RegulonDB RegulonDB 10.7: Operon Form
   

glnHPQ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: glnHPQ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: glnQ
Gene(s): glnQ   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: glnQp
+1: 846631
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 168
Sequence: actgcgtcgtatgctgccgccgctgggtaaccagtggatcatcagcattaaagacacctcGctgtttattgtgatcggcgt
                           -35                   -10        +1                   
Evidence: [AIPP]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fis1 repressor glnQp nd nd nd nd nd [GEA] [2]
Note(s): 1Fis negatively regulates glnQ gene expression, and RpoS lightly regulates its expression Xu J,1995.1Fis negatively regulates glnQ gene expression, and RpoS lightly regulates its expression Xu J,1995.


Transcription unit          
Name: glnHPQ
Synonym(s): OP00234
Gene(s): glnQ, glnP, glnH   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [3] Nohno T., et al., 1987
[4] Nohno T., et al., 1986
Promoter
Name: glnHp2
+1: 848047
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 43
Sequence: gccgcatctcgaaaaatcaaggagttgcaaaactggcacgattttttcatatatgtgaatGtcacgcaggggatcgtcccg
                                  -24         -12           +1                   
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [3] Nohno T., et al., 1987
[5] Salgado H, et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF1 activator glnHp2 848088 848100 -47.0 tttgccgcatCTCGAAAAATCAAggagttgcaa nd [APIORCISFBSCS], [BPP], [SM] [6], [7]
remote IHF activator glnHp2 848193 848205 -152.0 tacgctaaatAATCACTGTGTTGagtgcacaat nd [APIORCISFBSCS] [6], [7], [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NtrC-Pasp activator glnHp2 848148 848164 -109.0 accagattggTGCCCCAGAATGGTGCAtcttcagggt nd [APIORCISFBSCS], [BPP] [7]
remote NtrC-Pasp activator glnHp2 848161 848177 -122.0 acaattttagCGCACCAGATTGGTGCCccagaatggt nd [APIORCISFBSCS], [BPP] [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NtrC-Pasp repressor glnHp2 848118 848134 -79.0 tcagggtattGCCCTATAAATCGTGCAtcacgttttt nd [APIORCISFBSCS], [BPP] [7]
remote NtrC-Pasp repressor glnHp2 848174 848190 -135.0 ctgtgttgagTGCACAATTTTAGCGCAccagattggt nd [APIORCISFBSCS], [BPP] [7]
Note(s): 1IHF binds to a site immediately upstream of glnHp2 and enhances the activation of open complex formation by NRI phosphate.
6IHF binds to a site immediately upstream of glnHp2 and enhances the activation of open complex formation by NRI phosphate.


Transcription unit       
Name: glnHPQ
Gene(s): glnQ, glnP, glnH   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [3] Nohno T., et al., 1987
Promoter
Name: glnHp1
+1: 848198
Distance from start of the gene: 194
Sequence: catcacacaatcgttacataaagattgttttttcatcaggttttacgctaaataatcactGtgttgagtgcacaattttag
Evidence: [GEA]
[IMP]
[TIM]
Reference(s): [3] Nohno T., et al., 1987
[9] Typas A., et al., 2007


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [10] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.7 848107 848152 ccccagaatgGTGCATCTTCAGGGTATTGCCCTATAAATCGTGCATCACGTTTTTgccgcatctc
  anti-terminator -13.0 848149 848176 caattttagcGCACCAGATTGGTGCCCCAGAATGGTGcatcttcagg
  anti-anti-terminator -7.2 848162 848176 caattttagcGCACCAGATTGGTGccccagaatg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"




Reference(s)    

 [1] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [2] Xu J., Johnson RC., 1995, Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli., J Bacteriol 177(4):938-47

 [3] Nohno T., Saito T., 1987, Two transcriptional start sites found in the promoter region of Escherichia coli glutamine permease operon, glnHPQ., Nucleic Acids Res 15(6):2777

 [4] Nohno T., Saito T., Hong JS., 1986, Cloning and complete nucleotide sequence of the Escherichia coli glutamine permease operon (glnHPQ)., Mol Gen Genet 205(2):260-9

 [5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [6] Claverie-Martin F., Magasanik B., 1992, Positive and negative effects of DNA bending on activation of transcription from a distant site., J Mol Biol 227(4):996-1008

 [7] 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

 [8] Freundlich M., Ramani N., Mathew E., Sirko A., Tsui P., 1992, The role of integration host factor in gene expression in Escherichia coli., Mol Microbiol 6(18):2557-63

 [9] Typas A., Barembruch C., Possling A., Hengge R., 2007, Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of sigma(s) activity and levels., EMBO J 26(6):1569-78

 [10] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.


RegulonDB