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AsnC DNA-binding transcriptional dual regulator

Synonyms: AsnC-L-asparagine, AsnC
Summary:
AsnC is a transcriptional regulator that activates the expression of asnA, a gene involved in the synthesis of asparagine [2, 4] However, when asparagine is present the activation of asnA is turned off. On the other hand, AsnC is negatively autoregulated, but the presence of asparagine does not affect this regulation [2] AsnC belongs to the AsnC family of regulatory proteins whose members are widely distributed in archaea and bacteria [5] It has been postulated that AsnC is very ascient; it appears that it was present before the divergence of archea and bacteria [5] This protein has a DNA-binding domain with a helix-turn-helix motif in the N terminus and an effector-binding C-terminal domain [1] A crystal structure of AsnC complexed with the ligand l-asparagine has been solved at 2.4-Å resolution.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
AsnC Functional   Apo [IPI] [1]
AsnC-L-asparagine Non-Functional Allosteric Holo [IPI] [1]
Evolutionary Family: AsnC
Sensing class: Sensing external and internal signals
Connectivity class: Local Regulator
Gene name: asnC
  Genome position: 3926545-3927003
  Length: 459 bp / 152 aa
Operon name: asnC-mioC-mnmG-rsmG
TU(s) encoding the TF:
Transcription unit        Promoter
asnC
asnCp
asnC-mioC
asnCp
asnC-mioC-mnmG
asnCp


Regulon       
Regulated gene(s) asnA, asnC, mioC, mnmG
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
asparagine (2)
Transcription related (1)
activator (1)
repressor (1)
regulon (1)
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Regulated operon(s) asnA, asnC-mioC-mnmG-rsmG
First gene in the operon(s) asnA, asnC
Simple and complex regulons AsnC
AsnC,Nac
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[AsnC,-](1)
[AsnC,+](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
  AsnC activator asnAp Sigma70 -109.5 -135.5 asnA
taggattttcTTATGCGGATTGATgattcattct
 3927013 3927026 [GEA], [AIBSCS] [2]
  AsnC activator asnAp Sigma70 -75.5 -101.5 asnA
attttagcctTCTTTTTTAATGAAtcaaaagtga
 3927047 3927060 [GEA], [AIBSCS] [2]
  AsnC activator asnAp Sigma70 -43.5 -69.5 asnA
gagttaggctTTTTATTGAATGATtattgcatgt
 3927079 3927092 [GEA], [AIBSCS] [2], [3]
  AsnC activator asnAp Sigma70 -12.5 -38.5 asnA
tgtgtgtcggTTTTTGTTGCTTAAtcataagcaa
 3927110 3927123 [GEA], [AIBSCS] [2]
  AsnC repressor asnCp Sigma70 -85.5 -113.5 asnC, mioC, mnmG
ttgcttatgaTTAAGCAACAAAAAccgacacaca
 3927110 3927123 [GEA], [AIBSCS] [2]
  AsnC repressor asnCp Sigma70 -54.5 -82.5 asnC, mioC, mnmG
acatgcaataATCATTCAATAAAAagcctaactc
 3927079 3927092 [GEA], [AIBSCS] [2]
  AsnC repressor asnCp Sigma70 -22.5 -50.5 asnC, mioC, mnmG
tcacttttgaTTCATTAAAAAAGAaggctaaaat
 3927047 3927060 [GEA], [AIBSCS] [2]
  AsnC repressor asnCp Sigma70 12.5 -16.5 asnC, mioC, mnmG
agaatgaatcATCAATCCGCATAAgaaaatccta
 3927013 3927026 [GEA], [AIBSCS] [2]


Alignment and PSSM for AsnC TFBSs    

Aligned TFBS of AsnC   
  Sequence
  TGATTCATTAAAAAAGA
  TGATTAAGCAACAAAAA
  TCATTCAATAAAAAGCC
  TCAATCCGCATAAGAAA

Position weight matrix (PWM). AsnC matrix-quality result    
A	0	0	4	1	0	1	3	1	0	4	3	3	4	3	3	2	3
C	0	2	0	0	0	3	1	0	2	0	0	1	0	0	0	1	1
G	0	2	0	0	0	0	0	2	0	0	0	0	0	1	1	1	0
T	4	0	0	3	4	0	0	1	2	0	1	0	0	0	0	0	0

Consensus    
;	consensus.strict             	TgAtTCagcAaaAaaaa
;	consensus.strict.rc          	TTTTTTTTGCTGAATCA
;	consensus.IUPAC              	TsAtTCmgyAamArrvm
;	consensus.IUPAC.rc           	KBYYTKTTRCKGAATSA
;	consensus.regexp             	T[cg]AtTC[ac]g[ct]Aa[ac]A[ag][ag][acg][ac]
;	consensus.regexp.rc          	[GT][CGT][CT][CT]T[GT]TT[AG]C[GT]GAAT[CG]A

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    

 [IPI] Inferred from physical interaction

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] Thaw P., Sedelnikova SE., Muranova T., Wiese S., Ayora S., Alonso JC., Brinkman AB., Akerboom J., van der Oost J., Rafferty JB., 2006, Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family., Nucleic Acids Res 34(5):1439-1449

 [2] Kolling R., Lother H., 1985, AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli., J Bacteriol 164(1):310-5

 [3] Tobia AJ., Couri D., Sagone A., 1985, The effects of the quinone type drugs on hydroxyl radical (OH.) production by rat liver microsomes., J Toxicol Environ Health 15(2):265-77

 [4] de Wind N, de Jong M, Meijer M, Stuitje AR, 1985, Site-directed mutagenesis of the Escherichia coli chromosome near oriC: identification and characterization of asnC, a regulatory element in E. coli asparagine metabolism., Nucleic Acids Res, 13(24):8797 10.1093/nar/13.24.8797

 [5] Pérez-Rueda E, Collado-Vides J, 2001, Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria., J Mol Evol, 53(3):172 10.1007/s002390010207

 [6] Kolling R., Gielow A., Seufert W., Kucherer C., Messer W., 1988, AsnC, a multifunctional regulator of genes located around the replication origin of Escherichia coli, oriC., Mol Gen Genet 212(1):99-104

 [7] Gielow A., Kucherer C., Kolling R., Messer W., 1988, Transcription in the region of the replication origin, oriC, of Escherichia coli: termination of asnC transcripts., Mol Gen Genet 214(3):474-81

 [8] Schaefer C, Messer W, 1988, Termination of the Escherichia coli asnC transcript. The DnaA protein/dnaA box complex blocks transcribing RNA polymerase., Gene, 73(2):347 10.1016/0378-1119(88)90499-4

 [9] 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

 [10] Yokoyama K, Ishijima SA, Clowney L, Koike H, Aramaki H, Tanaka C, Makino K, Suzuki M, 2006, Feast/famine regulatory proteins (FFRPs): Escherichia coli Lrp, AsnC and related archaeal transcription factors., FEMS Microbiol Rev, 30(1):89 10.1111/j.1574-6976.2005.00005.x


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