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NanR DNA-binding transcriptional dual regulator

Synonyms: NanR-NANA, NanR
Summary:
The genes regulated by NanR, "N-acetyl-neuraminic acid regulator," are involved in N-acetyl-neuraminic acid (or sialic acid) transport and metabolism [1]and in OFF/ON switching of type 1 fimbriation. N-acetylneuraminate (Neu5Ac), which is the most common sialic acid, induces the catabolism of sialic acids operons by directly inactivating NanR [2] converting the predominantly dimeric form of the repressor to an inactive monomer [5] NanR is a member of the FadR/GntR family. Members of this family have two domains, an N-terminal domain with a helix-turn-helix DNA-binding motif and a C-terminal domain with dimerization and effector-binding motifs. Three-dimensional models of the N terminus of FadR and NanR show topological similarities and a ~26% sequence identity between them [1] NanR regulates transcription when it binds to a region of ~30 bp that contains three conserved motifs in tandem.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NanR Functional   Apo [APPH], [BPP], [IFC] [1], [2]
NanR-NANA Non-Functional Allosteric Holo [BPP] [2]
Evolutionary Family: GntR
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: nanR
  Genome position: 3373698-3374489
  Length: 792 bp / 263 aa
Operon name: nanR
TU(s) encoding the TF:
Transcription unit        Promoter
 
 


Regulon       
Regulated gene(s) fimB, nanA, nanC, nanE, nanK, nanM, nanS, nanT, yhcH, yjhB, yjhC
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
amino sugar conversions (4)
carbon compounds (2)
Porters (Uni-, Sym- and Antiporters) (2)
membrane (2)
fimbri, pili (1)
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Regulated operon(s) fimB, nanATEK-yhcH, nanCMS, yjhBC
First gene in the operon(s) fimB, nanA, nanC, yjhB
Simple and complex regulons BasR,DksA,DksA-ppGpp,H-NS,IHF,NagC,NanR,ppGpp
CRP,Fis,NanR
CRP,NagC,NanR
NanR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[NanR,-](3)
[NanR,+](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
  NanR activator fimBp2 nd -744.5 -1034.5 fimB
actatcttggTGCACCtttatacctg
 4539920 4539925 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/GS)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [CV(GEA/SM/GS)], [GEA], [GS], [SM] [2], [3], [4], [5], [6], [7]
  NanR activator fimBp2 nd -736.5 -1026.5 fimB
ggtgcaccttTATACCtgttatacca
 4539928 4539933 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/GS)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [CV(GEA/SM/GS)], [GEA], [GS], [SM] [2], [3], [4], [5], [6], [7]
  NanR activator fimBp2 nd -727.5 -1017.5 fimB
ttatacctgtTATACCagatcaaaaa
 4539937 4539942 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/GS)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [CV(GEA/SM/GS)], [GEA], [GS], [SM] [2], [3], [4], [5], [6], [7]
  NanR repressor nanAp Sigma70 -11.5 -55.5 nanA, nanT, nanE, nanK, yhcH
taattgatctGGTATAacaggtataa
 3373629 3373634 [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [1], [5], [8]
  NanR repressor nanAp Sigma70 -2.5 -46.5 nanA, nanT, nanE, nanK, yhcH
tggtataacaGGTATAaaggtatatc
 3373620 3373625 [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [1], [5], [8]
  NanR repressor nanAp Sigma70 6.5 -38.5 nanA, nanT, nanE, nanK, yhcH
caggtataaaGGTATAtcgtttatca
 3373612 3373617 [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [1], [5], [8]
  NanR repressor nanCp nd -11.5 -438.5 nanC, nanM, nanS
tttttgatctGGTATAacaggtataa
 4539937 4539942 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/GS)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [CV(GEA/SM/GS)], [GEA], [GS], [SM] [2], [3], [4], [5], [6], [7]
  NanR repressor nanCp nd -2.5 -429.5 nanC, nanM, nanS
tggtataacaGGTATAaaggtgcacc
 4539928 4539933 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/GS)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [CV(GEA/SM/GS)], [GEA], [GS], [SM] [2], [3], [4], [5], [6], [7]
  NanR repressor nanCp nd 6.5 -421.5 nanC, nanM, nanS
caggtataaaGGTGCAccaagatagt
 4539920 4539925 [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/GS)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [CV(GEA/SM/GS)], [GEA], [GS], [SM] [2], [3], [4], [5], [6], [7]
  NanR repressor yjhBp2 Sigma32 -393.5 -431.5 yjhB, yjhC
tttttgatctGGTATAacaggtataa
 4503624 4503629 [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [5]
  NanR repressor yjhBp2 Sigma32 -384.5 -422.5 yjhB, yjhC
tggtataacaGGTATAaaggtataca
 4503633 4503638 [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [5]
  NanR repressor yjhBp2 Sigma32 -376.5 -414.5 yjhB, yjhC
caggtataaaGGTATAcagaaaagca
 4503641 4503646 [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [5]


Alignment and PSSM for NanR TFBSs    

Aligned TFBS of NanR   
  Sequence
  TATACCT
  TATACCT
  TATACCT
  TATACCT
  TATACCT
  TATACCA
  TATACCA
  TATACCA
  TGCACCT

Position weight matrix (PWM). NanR matrix-quality result    
A	0	8	0	9	0	0	3
C	0	0	1	0	9	9	0
G	0	1	0	0	0	0	0
T	9	0	8	0	0	0	6

Consensus    
;	consensus.strict             	TATACCt
;	consensus.strict.rc          	AGGTATA
;	consensus.IUPAC              	TATACCw
;	consensus.IUPAC.rc           	WGGTATA
;	consensus.regexp             	TATACC[at]
;	consensus.regexp.rc          	[AT]GGTATA

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

 [IFC] Inferred by functional complementation

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

 [CV(CHIP-SV/GEA/GS)] cross validation(CHIP-SV/GEA/GS)

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)

 [CV(GEA/GS)] cross validation(GEA/GS)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)

 [CV(GEA/SM/GS)] cross validation(GEA/SM/GS)

 [GEA] Gene expression analysis

 [GS] genomic SELEX

 [SM] Site mutation


Reference(s)    

 [1] Kalivoda KA., Steenbergen SM., Vimr ER., Plumbridge J., 2003, Regulation of sialic acid catabolism by the DNA binding protein NanR in Escherichia coli., J Bacteriol 185(16):4806-15

 [2] 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

 [3] 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

 [4] El-Labany S., Sohanpal BK., Lahooti M., Akerman R., Blomfield IC., 2003, Distant cis-active sequences and sialic acid control the expression of fimB in Escherichia coli K-12., Mol Microbiol 49(4):1109-18

 [5] Kalivoda KA., Steenbergen SM., Vimr ER., 2013, Control of the Escherichia coli sialoregulon by transcriptional repressor NanR., J Bacteriol 195(20):4689-701

 [6] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936

 [7] 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

 [8] Plumbridge J., Vimr E., 1999, Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid by Escherichia coli., J Bacteriol 181(1):47-54


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