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NagC DNA-binding transcriptional dual regulator

Synonyms: NagC, NagC-N-acetyl-D-glucosamine 6-phosphate
Summary:
The NagC, "N-acetylglucosamine," transcriptional dual regulator participates in regulating the phosphotransferase system (PTS) [19] Its function is to coordinate the biosynthesis of the amino sugars, D-glucosamine (GlcN) and N-acetylglucosamine (GlcNAc) with their catabolism [3, 6, 7, 20]. The specific inducer for NagC is GlcNAc-6-P, the product of GlcNAc transport by the PTS [7, 20] NagC is displaced from its DNA targets by interacting with GlcNAc-6-P [7] Mutation in the first two amino acids of the recognition helix of the DNA-binding motif causes GlcNAc6P to act with NagC as a corepressor instead of as an inducer [16]. Proline at the first position of this helix seems to contribute to the distinction between the NagC binding sites and suboptimal sites [16]. Based on the structure of |FRAME: PD01896|, models for the three-dimensional structure of NagC and for the binding of GlcNAc-6-P were developed [19] The Nag regulon consists of two divergent operons, nagE and nagBACD.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NagC Functional   Apo [APPH], [BPP], [IMP] [1], [2], [3], [4], [5], [6], [7], [8], [9], [10]
NagC-N-acetyl-D-glucosamine 6-phosphate Non-Functional Allosteric Holo [BPP], [IMP] [7]
Evolutionary Family: MarR
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: nagC
  Genome position: 700374-701594
  Length: 1221 bp / 406 aa
Operon name: nagBAC-umpH
TU(s) encoding the TF:
Transcription unit        Promoter
nagBACD
nagBp
nagC
nagCp1
nagC
nagCp2


Regulon       
Regulated gene(s) chbA, chbB, chbC, chbF, chbG, chbR, chiP, chiQ, creA, creB, creC, creD, crr, dinI, feoA, feoB, feoC, fimB, galP, glmS, glmU, manX, manY, manZ, nagA, nagB, nagC, nagE, nanC, nanM, nanS, ptsH, ptsI, umpH, ydeM, ydeN, ydeP
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (14)
membrane (9)
Phosphotransferase Systems (PEP-dependent PTS) (8)
amino sugar conversions (5)
operon (4)
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Regulated operon(s) chbBCARFG, chiPQ, creABCD, dinI, feoABC, fimB, galP, glmUS, manXYZ, nagBAC-umpH, nagE, nanCMS, ptsHI-crr, ydeNM, ydeP
First gene in the operon(s) chbB, chiP, creA, feoA, fimB, galP, glmU, glmU, manX, nagB, nagE, nanC, ptsH, ptsH, ptsH, ydeP, nanC, dinI, ydeN
Simple and complex regulons AraC,GadX,NagC
BasR,DksA,DksA-ppGpp,H-NS,IHF,NagC,NanR,ppGpp
CRP,ChbR,NagC
CRP,Cra,Mlc,NagC
CRP,GalR,GalS,NagC
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[NagC,+](2)
[NagC,-](15)


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
  NagC repressor chbBp nd -112.0 -219.0 chbB, chbC, chbA, chbR, chbF, chbG
ggcctgagttCTTAATTATCTTCGCGAATTATTtgcccgaaat
1821827 1821849 [AIBSCS], [APIORCISFBSCS], [BPP], [GEA], [SM] [6], [11], [12]
  NagC repressor chbBp nd 1.0 -107.0 chbB, chbC, chbA, chbR, chbF, chbG
tctataccgtATACTCCTTTCAGCCACAAAAAAagtcatgttg
1821715 1821737 [APIORCISFBSCS], [BPP], [GEA] [6]
  NagC repressor chiPp nd -244.0 -342.0 chiP, chiQ
cggcgtttttTCTGCTTTTCTTCGCGAATTAATTCcgcttcgcaa
707980 708004 [BPP], [GEA] [13]
  NagC repressor chiPp nd -22.0 -120.0 chiP, chiQ
gaaagagattGATAATTCGCGTCGCGAAAAATAgtctgttcct
708203 708225 [AIBSCS], [BPP], [GEA] [12], [13]
  NagC repressor creAp Sigma70 2.0 -43.0 creA, creB, creC, creD
taatcaatatGTTATTTACCGTGACGAACTAATtgctcgtgta
4635467 4635489 [AIBSCS] [12]
  NagC repressor dinIp Sigma70 -14.0 -36.0 dinI
ttgtcattagGTTATTTTACCTGTATAAATAACcagtatattc
1121512 1121534 [AIBSCS] [12]
  NagC unknown feoAp Sigma70 -128.0 -234.0 feoA, feoB, feoC
agccagtccgGGTAATTCACTATTCGAATTATAttttcgctgc
3539918 3539940 [AIBSCS] [12]
  NagC activator fimBp2 nd -674.0 -964.0 fimB
aaaccagattTGCAATTCGTGTCACAAAATATGtcgatctttt
4539982 4540004 [AIBSCS], [APIORCISFBSCS], [BPP], [GEA], [SM] [1], [9], [10]
  NagC activator fimBp2 nd -462.0 -752.0 fimB
tcaggctgagCATAATTCTCATCATGAAATATGtttcctggtt
4540194 4540216 [AIBSCS], [APIORCISFBSCS], [BPP], [SM] [9], [10], [12]
  NagC repressor galPp Sigma70 2.0 -28.0 galP
actcacctatCTTAATTCACAATAAAAAATAACcatattggag
3088245 3088267 [AIBSCS], [BPP], [SM] [12], [14]
  NagC activator glmUp1 Sigma70 -199.0 -222.0 glmU, glmS
ctgttttcctGTTTATTCATTGATCGAAATAAGagcaaaaaca
3915411 3915433 [APIORCISFBSCS], [BPP], [SM] [3], [4]
  NagC activator glmUp1 Sigma70 -46.0 -69.0 glmU, glmS
ttatcctctgTCCATTTCACGATGAAAAAAATGtagttttttc
3915258 3915280 [APIORCISFBSCS], [BPP], [SM] [3], [4]
  NagC repressor glmUp2 Sigma70 -96.0 -222.0 glmU, glmS
ctgttttcctGTTTATTCATTGATCGAAATAAGagcaaaaaca
3915411 3915433 [APIORCISFBSCS], [BPP], [SM] [3], [4]
  NagC repressor glmUp2 Sigma70 58.0 -69.0 glmU, glmS
ttatcctctgTCCATTTCACGATGAAAAAAATGtagttttttc
3915258 3915280 [APIORCISFBSCS], [BPP], [SM] [3], [4]
  NagC repressor manXp Sigma70 -80.0 -195.0 manX, manY, manZ
atgtgacaagGATATTTTACCTTTCGAAATTTCtgctaatcga
1901842 1901864 [AIBSCS], [APIORCISFBSCS], [BCE], [GEA] [3], [5], [12], [15]
  NagC repressor manXp Sigma70 4.0 -112.0 manX, manY, manZ
cgatatctaaAATAAATCGCGAAACGCAGGGGTttttggttgt
1901925 1901947 [BCE], [GEA] [5], [15]
  NagC repressor nagBp Sigma70 -101.0 -198.0 nagB, nagA, nagC, umpH
tgtgtgaaaaTTTAATTCGTATCGCAAATTAAAcgcgtgtctt
703798 703820 [BPP], [GEA], [SM] [3], [5], [16], [17], [18]
  NagC repressor nagBp Sigma70 -7.0 -104.0 nagB, nagA, nagC, umpH
aaccagaaaaCTTATTTTATCATTCAAAAAATCaggtcggatt
703704 703726 [BPP], [GEA], [SM] [3], [5], [16], [17], [18]
  NagC repressor nagEp Sigma70 -125.0 -229.0 nagE
aatccgacctGATTTTTTGAATGATAAAATAAGttttctggtt
703704 703726 [BPP], [GEA], [SM] [3], [5], [16], [17], [18]
  NagC repressor nagEp Sigma70 -31.0 -135.0 nagE
aagacacgcgTTTAATTTGCGATACGAATTAAAttttcacaca
703798 703820 [BPP], [GEA], [SM] [3], [5], [16], [17], [18]
  NagC repressor nanCp nd -277.0 -704.0 nanC, nanM, nanS
aaccaggaaaCATATTTCATGATGAGAATTATGctcagcctga
4540194 4540216 [AIBSCS], [APIORCISFBSCS], [BPP], [SM] [9], [10], [12]
  NagC repressor nanCp nd -65.0 -492.0 nanC, nanM, nanS
aaaagatcgaCATATTTTGTGACACGAATTGCAaatctggttt
4539982 4540004 [AIBSCS], [APIORCISFBSCS], [BPP], [GEA], [SM] [1], [9], [10]
  NagC repressor ptsHp3 nd 7.0 -251.0 ptsH, ptsI, crr
aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg
2533502 2533524 [AIBSCS] [12]
  NagC repressor ptsHp4 Sigma32, Sigma70 13.0 -251.0 ptsH, ptsI, crr
aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg
2533502 2533524 [AIBSCS] [12]
  NagC repressor ptsHp5 Sigma32 16.0 -251.0 ptsH, ptsI, crr
aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg
2533502 2533524 [AIBSCS] [12]
  NagC repressor ydeNp Sigma70 -140.0 -170.0 ydeN, ydeM
caataaattaGTTGTTTATCGGCGAGAAATTACttaatagaac
1582683 1582705 [AIBSCS] [12]
  NagC repressor ydeNp Sigma70 -16.0 -46.0 ydeN, ydeM
cttacatccaCTTATTTCTCTTCGTAAAATTACtttggaatta
1582559 1582581 [AIBSCS] [12]
  NagC repressor ydePp Sigma70 -28.0 -206.0 ydeP
aagccagagtCTTATTTTTTATATTGAAAAATAtgttaattta
1586681 1586703 [AIBSCS] [12]



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
  NagC unknown nd nd nd nd nd nd [AIBSCS] [12]


Alignment and PSSM for NagC TFBSs    

Aligned TFBS of NagC   
  Sequence
  AAATAATTCGCGAAGATAATTAAGA
  ACATATTTCATGATGAGAATTATGC
  AGTAATTTTACGAAGAGAAATAAGT
  CTATTTTTCGCGACGCGAATTATCA
  AATTAATTCGCGAAGAAAAGCAGAA
  ATTAATTTCGCGCATCAAAATAATT
  ATTTAATTCGTATCGCAAATTAAAC
  TCTTAATTCACAATAAAAAATAACC
  AATTAGTTCGTCACGGTAAATAACA
  AGAAATTTCGAAAGGTAAAATATCC
  ATATAATTCGAATAGTGAATTACCC
  ACATATTTTGTGACACGAATTGCAA
  ACTTATTTTATCATTCAAAAAATCA
  AGTAATTTCTCGCCGATAAACAACT
  ATATTTTTCAATATAAAAAATAAGA
  TCTTATTTCGATCAATGAATAAACA
  GGTTATTTTACCTGTATAAATAACC
  GTCCATTTCACGATGAAAAAAATGT
  ACTTTTTTTGTGGCTGAAAGGAGTA
  AAATAAATCGCGAAACGCAGGGGTT

Position weight matrix (PWM). NagC matrix-quality result   
A	15	4	8	4	17	6	1	0	0	7	4	4	13	7	5	9	9	19	20	10	3	18	10	3	9
C	1	6	1	1	0	0	0	0	15	0	10	3	3	6	0	6	0	1	0	0	2	0	2	9	6
G	2	4	0	0	0	1	0	0	0	12	0	11	1	2	11	2	7	0	0	3	2	2	3	5	0
T	2	6	11	15	3	13	19	20	5	1	6	2	3	5	4	3	4	0	0	7	13	0	5	3	5

Consensus   
;	consensus.strict             	acttAtTTCGcgacgagAAatAaca
;	consensus.strict.rc          	TGTTATTTCTCGTCGCGAAATAAGT
;	consensus.IUPAC              	aywtAwTTCRygamgmrAAwtAasm
;	consensus.IUPAC.rc           	KSTTAWTTYKCKTCRYGAAWTAWRT
;	consensus.regexp             	a[ct][at]tA[at]TTC[AG][ct]ga[ac]g[ac][ag]AA[at]tAa[cg][ac]
;	consensus.regexp.rc          	[GT][CG]TTA[AT]TT[CT][GT]C[GT]TC[AG][CT]GAA[AT]TA[AT][AG]T

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    

 [APPH] Assay of protein purified to homogeneity

 [BPP] Binding of purified proteins

 [IMP] Inferred from mutant phenotype

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

 [GEA] Gene expression analysis

 [SM] Site mutation

 [BCE] Binding of cellular extracts



Reference(s)    

 [1] Condemine G., Berrier C., Plumbridge J., Ghazi A., 2005, Function and expression of an N-acetylneuraminic acid-inducible outer membrane channel in Escherichia coli., J Bacteriol 187(6):1959-65

 [2] Peri KG., Goldie H., Waygood EB., 1990, Cloning and characterization of the N-acetylglucosamine operon of Escherichia coli., Biochem Cell Biol 68(1):123-37

 [3] Plumbridge J., 2001, DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli., Nucleic Acids Res 29(2):506-14

 [4] Plumbridge J., 1995, Co-ordinated regulation of amino sugar biosynthesis and degradation: the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon and requires two separated NagC binding sites., EMBO J 14(16):3958-65

 [5] Plumbridge J., Kolb A., 1991, CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli., J Mol Biol 217(4):661-79

 [6] Plumbridge J., Pellegrini O., 2004, Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC, ChbR and CAP., Mol Microbiol 52(2):437-49

 [7] Plumbridge JA., 1991, Repression and induction of the nag regulon of Escherichia coli K-12: the roles of nagC and nagA in maintenance of the uninduced state., Mol Microbiol 5(8):2053-62

 [8] Plumbridge JA., 1989, Sequence of the nagBACD operon in Escherichia coli K12 and pattern of transcription within the nag regulon., Mol Microbiol 3(4):505-15

 [9] Sohanpal BK., El-Labany S., Lahooti M., Plumbridge JA., Blomfield IC., 2004, Integrated regulatory responses of fimB to N-acetylneuraminic (sialic) acid and GlcNAc in Escherichia coli K-12., Proc Natl Acad Sci U S A 101(46):16322-7

 [10] Sohanpal BK., Friar S., Roobol J., Plumbridge JA., Blomfield IC., 2007, Multiple co-regulatory elements and IHF are necessary for the control of fimB expression in response to sialic acid and N-acetylglucosamine in Escherichia coli K-12., Mol Microbiol 63(4):1223-36

 [11] Kachroo AH., Kancherla AK., Singh NS., Varshney U., Mahadevan S., 2007, Mutations that alter the regulation of the chb operon of Escherichia coli allow utilization of cellobiose., Mol Microbiol 66(6):1382-95

 [12] Oberto J., 2010, FITBAR: a web tool for the robust prediction of prokaryotic regulons., BMC Bioinformatics 11:554

 [13] Plumbridge J., Bossi L., Oberto J., Wade JT., Figueroa-Bossi N., 2014, Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella., Mol Microbiol 92(4):648-58

 [14] El Qaidi S., Allemand F., Oberto J., Plumbridge J., 2009, Repression of galP, the galactose transporter in Escherichia coli, requires the specific regulator of N-acetylglucosamine metabolism., Mol Microbiol 71(1):146-57

 [15] Plumbridge J., 1998, Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS., Mol Microbiol 27(2):369-80

 [16] Fernandez M., Plumbridge J., 2019, Complex synergistic amino acid-nucleotide interactions contribute to the specificity of NagC operator recognition and induction., Microbiology 165(7):792-803

 [17] Plumbridge J., Kolb A., 1993, DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo., Mol Microbiol 10(5):973-81

 [18] Plumbridge J., Kolb A., 1998, DNA bending and expression of the divergent nagE-B operons., Nucleic Acids Res 26(5):1254-60

 [19] Pennetier C, Domínguez-Ramírez L, Plumbridge J, 2008, Different regions of Mlc and NagC, homologous transcriptional repressors controlling expression of the glucose and N-acetylglucosamine phosphotransferase systems in Escherichia coli, are required for inducer signal recognition., Mol Microbiol, 2008 Jan

 [20] Plumbridge J, 2001, Regulation of PTS gene expression by the homologous transcriptional regulators, Mlc and NagC, in Escherichia coli (or how two similar repressors can behave differently)., J Mol Microbiol Biotechnol, 2001 Jul

 [21] Titgemeyer F, Reizer J, Reizer A, Saier MH Jr, 1994, Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria., Microbiology, 1994 Sep

 [22] Hansen T, Reichstein B, Schmid R, Schönheit P, 2002, The first archaeal ATP-dependent glucokinase, from the hyperthermophilic crenarchaeon Aeropyrum pernix, represents a monomeric, extremely thermophilic ROK glucokinase with broad hexose specificity., J Bacteriol, 2002 Nov

 [23] Cho S., Shin D., Ji GE., Heu S., Ryu S., 2005, High-level recombinant protein production by overexpression of Mlc in Escherichia coli., J Biotechnol 119(2):197-203



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