RegulonDB RegulonDB 11.1: 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: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fis repressor glnQp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]


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: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Huerta AM., et al., 2003
[3] Nohno T., et al., 1987
[5] Salgado H, et al., 2012
TF binding sites (TFBSs)
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator glnHp2 848088 848100 -47.0 tttgccgcatCTCGAAAAATCAAggagttgcaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-PCR-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [8]
remote IHF activator glnHp2 848193 848205 -152.0 tacgctaaatAATCACTGTGTTGagtgcacaat nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [6], [7]
[NtrC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NtrC-phosphorylated activator glnHp2 848148 848164 -109.0 accagattggTGCCCCAGAATGGTGCAtcttcagggt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]
remote NtrC-phosphorylated activator glnHp2 848161 848177 -122.0 acaattttagCGCACCAGATTGGTGCCccagaatggt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]
[NtrC,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NtrC-phosphorylated repressor glnHp2 848118 848134 -79.0 tcagggtattGCCCTATAAATCGTGCAtcacgttttt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]
remote NtrC-phosphorylated repressor glnHp2 848174 848190 -135.0 ctgtgttgagTGCACAATTTTAGCGCAccagattggt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]


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: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Nohno T., et al., 1987


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-CHIP-PCR-MANUAL] ChIP-PCR evidence used in manual assertion

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation


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., 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

 [7] 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

 [8] 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

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