
gtacccagaaGTGAGTAatcttgctta
1298321 1298327 [GEA], [APIORCISFBSCS] [2], [3]
  NarL-phosphorylated repressor adhEp2 Sigma38 -24.0 -212.0 adhE
acgtaatcagTACCCAGaagtgagtaa
1298330 1298336 [GEA], [APIORCISFBSCS] [3]
  NarL-phosphorylated repressor adhEp2 Sigma38 -15.0 -203.0 adhE
gtacccagaaGTGAGTAatcttgctta
1298321 1298327 [GEA], [APIORCISFBSCS] [3]
  NarL-phosphorylated repressor aspAp Sigma70 -112.0 -217.0 aspA, dcuA
aactatttttGGTAGTAatcccaaagc
4368541 4368547 [GEA], [BPP] [4]
  NarL-phosphorylated repressor aspAp Sigma70 -76.0 -181.0 aspA, dcuA
tttcacaaatTAATAATtaaggggtaa
4368505 4368511 [GEA], [BPP] [4]
  NarL-phosphorylated repressor aspAp Sigma70 -67.0 -172.0 aspA, dcuA
ttaataattaAGGGGTAaaaaccgaca
4368496 4368502 [GEA], [BPP] [4]
  NarL-phosphorylated repressor caiFp Sigma70 nd nd caiF nd nd [GEA], [BPP] [5]
  NarL-phosphorylated repressor citCp2 nd 37.0 -147.0 citC, citD, citE, citF, citX, citG
tcacgccgaaATACTCCTtaggatgtat
652000 652007 [AIBSCS], [AIBSCS] [6]
  NarL-phosphorylated activator cydDp Sigma70 -126.0 -195.0 cydD, cydC
gccaggccatTACTTCGgccggtacag
931154 931160 [GEA], [APIORCISFBSCS] [7]
  NarL-phosphorylated activator cydDp Sigma70 -80.0 -149.0 cydD, cydC
tgcggaacgcTACCTCGatggtttagc
931108 931114 [GEA], [APIORCISFBSCS] [7]
  NarL-phosphorylated repressor dcuBp1 Sigma70 -109.0 -129.0 dcuB, fumB
atattcactgTGAGGTAtttgctaaag
4348870 4348876 [GEA], [APIORCISFBSCS] [8]
  NarL-phosphorylated repressor dcuBp1 Sigma70 -45.0 -65.0 dcuB, fumB
aaacagttcaTACAAAAcagaacgtga
4348806 4348812 [GEA], [APIORCISFBSCS] [8]
  NarL-phosphorylated repressor dcuBp1 Sigma70 2.0 -19.0 dcuB, fumB
aatttaaataGGATTATcgcgagggtt
4348760 4348766 [GEA], [APIORCISFBSCS] [8]
  NarL-phosphorylated repressor dcuBp1 Sigma70 19.0 -2.0 dcuB, fumB
cgcgagggttCACACATgttatttact
4348743 4348749 [GEA], [APIORCISFBSCS] [8]
  NarL-phosphorylated repressor dcuBp1 Sigma70 24.0 4.0 dcuB, fumB
gggttcacacATGTTATttactatcca
4348738 4348744 [GEA], [APIORCISFBSCS] [8]
  NarL-phosphorylated repressor dcuBp1 Sigma70 43.0 23.0 dcuB, fumB
actatccaacTTATCATaatactgata
4348719 4348725 [GEA], [APIORCISFBSCS] [8]
  NarL-phosphorylated repressor dcuSp Sigma70 -40.0 -63.0 dcuS, dcuR
caatcattctTACTCCCtttgaattac
4351722 4351728 [GEA], [APIORCISFBSCS], [BPP] [4]
  NarL-phosphorylated repressor dcuSp Sigma70 -31.0 -54.0 dcuS, dcuR
ttactcccttTGAATTAcccgcctcat
4351713 4351719 [GEA], [APIORCISFBSCS], [BPP] [4]
  NarL-phosphorylated repressor dmsAp1 Sigma70 -27.0 -163.0 dmsA, dmsB, dmsC
gaacaataatTACTCCTcacttacacg
940793 940799 [BCE], [BPP] [9]
  NarL-phosphorylated repressor dmsAp1 Sigma70 -7.0 -143.0 dmsA, dmsB, dmsC
ttacacgtaaTACTACTttcgagtgaa
940813 940819 [BCE], [BPP] [9]
  NarL-phosphorylated repressor dmsAp1 Sigma70 15.0 -122.0 dmsA, dmsB, dmsC
agtgaaaatcTACCTATctctttgatt
940834 940840 [APIORCISFBSCS], [BPP] [9]
  NarL-phosphorylated repressor dpiBp1 nd 20.0 -232.0 dpiB, dpiA
atacatcctaAGGAGTATttcggcgtga
652000 652007 [AIBSCS] [6]
  NarL-phosphorylated repressor dpiBp2 nd 25.0 -39.0 dpiB, dpiA
acattttaatTACATCCGtcaaagaggc
652193 652200 [AIBSCS] [6]
  NarL-phosphorylated repressor fdhFp Sigma54 nd nd fdhF nd nd [GEA], [BPP] [10]
  NarL-phosphorylated activator fdnGp Sigma70 -124.0 -153.0 fdnG, fdnH, fdnI
cctgtcaggcAGTGGTGcgtttttcta
1547245 1547251 [GEA], [APIORCISFBSCS], [BCE], [SM] [10], [11], [12], [13], [14]
  NarL-phosphorylated activator fdnGp Sigma70 -109.0 -138.0 fdnG, fdnH, fdnI
tgcgtttttcTACCGCTattgaggtag
1547260 1547266 [GEA], [BCE], [SM] [10], [15]
  NarL-phosphorylated activator fdnGp Sigma70 -100.0 -129.0 fdnG, fdnH, fdnI
ctaccgctatTGAGGTAggtcaatttg
1547269 1547275 [GEA], [APIORCISFBSCS], [BPP], [SM] [10], [11], [12], [14]
  NarL-phosphorylated activator fdnGp Sigma70 -77.0 -106.0 fdnG, fdnH, fdnI
tttgcgaaggCGGATTAttttgtggca
1547292 1547298 [GEA], [APIORCISFBSCS], [BCE], [SM] [10], [11], [12], [14]
  NarL-phosphorylated repressor focAp1 Sigma70 -348.0 -375.0 focA, pflB
aatgtaggctTAATGATtagtctgagt
954838 954844 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -346.0 -373.0 focA, pflB
tgtaggcttaATGATTAgtctgagtta
954836 954842 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -286.0 -313.0 focA, pflB
catatatttgCATTAATaaaataattg
954776 954782 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -270.0 -297.0 focA, pflB
taaaataattGTAATTAtaaggttaaa
954760 954766 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -253.0 -280.0 focA, pflB
taaggttaaaTATCGGTaatttgtatt
954743 954749 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -235.0 -262.0 focA, pflB
atttgtatttAATAAATacgatcgata
954725 954731 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -226.0 -253.0 focA, pflB
taataaatacGATCGATattgttactt
954716 954722 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -152.0 -179.0 focA, pflB
ggaaaaaattCAACTCAtttgttaatt
954642 954648 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -101.0 -128.0 focA, pflB
aatcaaatatTTACTCCgtatttgcat
954591 954597 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -37.0 -64.0 focA, pflB
gatatgatctATATCAAtttctcatct
954527 954533 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp1 Sigma70 -20.0 -47.0 focA, pflB
tttctcatctATAATGCtttgttagta
954510 954516 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 -27.0 -375.0 focA, pflB
aatgtaggctTAATGATtagtctgagt
954838 954844 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 -25.0 -373.0 focA, pflB
tgtaggcttaATGATTAgtctgagtta
954836 954842 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 36.0 -313.0 focA, pflB
catatatttgCATTAATaaaataattg
954776 954782 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 52.0 -297.0 focA, pflB
taaaataattGTAATTAtaaggttaaa
954760 954766 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 69.0 -280.0 focA, pflB
taaggttaaaTATCGGTaatttgtatt
954743 954749 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 87.0 -262.0 focA, pflB
atttgtatttAATAAATacgatcgata
954725 954731 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 96.0 -253.0 focA, pflB
taataaatacGATCGATattgttactt
954716 954722 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 170.0 -179.0 focA, pflB
ggaaaaaattCAACTCAtttgttaatt
954642 954648 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 221.0 -128.0 focA, pflB
aatcaaatatTTACTCCgtatttgcat
954591 954597 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 285.0 -64.0 focA, pflB
gatatgatctATATCAAtttctcatct
954527 954533 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor focAp3 Sigma70 302.0 -47.0 focA, pflB
tttctcatctATAATGCtttgttagta
954510 954516 [GEA], [APIORCISFBSCS], [BPP] [16]
  NarL-phosphorylated repressor frdAp Sigma70 -26.0 -120.0 frdA, frdB, frdC, frdD
atttcagactTATCCATcagactatac
4382435 4382441 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor frdAp Sigma70 -12.0 -106.0 frdA, frdB, frdC, frdD
catcagactaTACTGTTgtacctataa
4382421 4382427 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor frdAp Sigma70 -4.0 -98.0 frdA, frdB, frdC, frdD
tatactgttgTACCTATaaaggagcag
4382413 4382419 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor frdAp Sigma70 6.0 -89.0 frdA, frdB, frdC, frdD
gtacctataaAGGAGCAgtggaatagc
4382404 4382410 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor frdAp Sigma70 14.0 -81.0 frdA, frdB, frdC, frdD
aaaggagcagTGGAATAgcgttcgcag
4382396 4382402 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor frdAp2 Sigma38 -26.0 -120.0 frdA, frdB, frdC, frdD
atttcagactTATCCATcagactatac
4382435 4382441 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor frdAp2 Sigma38 -12.0 -106.0 frdA, frdB, frdC, frdD
catcagactaTACTGTTgtacctataa
4382421 4382427 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor frdAp2 Sigma38 -4.0 -98.0 frdA, frdB, frdC, frdD
tatactgttgTACCTATaaaggagcag
4382413 4382419 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor frdAp2 Sigma38 6.0 -89.0 frdA, frdB, frdC, frdD
gtacctataaAGGAGCAgtggaatagc
4382404 4382410 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor frdAp2 Sigma38 14.0 -81.0 frdA, frdB, frdC, frdD
aaaggagcagTGGAATAgcgttcgcag
4382396 4382402 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated activator hcpp1 nd -109.0 -140.0 hcp, hcr, poxB
ctctgcgtaaTACCTCTctggcggtag
913951 913957 [GEA], [APIORCISFBSCS], [BPP] [17], [18]
  NarL-phosphorylated activator hcpp1 nd -100.0 -131.0 hcp, hcr, poxB
atacctctctGGCGGTAgatccctgcc
913942 913948 [GEA], [APIORCISFBSCS], [BPP] [17], [18]
  NarL-phosphorylated repressor hyaAp Sigma70 -10.0 -165.0 hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
aaagtttcacTACGCTTtattaacaat
1031971 1031977 [GEA], [APIORCISFBSCS]
  NarL-phosphorylated repressor hyaAp Sigma70 7.0 -149.0 hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
ttattaacaaTACTTTCtggcgacgtg
1031987 1031993 [GEA], [APIORCISFBSCS]
  NarL-phosphorylated repressor hyaAp2 Sigma38 -10.0 -165.0 hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
aaagtttcacTACGCTTtattaacaat
1031971 1031977 [GEA], [APIORCISFBSCS]
  NarL-phosphorylated repressor hyaAp2 Sigma38 7.0 -149.0 hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
ttattaacaaTACTTTCtggcgacgtg
1031987 1031993 [GEA], [APIORCISFBSCS]
  NarL-phosphorylated repressor hybOp1 Sigma70 -76.0 -178.0 hybO, hybA, hybB, hybC, hybD, hybE, hybF, hybG
tgatcaaacaTACGTATtatcttgctt
3146436 3146442 [GEA], [APIORCISFBSCS] [19]
  NarL-phosphorylated repressor hybOp1 Sigma70 -51.0 -153.0 hybO, hybA, hybB, hybC, hybD, hybE, hybF, hybG
tttaattaatTACACTAatgcttcttc
3146411 3146417 [GEA], [APIORCISFBSCS] [19]
  NarL-phosphorylated repressor hybOp1 Sigma70 21.0 -82.0 hybO, hybA, hybB, hybC, hybD, hybE, hybF, hybG
ataataaatgTGTGGTAaatggcgcat
3146340 3146346 [GEA], [APIORCISFBSCS] [19]
  NarL-phosphorylated activator moeAp Sigma70 -177.0 -207.0 moeA, moeB
atgactgcttTGCCCATagtattcgtc
866568 866574 [GEA], [AIBSCS] [20]
  NarL-phosphorylated activator moeAp Sigma70 -109.0 -139.0 moeA, moeB
ttttatgaatTACTCATtcaatttttg
866500 866506 [GEA], [AIBSCS] [20]
  NarL-phosphorylated repressor napFp1 Sigma70 -49.0 -126.0 napF, napD, napA, napG, napH, napB, napC, ccmA, ccmB, ccmC, ccmD, ccmE, ccmF, ccmG, ccmH
ctacaggtttTACCCCGatcggggtat
2303620 2303626 [GEA], [APIORCISFBSCS], [SM] [21], [22], [23]
  NarL-phosphorylated repressor napFp1 Sigma70 -40.0 -117.0 napF, napD, napA, napG, napH, napB, napC, ccmA, ccmB, ccmC, ccmD, ccmE, ccmF, ccmG, ccmH
ttaccccgatCGGGGTAtgcatctttg
2303611 2303617 [GEA], [APIORCISFBSCS], [SM] [21], [22], [23]
  NarL-phosphorylated repressor napFp2 Sigma70 -46.0 -126.0 napF, napD, napA, napG, napH, napB, napC, ccmA, ccmB, ccmC, ccmD, ccmE, ccmF, ccmG, ccmH
ctacaggtttTACCCCGatcggggtat
2303620 2303626 [GEA], [APIORCISFBSCS], [SM] [23]
  NarL-phosphorylated repressor napFp2 Sigma70 -37.0 -117.0 napF, napD, napA, napG, napH, napB, napC, ccmA, ccmB, ccmC, ccmD, ccmE, ccmF, ccmG, ccmH
ttaccccgatCGGGGTAtgcatctttg
2303611 2303617 [GEA], [APIORCISFBSCS], [SM] [23]
  NarL-phosphorylated activator narGp Sigma70 -208.0 -265.0 narG, narH, narJ, narI
attaatatgtTACCCATggggaatact
1279596 1279602 [GEA], [APIORCISFBSCS], [BPP] [13], [24], [25]
  NarL-phosphorylated activator narGp Sigma70 -195.0 -252.0 narG, narH, narJ, narI
ccatggggaaTACTCCTtaatacccat
1279609 1279615 [GEA], [APIORCISFBSCS], [BPP], [SM] [13], [24], [25], [26]
  NarL-phosphorylated activator narGp Sigma70 -185.0 -242.0 narG, narH, narJ, narI
tactccttaaTACCCATctgcataaaa
1279619 1279625 [GEA], [APIORCISFBSCS], [BPP], [SM] [13], [24], [25], [26]
  NarL-phosphorylated activator narGp Sigma70 -101.0 -158.0 narG, narH, narJ, narI
tggtggctgtTAATTATcctaaagggg
1279703 1279709 [GEA], [APIORCISFBSCS], [BPP], [SM] [12], [13], [14], [24], [25], [26]
  NarL-phosphorylated activator narGp Sigma70 -89.0 -146.0 narG, narH, narJ, narI
attatcctaaAGGGGTAtcttaggaat
1279715 1279721 [GEA], [APIORCISFBSCS], [BPP], [SM] [13], [24], [25], [26]
  NarL-phosphorylated activator narGp Sigma70 -79.0 -136.0 narG, narH, narJ, narI
aggggtatctTAGGAATttactttatt
1279725 1279731 [GEA], [APIORCISFBSCS], [BPP] [13], [24], [25]
  NarL-phosphorylated activator narGp Sigma70 -71.0 -128.0 narG, narH, narJ, narI
cttaggaattTACTTTAtttttcatcc
1279733 1279739 [GEA], [APIORCISFBSCS], [BPP] [13], [24], [25]
  NarL-phosphorylated activator narGp Sigma70 -57.0 -114.0 narG, narH, narJ, narI
ttatttttcaTCCCCATcactcttgat
1279747 1279753 [GEA], [APIORCISFBSCS], [BPP] [13], [24], [25]
  NarL-phosphorylated activator narKp1 Sigma70 -214.0 -239.0 narK
ggctgaagtaTACCCATacccggaaag
1277715 1277721 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated activator narKp1 Sigma70 -194.0 -219.0 narK
cggaaagagtTACTCCTtatttgccgt
1277735 1277741 [APIORCISFBSCS], [BPP], [SM] [13], [27]
  NarL-phosphorylated activator narKp1 Sigma70 -177.0 -202.0 narK
tatttgccgtGTGGTTAgtcgctttac
1277752 1277758 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated activator narKp1 Sigma70 -160.0 -185.0 narK
gtcgctttacATCGGTAagggtaggga
1277769 1277775 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated activator narKp1 Sigma70 -154.0 -179.0 narK
ttacatcggtAAGGGTAgggattttac
1277775 1277781 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated activator narKp1 Sigma70 -103.0 -128.0 narK
tttatgaagtCACTGTActcactatgg
1277826 1277832 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated activator narKp1 Sigma70 -98.0 -123.0 narK
gaagtcactgTACTCACtatgggtaat
1277831 1277837 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated activator narKp1 Sigma70 -90.0 -115.0 narK
tgtactcactATGGGTAatgataaata
1277839 1277845 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated activator narKp1 Sigma70 -80.0 -105.0 narK
atgggtaatgATAAATAtcaatgatag
1277849 1277855 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated activator narKp1 Sigma70 -67.0 -92.0 narK
aatatcaatgATAGATAaagttatctt
1277862 1277868 [APIORCISFBSCS], [BPP] [13]
  NarL-phosphorylated repressor nikAp1 nd nd nd nikA, nikB, nikC, nikD, nikE, nikR nd nd [GEA], [BPP] [28]
  NarL-phosphorylated activator nirBp Sigma70 -74.0 -98.0 nirB, nirD, nirC, cysG
atcagcaataTACCCATtaaggagtat
3493910 3493916 [GEA], [BCE], [BPP], [SM] [12], [29], [30]
  NarL-phosphorylated activator nirBp Sigma70 -65.0 -89.0 nirB, nirD, nirC, cysG
atacccattaAGGAGTAtataaaggtg
3493919 3493925 [GEA], [BCE], [BPP], [SM] [12], [29], [30]
  NarL-phosphorylated repressor norVp Sigma54 -78.0 -115.0 norV, norW
tcattttgacTACTCATtaatgggcat
2832358 2832364 [GEA], [APIORCISFBSCS] [31]
  NarL-phosphorylated repressor norVp Sigma54 -69.0 -106.0 norV, norW
ctactcattaATGGGCAtaattttatt
2832367 2832373 [GEA], [APIORCISFBSCS] [31]
  NarL-phosphorylated activator nrfAp Sigma70 -79.0 -172.0 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
agatactgacTAACTCTaaagtggtat
4287589 4287595 [GEA], [AIBSCS], [BPP], [SM] [12], [14], [30], [32], [33], [34]
  NarL-phosphorylated activator nrfAp Sigma70 -70.0 -163.0 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
ctaactctaaAGTGGTAttttacatgc
4287598 4287604 [GEA], [APIORCISFBSCS], [BPP], [SM] [12], [14], [30], [32], [33], [34]
  NarL-phosphorylated activator nrfAp Sigma70 -50.0 -143.0 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
tacatgcactTACAATTgattaaagac
4287618 4287624 [GEA], [APIORCISFBSCS], [BPP], [SM] [12], [14], [30], [32], [34]
  NarL-phosphorylated repressor nrfAp Sigma70 -50.0 -143.0 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
tacatgcactTACAATTgattaaagac
4287618 4287624 [GEA], [APIORCISFBSCS], [BPP], [SM] [12], [14], [30], [32], [34]
  NarL-phosphorylated repressor nrfAp Sigma70 -22.0 -115.0 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
acattcacagTGTGGTTatttgttaca
4287646 4287652 [GEA], [APIORCISFBSCS], [BPP], [SM] [12], [14], [30], [32], [34]
  NarL-phosphorylated activator nuoAp2 Sigma70 -122.0 -212.0 nuoA, nuoB, nuoC, nuoE, nuoF, nuoG, nuoH, nuoI, nuoJ, nuoK, nuoL, nuoM, nuoN
gggcattaaaTGCTAATggtgttgata
2405281 2405287 [GEA], [APIORCISFBSCS]
  NarL-phosphorylated activator ogtp nd -83.0 -131.0 ogt
gcgaaactggGTACTTACtattcgttag
1400364 1400371 [GEA], [BPP], [SM] [35], [36]
  NarL-phosphorylated activator ogtp nd -74.0 -122.0 ogt
ggtacttactATTCGTTAgtcttgccct
1400355 1400362 [GEA], [BPP], [SM] [35], [36]
  NarL-phosphorylated activator ogtp nd -50.0 -98.0 ogt
ccctatccacTTATCTTTttggtggtat
1400331 1400338 [GEA], [BPP], [SM] [35], [36]
  NarL-phosphorylated activator ogtp nd -41.0 -89.0 ogt
cttatcttttTGGTGGTAtggctgctga
1400322 1400329 [GEA], [BPP], [SM] [35], [36]
  NarL-phosphorylated repressor ompWp nd -18.5 -47.5 ompW
gatcatttgtTACTCCAATGTAGGTATattcgtcacg
1313965 1313981 [GEA], [AIBSCS], [BPP] [37]
  NarL-phosphorylated repressor torCp Sigma70 nd nd torC, torA, torD nd nd [IMP], [BPP] [38]
  NarL-phosphorylated repressor ubiCp Sigma70 nd nd ubiC, ubiA nd nd [GEA], [BPP] [39]
  NarL-phosphorylated activator ydePp Sigma70 nd nd ydeP nd nd [GEA], [BPP] [40]
  NarL-phosphorylated repressor ydhYp Sigma38 -42.0 -207.0 ydhY, ydhV, ydhW, ydhX, ydhU, ydhT
ttttaattgaTAACGATcaatgttaag
1754681 1754687 [GEA], [APIORCISFBSCS] [41]
  NarL-phosphorylated repressor ydhYp Sigma38 -16.0 -181.0 ydhY, ydhV, ydhW, ydhX, ydhU, ydhT
gggctcagaaTAATCACattatttttt
1754655 1754661 [GEA], [APIORCISFBSCS], [BPP], [SM] [41]
  NarL-phosphorylated repressor ydhYp Sigma38 6.0 -160.0 ydhY, ydhV, ydhW, ydhX, ydhU, ydhT
attttttctcCTAACCATaaaggattag
1754634 1754641 [GEA], [APIORCISFBSCS], [BPP], [SM] [41]
  NarL-phosphorylated repressor ydhYp Sigma38 15.0 -151.0 ydhY, ydhV, ydhW, ydhX, ydhU, ydhT
cctaaccataAAGGATTAgtttatcggc
1754625 1754632 [GEA], [APIORCISFBSCS], [BPP], [SM] [41]
  NarL-phosphorylated activator yeaRp Sigma70 -48.0 -94.0 yeaR, yoaG
tgctaaaaagTAACCAAtaaatggtat
1880039 1880045 [GEA], [AIBSCS], [BPP] [36], [42]
  NarL-phosphorylated activator yeaRp Sigma70 -39.0 -85.0 yeaR, yoaG
gtaaccaataAATGGTAtttaaaatgc
1880030 1880036 [GEA], [AIBSCS], [BPP] [36], [42]
  NarL-phosphorylated repressor ynfEp Sigma70 -23.0 -89.0 ynfE, ynfF, ynfG, ynfH, dmsD
taataattctTAACCCAaaatgggtag
1657977 1657983 [AIBSCS], [BPP] [43]
  NarL-phosphorylated repressor ynfEp Sigma70 -14.0 -80.0 ynfE, ynfF, ynfG, ynfH, dmsD
ttaacccaaaATGGGTAgactccctct
1657986 1657992 [AIBSCS], [BPP] [43]
  NarL-phosphorylated repressor ynfEp2 Sigma38 -23.0 -89.0 ynfE, ynfF, ynfG, ynfH, dmsD
taataattctTAACCCAaaatgggtag
1657977 1657983 [AIBSCS], [BPP] [43]
  NarL-phosphorylated repressor ynfEp2 Sigma38 -14.0 -80.0 ynfE, ynfF, ynfG, ynfH, dmsD
ttaacccaaaATGGGTAgactccctct
1657986 1657992 [AIBSCS], [BPP] [43]
  NarL-phosphorylated activator ytfEp nd -50.0 -76.0 ytfE
aataagcctcTGCTACGtaagggttat
4432056 4432062 [AIBSCS] [44]
  NarL-phosphorylated activator ytfEp nd -41.0 -67.0 ytfE
ctgctacgtaAGGGTTAtagcttttgc
4432047 4432053 [AIBSCS] [44]


Alignment and PSSM for NarL TFBSs    

Aligned TFBS of NarL   
  Sequence
  ATACCCATTAAGGAGTA
  ATACCCCGATCGGGGTA
  ATAACCCTTACGTAGCA
  ATACCCCTTTAGGATAA
  CTACTCATTAATGGGCA
  CTACCGCTATTGAGGTA
  TTACTCACTTCTGGGTA
  TTACCCCTTAATTATTA
  CTAACTCTAAAGTGGTA
  CTAATCCTTTATGGTTA
  ATACCTACATTGGAGTA
  ATAATGCTTTGTTAGTA
  TTAACCCAAAATGGGTA
  GTACCTATAAAGGAGCA
  GTACTCACTATGGGTAA
  ATAACGATCAATGTTAA
  CTACCCTTACCGATGTA
  ATACCCATACCCGGAAA
  CTACCTATCTCTTTGAT
  ATACCATTTATTGGTTA
  TTACTCCTTATTTGCCG
  TTACTCCGTATTTGCAT
  ATACTACTTTCGAGTGA
  GTAATTCAAAGGGAGTA
  ATACCTCACAGTGAATA
  CTAACGAATAGTAAGTA
  GTAATTATAAGGTTAAA
  TTACCGATATTTAACCT
  TTAATGATTAGTCTGAG
  ATACTCCTTAATACCCA
  TTACTCCTCACTTACAC
  ATAATCCGCCTTCGCAA
  ATAACCACACTGTGAAT
  TTAATTACATCCGTCAA
  TTACCACACATTTATTA
  CTAACCACACGGCAAAT
  CTACCTCGATGGTTTAG
  ATACCACCAAAAAGATA
  ATAACTTTATCTATCAT
  CTACCGCCAGAGAGGTA
  ATTATGATAAGTTGGAT
  ATAATACGTATGTTTGA
  TAAATGCTAATGGTGTT
  GTAACAATATCGATCGT
  GTATTCCCCATGGGTAA
  TTAATCAATTGTAAGTG
  ATAATCACATTATTTTT
  ATCCCCATCACTCTTGA
  TTACTCATTCAATTTTT
  TAAATAACATGTGTGAA
  ACAATACTTTCTGGCGA
  CAACTCATTTGTTAATT
  CTACGCTTTATTAACAA
  ATTACACTAATGCTTCT
  TTATCCATCAGACTATA
  GTTCTGTTTTGTATGAA
  ATATCAATTTCTCATCT
  TTACTTCGGCCGGTACA
  ATAATTAACAGCCACCA
  CGAATACTATGGGCAAA
  TTACTACCAAAAATAGT
  TTTACTTTATTTTTCAT
  CGAACGCTATTCCACTG
  ATTATTTTATTAATGCA
  ATAGTGAGTACAGTGAC
  GCACCACTGCCTGACAG
  CTCGCGATAATCCTATT
  CGAAATACTCCTTAGGA

Position weight matrix (PWM). NarL matrix-quality result   
A	26	3	61	30	1	13	30	7	30	33	14	7	15	22	12	24	43
C	16	2	2	33	34	27	31	13	10	9	18	5	10	2	15	11	2
G	8	3	0	2	1	13	0	7	2	1	16	24	24	20	25	7	6
T	18	60	5	3	32	15	7	41	26	25	20	32	19	24	16	26	17

Consensus   
;	consensus.strict             	aTAcccctaacggggta
;	consensus.strict.rc          	TACCCCGTTAGGGGTAT
;	consensus.IUPAC              	mTAmycmtwwskgdswa
;	consensus.IUPAC.rc           	TWSHCMSWWAKGRKTAK
;	consensus.regexp             	[ac]TA[ac][ct]c[ac]t[at][at][cg][gt]g[agt][cg][at]a
;	consensus.regexp.rc          	T[AT][CG][ACT]C[AC][CG][AT][AT]A[GT]G[AG][GT]TA[GT]

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




Reference(s)    

 [1] 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

 [2] Chen YM., Lin EC., 1991, Regulation of the adhE gene, which encodes ethanol dehydrogenase in Escherichia coli., J Bacteriol 173(24):8009-13

 [3] Membrillo-Hernandez J., Lin EC., 1999, Regulation of expression of the adhE gene, encoding ethanol oxidoreductase in Escherichia coli: transcription from a downstream promoter and regulation by fnr and RpoS., J Bacteriol 181(24):7571-9

 [4] Goh EB., Bledsoe PJ., Chen LL., Gyaneshwar P., Stewart V., Igo MM., 2005, Hierarchical control of anaerobic gene expression in Escherichia coli K-12: the nitrate-responsive NarX-NarL regulatory system represses synthesis of the fumarate-responsive DcuS-DcuR regulatory system., J Bacteriol 187(14):4890-9

 [5] Eichler K., Buchet A., Lemke R., Kleber HP., Mandrand-Berthelot MA., 1996, Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli., J Bacteriol 178(5):1248-57

 [6] Scheu PD., Witan J., Rauschmeier M., Graf S., Liao YF., Ebert-Jung A., Basche T., Erker W., Unden G., 2012, CitA/CitB two-component system regulating citrate fermentation in Escherichia coli and its relation to the DcuS/DcuR system in vivo., J Bacteriol 194(3):636-45

 [7] Cook GM., Membrillo-Hernandez J., Poole RK., 1997, Transcriptional regulation of the cydDC operon, encoding a heterodimeric ABC transporter required for assembly of cytochromes c and bd in Escherichia coli K-12: regulation by oxygen and alternative electron acceptors., J Bacteriol 179(20):6525-30

 [8] Golby P., Kelly DJ., Guest JR., Andrews SC., 1998, Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli., J Bacteriol 180(24):6586-96

 [9] Bearson SM., Albrecht JA., Gunsalus RP., 2002, Oxygen and nitrate-dependent regulation of dmsABC operon expression in Escherichia coli: sites for Fnr and NarL protein interactions., BMC Microbiol 2(1):13

 [10] Wang H., Gunsalus RP., 2003, Coordinate regulation of the Escherichia coli formate dehydrogenase fdnGHI and fdhF genes in response to nitrate, nitrite, and formate: roles for NarL and NarP., J Bacteriol 185(17):5076-85

 [11] Berg BL., Stewart V., 1990, Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12., Genetics 125(4):691-702

 [12] Darwin AJ., Tyson KL., Busby SJ., Stewart V., 1997, Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement., Mol Microbiol 25(3):583-95

 [13] Li J., Kustu S., Stewart V., 1994, In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12., J Mol Biol 241(2):150-65

 [14] Rabin RS., Stewart V., 1993, Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate- and nitrite-regulated gene expression in Escherichia coli K-12., J Bacteriol 175(11):3259-68

 [15] Li J., Stewart V., 1992, Localization of upstream sequence elements required for nitrate and anaerobic induction of fdn (formate dehydrogenase-N) operon expression in Escherichia coli K-12., J Bacteriol 174(15):4935-42

 [16] Kaiser M., Sawers G., 1995, Nitrate repression of the Escherichia coli pfl operon is mediated by the dual sensors NarQ and NarX and the dual regulators NarL and NarP., J Bacteriol 177(13):3647-55

 [17] Filenko N., Spiro S., Browning DF., Squire D., Overton TW., Cole J., Constantinidou C., 2007, The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase., J Bacteriol 189(12):4410-7

 [18] Filenko NA., Browning DF., Cole JA., 2005, Transcriptional regulation of a hybrid cluster (prismane) protein., Biochem Soc Trans 33(Pt 1):195-7

 [19] Richard DJ., Sawers G., Sargent F., McWalter L., Boxer DH., 1999, Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli., Microbiology 145 ( Pt 10):2903-12

 [20] Hasona A., Self WT., Shanmugam KT., 2001, Transcriptional regulation of the moe (molybdate metabolism) operon of Escherichia coli., Arch Microbiol 175(3):178-88

 [21] Darwin AJ., Stewart V., 1995, Nitrate and nitrite regulation of the Fnr-dependent aeg-46.5 promoter of Escherichia coli K-12 is mediated by competition between homologous respon