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NtrC DNA-binding transcriptional dual regulator

Synonyms: NtrC-phosphorylated


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NtrC-phosphorylated Functional Covalent Holo nd nd
TFBs symmetry: inverted-repeat
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: glnG
  Genome position: 4053869-4055278
  Length: 1410 bp / 469 aa
Operon name: glnALG
TU(s) encoding the TF:
Transcription unit        Promoter
glnALG
glnAp1
glnALG
glnAp2
glnLG
glnLp


Regulon       
Regulated gene(s) amtB, argT, astA, astB, astC, astD, astE, cbl, ddpA, ddpB, ddpC, ddpD, ddpF, ddpX, glnA, glnG, glnH, glnK, glnL, glnP, glnQ, hisJ, hisM, hisP, hisQ, nac, patA, potF, potG, potH, potI, relA, rpoE, rseA, rseB, rseC, rseD, rutA, rutB, rutC, rutD, rutE, rutF, rutG, yeaG, yeaH, yhdW, yhdX, yhdY, yhdZ
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (12)
nitrogen metabolism (11)
ABC superfamily, membrane component (9)
other (mechanical, nutritional, oxidative stress) (8)
Transcription related (7)
Read more >
Regulated operon(s) argT-hisJQMP, astCADBE, cbl, ddpXABCDF, glnALG, glnHPQ, glnK-amtB, nac, patA, potFGHI, relA-mazEFG, rseD-rpoE-rseABC, rutABCDEFG, yeaGH, yhdWXYZ
First gene in the operon(s) argT, astC, cbl, ddpX, glnA, glnH, glnK, glnL, nac, patA, potF, relA, rseD, rutA, yeaG, yhdW
Simple and complex regulons ArcA,NtrC,PhoP,RutR
ArgR,NtrC
CRP,Fis,NtrC
CRP,GlrR,NtrC,RcsB
CRP,NtrC
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[NtrC,-](3)
[NtrC,+](18)


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
  NtrC-phosphorylated activator argTp Sigma54 -190.0 -248.0 argT, hisJ, hisQ, hisM, hisP
actccgctgtTGCCCTGTTTCAGGGCAattttgcaac
 2428031 2428047 [GEA], [AIBSCS] [1]
  NtrC-phosphorylated activator argTp Sigma54 -83.0 -141.0 argT, hisJ, hisQ, hisM, hisP
tatcttcaacTTCAGGACAATAATGCAacgtcttatt
 2427924 2427940 [GEA], [AIBSCS] [1]
  NtrC-phosphorylated activator astCp2 Sigma54 -275.0 -337.0 astC, astA, astD, astB, astE
gttgttaatgATGTCAACGATGGCGCAaaaaatgccc
 1832311 1832327 [GEA], [AIBSCS], [BPP] [2]
  NtrC-phosphorylated activator astCp2 Sigma54 -253.0 -315.0 astC, astA, astD, astB, astE
gcgcaaaaaaTGCCCGCTTTTGGTGCGcgctgcgtca
 1832289 1832305 [GEA], [AIBSCS], [BPP] [2]
  NtrC-phosphorylated activator astCp2 Sigma54 -233.0 -295.0 astC, astA, astD, astB, astE
tggtgcgcgcTGCGTCAGAATGGCGCAgtaatttcca
 1832269 1832285 [GEA], [AIBSCS], [BPP] [2]
  NtrC-phosphorylated activator cblp Sigma70 nd nd cbl
nd
 nd nd [GEA], [BPP] [1]
  NtrC-phosphorylated activator ddpXp1 Sigma54 -109.0 -140.0 ddpX, ddpA, ddpB, ddpC, ddpD, ddpF
cttcccctctTGCACCAAAACTGCACTacgctgcaca
 1563208 1563224 [GEA], [AIBSCS] [1]
  NtrC-phosphorylated activator ddpXp1 Sigma54 -88.0 -119.0 ddpX, ddpA, ddpB, ddpC, ddpD, ddpF
tgcactacgcTGCACAAATGTTGATCAaaagttaaaa
 1563187 1563203 [GEA], [AIBSCS] [1]
  NtrC-phosphorylated repressor glnAp1 Sigma70 -25.0 -213.0 glnA, glnL, glnG
caaaggtcatTGCACCAACATGGTGCTtaatgtttcc
 4058239 4058255 [GEA], [APIORCISFBSCS], [BPP], [SM] [3], [4]
  NtrC-phosphorylated repressor glnAp1 Sigma70 8.0 -181.0 glnA, glnL, glnG
tttccattgaAGCACTATATTGGTGCAacattcacat
 4058207 4058223 [GEA], [APIORCISFBSCS], [BPP], [SM] [3], [4]
  NtrC-phosphorylated repressor glnAp1 Sigma70 27.0 -162.0 glnA, glnL, glnG
ttggtgcaacATTCACATCGTGGTGCAgcccttttgc
 4058188 4058204 [GEA], [APIORCISFBSCS], [BPP], [SM] [3], [5]
  NtrC-phosphorylated repressor glnAp1 Sigma70 48.0 -141.0 glnA, glnL, glnG
ggtgcagcccTTTTGCACGATGGTGCGcatgataacg
 4058167 4058183 [GEA], [APIORCISFBSCS], [SM] [3], [5]
  NtrC-phosphorylated repressor glnAp1 Sigma70 71.0 -118.0 glnA, glnL, glnG
tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt
 4058144 4058160 [GEA], [APIORCISFBSCS] [3], [5]
  NtrC-phosphorylated activator glnAp2 Sigma54 -140.0 -213.0 glnA, glnL, glnG
caaaggtcatTGCACCAACATGGTGCTtaatgtttcc
 4058239 4058255 [GEA], [APIORCISFBSCS], [BPP], [SM] [4], [6], [7]
  NtrC-phosphorylated activator glnAp2 Sigma54 -108.0 -181.0 glnA, glnL, glnG
tttccattgaAGCACTATATTGGTGCAacattcacat
 4058207 4058223 [GEA], [APIORCISFBSCS], [BPP], [SM] [4], [7], [8]
  NtrC-phosphorylated activator glnAp2 Sigma54 -89.0 -162.0 glnA, glnL, glnG
ttggtgcaacATTCACATCGTGGTGCAgcccttttgc
 4058188 4058204 [GEA], [APIORCISFBSCS], [BPP], [SM] [3], [4], [5], [6], [7]
  NtrC-phosphorylated activator glnAp2 Sigma54 -68.0 -141.0 glnA, glnL, glnG
ggtgcagcccTTTTGCACGATGGTGCGcatgataacg
 4058167 4058183 [GEA], [APIORCISFBSCS], [SM] [3], [5]
  NtrC-phosphorylated activator glnAp2 Sigma54 -45.0 -118.0 glnA, glnL, glnG
tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt
 4058144 4058160 [GEA], [APIORCISFBSCS] [3], [5]
  NtrC-phosphorylated repressor glnHp2 Sigma54 -135.0 -178.0 glnH, glnP, glnQ
ctgtgttgagTGCACAATTTTAGCGCAccagattggt
 848174 848190 [APIORCISFBSCS], [BPP] [9]
  NtrC-phosphorylated activator glnHp2 Sigma54 -122.0 -165.0 glnH, glnP, glnQ
acaattttagCGCACCAGATTGGTGCCccagaatggt
 848161 848177 [APIORCISFBSCS], [BPP] [9]
  NtrC-phosphorylated activator glnHp2 Sigma54 -109.0 -152.0 glnH, glnP, glnQ
accagattggTGCCCCAGAATGGTGCAtcttcagggt
 848148 848164 [APIORCISFBSCS], [BPP] [9]
  NtrC-phosphorylated repressor glnHp2 Sigma54 -79.0 -122.0 glnH, glnP, glnQ
tcagggtattGCCCTATAAATCGTGCAtcacgttttt
 848118 848134 [APIORCISFBSCS], [BPP] [9]
  NtrC-phosphorylated activator glnKp Sigma54 -87.0 -129.0 glnK, amtB
taacgcactgTGCACTGTCATAGTGCGttttcatttt
 472461 472477 [APIORCISFBSCS] [10]
  NtrC-phosphorylated repressor glnLp Sigma70 3.0 -30.0 glnL, glnG
aaagctataaTGCACTAAAATGGTGCAacctgttcag
 4056361 4056377 [APIORCISFBSCS], [BPP], [SM] [11]
  NtrC-phosphorylated activator nacp Sigma54 -152.0 -197.0 nac
tattgggtaaTGAACCATCGTGGTGCAtaccctcctt
 2062122 2062138 [APIORCISFBSCS] [12]
  NtrC-phosphorylated activator patAp Sigma38 -543.0 -579.0 patA
atccgggtgaCGCACCATGTTGTGCGGCtgcccttgta
 3218907 3218924 [IEP], [AIBSCS] [13]
  NtrC-phosphorylated activator patAp Sigma38 -193.0 -229.0 patA
ttaattatctTGCCCAAAAATCAGGCAattattgccc
 3219257 3219273 [GEA], [AIBSCS] [14], [15]
  NtrC-phosphorylated activator patAp Sigma38 -171.0 -207.0 patA
aggcaattatTGCCCTGAAAACGTGCAtttgcgcagc
 3219279 3219295 [GEA], [AIBSCS] [14], [15]
  NtrC-phosphorylated activator patAp2 Sigma54 -543.0 -579.0 patA
atccgggtgaCGCACCATGTTGTGCGGCtgcccttgta
 3218907 3218924 [IEP], [AIBSCS] [13]
  NtrC-phosphorylated activator patAp2 Sigma54 -193.0 -229.0 patA
ttaattatctTGCCCAAAAATCAGGCAattattgccc
 3219257 3219273 [GEA], [AIBSCS] [14], [15]
  NtrC-phosphorylated activator patAp2 Sigma54 -171.0 -207.0 patA
aggcaattatTGCCCTGAAAACGTGCAtttgcgcagc
 3219279 3219295 [GEA], [AIBSCS] [14], [15]
  NtrC-phosphorylated activator potFp1 Sigma54 nd nd potF, potG, potH, potI
nd
 nd nd [GEA], [BPP] [1]
  NtrC-phosphorylated activator relAp4 Sigma54 nd nd relA
nd
 nd nd [GEA], [BPP] [16]
  NtrC-phosphorylated activator rpoEp2b Sigma70 -33.5 -208.5 rseD, rpoE, rseA, rseB, rseC
tttggtcagcATAGCATCATGTTGTGCGGataaacacct
 2710364 2710382 [APIORCISFBSCS], [BPP] [17]
  NtrC-phosphorylated activator rseDp Sigma54 -33.5 -208.5 rseD, rpoE, rseA, rseB, rseC
tttggtcagcATAGCATCATGTTGTGCGGataaacacct
 2710364 2710382 [APIORCISFBSCS], [BPP] [17]
  NtrC-phosphorylated activator rutAp Sigma54 -145.0 -160.0 rutA, rutB, rutC, rutD, rutE, rutF, rutG
ctcgaccttcTGCACTCTCATCGCGCAcagatgcatg
 1074163 1074179 [GEA], [AIBSCS] [1]
  NtrC-phosphorylated activator rutAp Sigma54 -124.0 -139.0 rutA, rutB, rutC, rutD, rutE, rutF, rutG
cgcgcacagaTGCATGTTTTATGTGCAactgttttga
 1074142 1074158 [GEA], [AIBSCS] [1]
  NtrC-phosphorylated activator yeaGp1 Sigma54 nd nd yeaG, yeaH
nd
 nd nd [GEA], [BPP] [1]
  NtrC-phosphorylated activator yhdWp Sigma54 -126.0 -196.0 yhdW, yhdX, yhdY, yhdZ
gtaaatatttTGCGCCAAAATGTGGCGcatgtttcat
 3418838 3418854 [GEA], [AIBSCS] [1]
  NtrC-phosphorylated activator yhdWp Sigma54 -96.0 -166.0 yhdW, yhdX, yhdY, yhdZ
gtttcattttCGCACCATTGCGGGGCGctgtttttat
 3418868 3418884 [GEA], [AIBSCS] [1]


Alignment and PSSM for NtrC TFBSs    

Aligned TFBS of NtrC   
  Sequence
  GATGCACCATTCTGGGGCAC
  TAAGCACCATGTTGGTGCAA
  GTTGCACCATTTTAGTGCAT
  TTCGCACCATTGCGGGGCGC
  AGTGCACAATTTTAGCGCAC
  AATGCACGTTTTCAGGGCAA
  ATTGCCTGATTTTTGGGCAA
  GAAGCACTATATTGGTGCAA
  AATGCCCGCTTTTGGTGCGC
  GTTGCCCTGTTTCAGGGCAA
  TGCGCCACATTTTGGCGCAA
  GGGGCACCAATCTGGTGCGC
  GATGCATGTTTTATGTGCAA
  AACGCACTATGACAGTGCAC
  AATGAACCATCGTGGTGCAT
  GACGCACCATGTTGTGCGGC
  ACTGCGCCATTCTGACGCAG
  ATAACGCCTTTTAGGGGCAA
  GTAGTGCAGTTTTGGTGCAA
  TGTGCGCGATGAGAGTGCAG
  GATGCACGATTTATAGGGCA
  TTTGCACGATGGTGCGCATG
  ATAGCATCATGTTGTGCGGA
  GTTGCATTATTGTCCTGAAG
  GCTGCACAAATGTTGATCAA
  TTTGCGCCATCGTTGACATC
  TTCACATCGTGGTGCAGCCC

Position weight matrix (PWM). NtrC matrix-quality result    
A	9	10	5	2	1	18	1	3	20	2	1	2	3	6	2	3	0	3	18	12
C	0	2	5	0	25	4	21	13	1	0	2	3	4	1	3	3	4	21	2	9
G	11	4	1	25	0	5	0	7	3	0	7	7	1	15	20	10	22	3	5	4
T	7	11	16	0	1	0	5	4	3	25	17	15	19	5	2	11	1	0	2	2

Consensus    
;	consensus.strict             	gttGCaCcaTtttgGgGCac
;	consensus.strict.rc          	GTGCCCCAAAATGGTGCAAC
;	consensus.IUPAC              	rwtGCaCsaTkktgGkGCam
;	consensus.IUPAC.rc           	KTGCMCCAMMATSGTGCAWY
;	consensus.regexp             	[ag][at]tGCaC[cg]aT[gt][gt]tgG[gt]GCa[ac]
;	consensus.regexp.rc          	[GT]TGC[AC]CCA[AC][AC]AT[CG]GTGCA[AT][CT]

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    

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

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

 [SM] Site mutation

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9

 [2] Kiupakis AK., Reitzer L., 2002, ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli., J Bacteriol 184(11):2940-50

 [3] Reitzer LJ., Magasanik B., 1985, Expression of glnA in Escherichia coli is regulated at tandem promoters., Proc Natl Acad Sci U S A 82(7):1979-83

 [4] Reitzer LJ., Movsas B., Magasanik B., 1989, Activation of glnA transcription by nitrogen regulator I (NRI)-phosphate in Escherichia coli: evidence for a long-range physical interaction between NRI-phosphate and RNA polymerase., J Bacteriol 171(10):5512-22

 [5] Atkinson MR., Pattaramanon N., Ninfa AJ., 2002, Governor of the glnAp2 promoter of Escherichia coli., Mol Microbiol 46(5):1247-57

 [6] Collado-Vides J., Magasanik B., Gralla JD., 1991, Control site location and transcriptional regulation in Escherichia coli., Microbiol Rev 55(3):371-94

 [7] Ninfa AJ., Reitzer LJ., Magasanik B., 1987, Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers., Cell 50(7):1039-46

 [8] Reitzer LJ., Magasanik B., 1986, Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter., Cell 45(6):785-92

 [9] Claverie-Martin F., Magasanik B., 1991, Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli., Proc Natl Acad Sci U S A 88(5):1631-5

 [10] van Heeswijk WC., Hoving S., Molenaar D., Stegeman B., Kahn D., Westerhoff HV., 1996, An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli., Mol Microbiol 21(1):133-46

 [11] Ueno-Nishio S., Mango S., Reitzer LJ., Magasanik B., 1984, Identification and regulation of the glnL operator-promoter of the complex glnALG operon of Escherichia coli., J Bacteriol 160(1):379-84

 [12] Muse WB., Bender RA., 1998, The nac (nitrogen assimilation control) gene from Escherichia coli., J Bacteriol 180(5):1166-73

 [13] Robison K., McGuire AM., Church GM., 1998, A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome., J Mol Biol 284(2):241-54

 [14] Samsonova NN., Smirnov SV., Altman IB., Ptitsyn LR., 2003, Molecular cloning and characterization of Escherichia coli K12 ygjG gene., BMC Microbiol 3(1):2

 [15] Schneider BL., Hernandez VJ., Reitzer L., 2013, Putrescine catabolism is a metabolic response to several stresses in Escherichia coli., Mol Microbiol 88(3):537-50

 [16] Brown DR., Barton G., Pan Z., Buck M., Wigneshweraraj S., 2014, Nitrogen stress response and stringent response are coupled in Escherichia coli., Nat Commun 5:4115

 [17] Klein G., Stupak A., Biernacka D., Wojtkiewicz P., Lindner B., Raina S., 2016, Multiple Transcriptional Factors Regulate Transcription of the rpoE Gene in Escherichia coli under Different Growth Conditions and When the Lipopolysaccharide Biosynthesis Is Defective., J Biol Chem 291(44):22999-23019


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