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Nac DNA-binding transcriptional dual regulator

Synonyms: Nac
Summary:
Nac, Nitrogen assimilation control, regulates, without a coeffector, genes involved in nitrogen metabolism under nitrogen-limiting conditions [7]
The genes regulated by Nac are transcribed by RNA polymerase σ70. These genes are coupled to the nitrogen regulatory (Ntr) system, which is σ54 dependent, through Nac, whose transcription is activated by NtrC [7] Using DNA microarray analyses, it was shown that Nac could affect the expression of 25 genes [3] This transcriptional regulator is negatively autoregulated [7]and is expressed under nitrogen-limiting conditions [6]
Nac belongs to the LysR family [7]and features a helix-turn-helix motif located close to the N terminus [10] In contrast with most LysR family members, which are transcribed divergently from the gene they regulate, nac is distant on the genome from its regulated genes [7]
In Klebsiella pneumoniae, Nac functions as a dimer, and for some sites it can bind as a tetramer; it recognizes long and short sites in the absence of a coeffector [11] Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
Nac     nd nd
Evolutionary Family: LysR
Connectivity class: Local Regulator
Gene name: nac
  Genome position: 2061016-2061933
  Length: 918 bp / 305 aa
Operon name: nac
TU(s) encoding the TF:
Transcription unit        Promoter
nac
nacp


Regulon       
Regulated gene(s) asnC, codA, codB, feaR, gabD, gabP, gabT, gdhA, gltB, gltD, gltF, mioC, mnmG, nac, nupC, patD, serA, ydcS, ydcT, ydcU, ydcV
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (5)
nitrogen metabolism (4)
Transcription related (3)
activator (3)
nucleotide and nucleoside conversions (3)
Read more >
Regulated operon(s) asnC-mioC-mnmG-rsmG, codBA, csiD-lhgO-gabDTP, feaR, gdhA, gltBDF, nac, nupC, serA, ydcSTUV-patD
First gene in the operon(s) asnC, asnC, asnC, codB, feaR, gabD, gdhA, gltB, nac, nupC, serA, ydcS
Simple and complex regulons AdiY,ArgR,CRP,FNR,Fur,GadE,HdfR,IHF,Lrp,Nac
ArgP,CRP,FNR,Fur,Nac
AsnC,Nac
CRP,CytR,Nac
CRP,Nac,NsrR,PhoB
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[Nac,-](4)
[Nac,+](4)


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
  Nac repressor asnCp Sigma70 -64.0 -92.0 asnC, mioC, mnmG
aaaccgacacACATGCAATAATCATtcaataaaaa
3927088 3927102 [GEA], [HIBSCS] [1]
  Nac repressor asnCp Sigma70 -7.0 -35.0 asnC, mioC, mnmG
taaaaaagaaGGCTAAAATAGAATGaatcatcaat
3927031 3927045 [GEA], [HIBSCS] [1]
  Nac repressor asnCp Sigma70 16.0 -13.0 asnC, mioC, mnmG
atgaatcatcAATCCGCATAAGAAAatcctatgga
3927009 3927023 [GEA], [HIBSCS] [1]
  Nac activator codBp Sigma70 -58.0 -96.0 codB, codA
gcactcattcATATAAAAAATATATttccccacga
354819 354833 [AIBSCS], [BPP], [GEA], [SM] [2], [3]
  Nac activator feaRp2 Sigma70 -32.5 -58.0 feaR
gtcaggctcaTTAGCTTCGTTTATTgcaacacaaa
1447334 1447348 [IHBCE] [4]
  Nac activator gabDp1 Sigma70 -44.0 -145.0 gabD, gabT, gabP
cggcagcgacATCAGCAATTCCTATtggtgcgcat
2791121 2791135 [GEA], [HIBSCS] [3], [5]
  Nac repressor gdhAp1 Sigma70 -81.0 -144.0 gdhA
tcgcatttggTTATGAGATTACTCTcgttattaat
1842220 1842234 [GEA], [HIBSCS] [6]
  Nac repressor gdhAp1 Sigma70 -25.0 -88.0 gdhA
ttcttgcttaCCGTCACATTCTTGAtggtatagtc
1842276 1842290 [GEA], [HIBSCS] [6]
  Nac repressor gdhAp1 Sigma70 25.0 -39.0 gdhA
cacatgacatAAACAACATAAGCACaatcgtatta
1842325 1842339 [GEA], [HIBSCS] [6]
  Nac repressor gdhAp1 Sigma70 45.0 -19.0 gdhA
agcacaatcgTATTAATATATAAGGgttttatatc
1842345 1842359 [GEA], [HIBSCS] [6]
  Nac repressor gltBp Sigma70 nd nd gltB, gltD, gltF nd nd [GEA] [3]
  Nac repressor nacp Sigma54 -75.0 -120.0 nac
tgacgaatctATCATAATCTCTTATttgacagttg
2062046 2062060 [BPP], [GEA], [HIBSCS] [7]
  Nac activator nupCp Sigma70 nd nd nupC nd nd [GEA] [3]
  Nac repressor serAp1 Sigma70 -30.0 -76.0 serA
gcaaacgttcATATTGCCGCAATATtattttttga
3058479 3058493 [GEA], [HIBSCS] [8]
  Nac repressor serAp1 Sigma70 -19.0 -65.0 serA
tattgccgcaATATTATTTTTTGATatgttgaaag
3058468 3058482 [GEA], [HIBSCS] [8]
  Nac activator ydcSp1 Sigma38 -51.0 -106.0 ydcS, ydcT, ydcU, ydcV, patD
cacaacctgaATAAATTTTCTCAGGggcgaaggtg
1511541 1511555 [GEA], [HIBSCS], [IDA] [9]


Alignment and PSSM for Nac TFBSs    

Aligned TFBS of Nac   
  Sequence
 

Position weight matrix (PWM).   
A	3	3	1	6	3	11	1	9	12	5	10	7	10	10	2	3	5
C	3	4	8	5	6	1	2	2	1	0	3	0	1	0	1	4	5
G	2	3	5	1	0	1	0	3	0	7	0	3	0	1	1	2	0
T	6	4	0	2	5	1	11	0	1	2	1	4	3	3	10	5	4

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

 [HIBSCS] Human inference based on similarity to consensus sequences

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [IHBCE] Inferred by a human based on computational evidence

 [IDA] Inferred from direct assay



Reference(s)    

 [1] Poggio S., Domeinzain C., Osorio A., Camarena L., 2002, The nitrogen assimilation control (Nac) protein represses asnC and asnA transcription in Escherichia coli., FEMS Microbiol Lett. 206(2):151-6

 [2] Muse WB., Rosario CJ., Bender RA., 2003, Nitrogen regulation of the codBA (cytosine deaminase) operon from Escherichia coli by the nitrogen assimilation control protein, NAC., J Bacteriol. 185(9):2920-6

 [3] 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

 [4] Zeng J., Spiro S., 2013, Finely tuned regulation of the aromatic amine degradation pathway in Escherichia coli., J Bacteriol. 195(22):5141-50

 [5] Schneider BL., Ruback S., Kiupakis AK., Kasbarian H., Pybus C., Reitzer L., 2002, The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction., J Bacteriol. 184(24):6976-86

 [6] Camarena L., Poggio S., Garcia N., Osorio A., 1998, Transcriptional repression of gdhA in Escherichia coli is mediated by the Nac protein., FEMS Microbiol Lett. 167(1):51-6

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

 [8] Blauwkamp TA., Ninfa AJ., 2002, Nac-mediated repression of the serA promoter of Escherichia coli., Mol Microbiol. 45(2):351-63

 [9] 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

 [10] Muse WB., Bender RA., 1999, The amino-terminal 100 residues of the nitrogen assimilation control protein (NAC) encode all known properties of NAC from Klebsiella aerogenes and Escherichia coli., J Bacteriol. 181(3):934-40

 [11] Rosario CJ., Frisch RL., Bender RA., 2010, The LysR-type nitrogen assimilation control protein forms complexes with both long and short DNA binding sites in the absence of coeffectors., J Bacteriol. 192(19):4827-33



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