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NtrC DNA-binding transcriptional dual regulator

Synonyms: NtrC-Phosphorylated, NtrC


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NtrC Non-Functional   Apo [IDA] [1]
NtrC-Phosphorylated Functional Covalent Holo [APPHINH], [BPP], [GEA], [HIFS], [IDA], [IPI] [1], [2], [3], [4], [5], [6], [7], [8], [9]
Evolutionary Family: EBP
Sensing class: Using internal synthesized signals
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, glnA, glnA, 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,+](11)


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
gttgcaaaatTGCCCTGAAACAGGGCAacagcggagt
2428031 2428047 [AIBSCS], [GEA] [10]
  NtrC-Phosphorylated activator argTp Sigma54 -83.0 -141.0 argT, hisJ, hisQ, hisM, hisP
aataagacgtTGCATTATTGTCCTGAAgttgaagata
2427924 2427940 [AIBSCS], [GEA] [10]
  NtrC-Phosphorylated activator astCp2 Sigma54 -275.0 -337.0 astC, astA, astD, astB, astE
gggcatttttTGCGCCATCGTTGACATcattaacaac
1832311 1832327 [AIBSCS], [BPP], [GEA] [11]
  NtrC-Phosphorylated activator astCp2 Sigma54 -253.0 -315.0 astC, astA, astD, astB, astE
tgacgcagcgCGCACCAAAAGCGGGCAttttttgcgc
1832289 1832305 [AIBSCS], [BPP], [GEA] [11]
  NtrC-Phosphorylated activator astCp2 Sigma54 -233.0 -295.0 astC, astA, astD, astB, astE
tggaaattacTGCGCCATTCTGACGCAgcgcgcacca
1832269 1832285 [AIBSCS], [BPP], [GEA] [11]
  NtrC-Phosphorylated activator cblp Sigma70 nd 2060914.0 cbl nd nd [GEA] [10]
  NtrC-Phosphorylated activator ddpXp Sigma54 -109.0 -140.0 ddpX, ddpA, ddpB, ddpC, ddpD, ddpF
tgtgcagcgtAGTGCAGTTTTGGTGCAagaggggaag
1563208 1563224 [AIBSCS], [GEA] [10]
  NtrC-Phosphorylated activator ddpXp Sigma54 -88.0 -119.0 ddpX, ddpA, ddpB, ddpC, ddpD, ddpF
ttttaactttTGATCAACATTTGTGCAgcgtagtgca
1563187 1563203 [AIBSCS], [GEA] [10]
  NtrC-Phosphorylated repressor glnAp1 Sigma70 -25.0 -213.0 glnA, glnL, glnG
ggaaacattaAGCACCATGTTGGTGCAatgacctttg
4058239 4058255 [BPP], [GEA], [HIBSCS], [SM] [5], [12], [13], [14]
  NtrC-Phosphorylated repressor glnAp1 Sigma70 8.0 -181.0 glnA, glnL, glnG
atgtgaatgtTGCACCAATATAGTGCTtcaatggaaa
4058207 4058223 [BPP], [GEA], [HIBSCS], [SM] [5], [12], [13], [14]
  NtrC-Phosphorylated repressor glnAp1 Sigma70 27.0 -162.0 glnA, glnL, glnG
gcaaaagggcTGCACCACGATGTGAATgttgcaccaa
4058188 4058204 [BPP], [GEA], [HIBSCS], [SM] [5], [12], [14], [15]
  NtrC-Phosphorylated repressor glnAp1 Sigma70 48.0 -141.0 glnA, glnL, glnG
cgttatcatgCGCACCATCGTGCAAAAgggctgcacc
4058167 4058183 [GEA], [HIBSCS], [SM] [12], [15]
  NtrC-Phosphorylated repressor glnAp1 Sigma70 71.0 -118.0 glnA, glnL, glnG
acttttaaatTGCCCCTAAAAGGCGTTatcatgcgca
4058144 4058160 [GEA], [HIBSCS] [12], [15]
  NtrC-Phosphorylated activator glnAp2 Sigma54 -140.0 -213.0 glnA, glnL, glnG
ggaaacattaAGCACCATGTTGGTGCAatgacctttg
4058239 4058255 [BPP], [GEA], [HIBSCS], [SM] [5], [12], [13], [14], [16]
  NtrC-Phosphorylated activator glnAp2 Sigma54 -108.0 -181.0 glnA, glnL, glnG
atgtgaatgtTGCACCAATATAGTGCTtcaatggaaa
4058207 4058223 [BPP], [GEA], [HIBSCS], [SM] [5], [12], [13], [14]
  NtrC-Phosphorylated activator glnAp2 Sigma54 -89.0 -162.0 glnA, glnL, glnG
gcaaaagggcTGCACCACGATGTGAATgttgcaccaa
4058188 4058204 [BPP], [GEA], [HIBSCS], [SM] [5], [12], [14], [15], [16]
  NtrC-Phosphorylated activator glnAp2 Sigma54 -68.0 -141.0 glnA, glnL, glnG
cgttatcatgCGCACCATCGTGCAAAAgggctgcacc
4058167 4058183 [GEA], [HIBSCS], [SM] [12], [15]
  NtrC-Phosphorylated activator glnAp2 Sigma54 -45.0 -118.0 glnA, glnL, glnG
acttttaaatTGCCCCTAAAAGGCGTTatcatgcgca
4058144 4058160 [GEA], [HIBSCS] [12], [15]
  NtrC-Phosphorylated repressor glnHp2 Sigma54 -135.0 -178.0 glnH, glnP, glnQ
accaatctggTGCGCTAAAATTGTGCActcaacacag
848174 848190 [BPP], [HIBSCS] [17]
  NtrC-Phosphorylated activator glnHp2 Sigma54 -122.0 -165.0 glnH, glnP, glnQ
accattctggGGCACCAATCTGGTGCGctaaaattgt
848161 848177 [BPP], [HIBSCS] [17]
  NtrC-Phosphorylated activator glnHp2 Sigma54 -109.0 -152.0 glnH, glnP, glnQ
accctgaagaTGCACCATTCTGGGGCAccaatctggt
848148 848164 [BPP], [HIBSCS] [17]
  NtrC-Phosphorylated repressor glnHp2 Sigma54 -79.0 -122.0 glnH, glnP, glnQ
aaaaacgtgaTGCACGATTTATAGGGCaataccctga
848118 848134 [BPP], [HIBSCS] [17]
  NtrC-Phosphorylated activator glnKp Sigma54 -87.0 -129.0 glnK, amtB
taacgcactgTGCACTGTCATAGTGCGttttcatttt
472461 472477 [HIBSCS] [18]
  NtrC-Phosphorylated repressor glnLp Sigma70 3.0 -30.0 glnL, glnG
ctgaacaggtTGCACCATTTTAGTGCAttatagcttt
4056361 4056377 [BPP], [HIBSCS], [SM] [8], [19]
  NtrC-Phosphorylated activator nacp Sigma54 -152.0 -197.0 nac
aaggagggtaTGCACCACGATGGTTCAttacccaata
2062122 2062138 [HIBSCS] [20]
  NtrC-Phosphorylated activator patAp Sigma38, Sigma54 -543.0 -578.5 patA
atccgggtgaCGCACCATGTTGTGCGGctgcccttgt
3218907 3218924 [AIBSCS], [IEP] [21]
  NtrC-Phosphorylated activator patAp Sigma38, Sigma54 -193.0 -229.0 patA
ttaattatctTGCCCAAAAATCAGGCAattattgccc
3219257 3219273 [AIBSCS], [GEA] [22], [23]
  NtrC-Phosphorylated activator patAp Sigma38, Sigma54 -171.0 -207.0 patA
aggcaattatTGCCCTGAAAACGTGCAtttgcgcagc
3219279 3219295 [AIBSCS], [GEA] [22], [23]
  NtrC-Phosphorylated activator potFp1 Sigma54 nd -893784.0 potF, potG, potH, potI nd nd [GEA] [10]
  NtrC-Phosphorylated activator relAp4 Sigma54 nd 2913651.0 relA nd nd [BPP], [GEA] [24]
  NtrC-Phosphorylated activator rpoEp2b Sigma70, Sigma54 -33.5 -209.0 rseD, rpoE, rseA, rseB, rseC
aggtgtttatCCGCACAACATGATGCTAtgctgaccaa
2710364 2710382 [BPP], [HIBSCS] [25]
  NtrC-Phosphorylated activator rutAp Sigma54 -145.0 -160.0 rutA, rutB, rutC, rutD, rutE, rutF, rutG
catgcatctgTGCGCGATGAGAGTGCAgaaggtcgag
1074163 1074179 [AIBSCS], [GEA] [10]
  NtrC-Phosphorylated activator rutAp Sigma54 -124.0 -139.0 rutA, rutB, rutC, rutD, rutE, rutF, rutG
tcaaaacagtTGCACATAAAACATGCAtctgtgcgcg
1074142 1074158 [AIBSCS], [GEA] [10]
  NtrC-Phosphorylated activator yeaGp1 Sigma54 nd -1866908.0 yeaG, yeaH nd nd [GEA] [10]
  NtrC-Phosphorylated activator yhdWp Sigma54 -126.0 -303.0 yhdW, yhdX, yhdY, yhdZ
gtaaatatttTGCGCCAAAATGTGGCGcatgtttcat
3418838 3418854 [AIBSCS], [GEA] [10]
  NtrC-Phosphorylated activator yhdWp Sigma54 -96.0 -273.0 yhdW, yhdX, yhdY, yhdZ
gtttcattttCGCACCATTGCGGGGCGctgtttttat
3418868 3418884 [AIBSCS], [GEA] [10]


Alignment and PSSM for NtrC TFBSs    

Position weight matrix (PWM).   
A	0	0	0	14	1	3	17	15	13	20	3	3	1	3	3	4	14	6
C	4	2	24	7	21	15	1	3	6	1	2	6	2	4	1	20	0	5
G	2	23	1	4	0	0	4	2	2	4	1	12	20	4	19	0	5	4
T	19	0	0	0	3	7	3	5	4	0	19	4	2	14	2	1	6	10

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    

 [IDA] Inferred from direct assay

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

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIFS] Human inference of function from sequence

 [IPI] Inferred from physical interaction

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [IEP] Inferred from expression pattern



Reference(s)    

 [1] Nohaile M, Kern D, Wemmer D, Stedman K, Kustu S., 1997, Structural and functional analyses of activating amino acid substitutions in the receiver domain of NtrC: evidence for an activating surface., J Mol Biol.

 [2] Chen P, Reitzer LJ., 1995, Active contribution of two domains to cooperative DNA binding of the enhancer-binding protein nitrogen regulator I (NtrC) of Escherichia coli: stimulation by phosphorylation and the binding of ATP., J Bacteriol.

 [3] Fiedler U, Weiss V., 1995, A common switch in activation of the response regulators NtrC and PhoB: phosphorylation induces dimerization of the receiver modules., EMBO J.

 [4] Miranda-Rios J., Sanchez-Pescador R., Urdea M., Covarrubias AA., 1987, The complete nucleotide sequence of the glnALG operon of Escherichia coli K12., Nucleic Acids Res 15(6):2757-70

 [5] 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

 [6] Reitzer L., 2003, Nitrogen assimilation and global regulation in Escherichia coli., Annu Rev Microbiol 57:155-76

 [7] Rippe K, M¿¿¿cke N, Schulz A., 1998, Association states of the transcription activator protein NtrC from E. coli determined by analytical ultracentrifugation., J Mol Biol.

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [12] 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

 [13] 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

 [14] 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

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

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

 [17] 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

 [18] 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

 [19] Rocha M., Vazquez M., Garciarrubio A., Covarrubias AA., 1985, Nucleotide sequence of the glnA-glnL intercistronic region of Escherichia coli., Gene 37(1-3):91-9

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

 [21] 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

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

 [23] 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

 [24] 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

 [25] 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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