RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: galP
Gene(s): galP   Genome Browser M3D Gene expression COLOMBOS
Note(s): The regulation of the galP operon is unusual in that it is controlled by three repressors which are involved in two different areas of the metabolism El Qaidi S,2009
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for galP . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Promoter
Name: galPp
+1: 3088255
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: attacactgatgtgatttgcttcacatctttttacgtcgtactcacctatcttaattcacAataaaaaataaccatattgg
                     -35                        -10         +1                   
Evidence: [HIPP]
[ICWHO]
[NTAS]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[2] Salgado H, et al., 2012
[3] Semsey S., et al., 2007
[4] Weickert MJ., et al., 1993
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator galPp 3088202 3088224 -42.5 gcgattacacTGATGTGATTTGCTTCACATCTTtttacgtcgt nd [GEA], [AIBSCS], [APIORCISFBSCS] [3], [4], [7]
[GalR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GalR-D-galactose repressor galPp 3088004 3088019 -243.5 atcatcacaaCTGAAACCGATTACACcaaccacaac nd [AIBSCS], [BPP], [SM] [5]
remote GalR-D-galactose repressor galPp 3088040 3088055 -207.5 agacaaagatTTGTAATATTTTCATAttattattcg nd [BPP] [5]
remote GalR-D-galactose repressor galPp 3088069 3088084 -178.5 ttattcggttTTCACAGTTGTTACATttcttttcag nd [AIBSCS], [BPP], [SM] [5]
remote GalR-D-galactose repressor galPp 3088140 3088155 -107.5 tgatgatataACTCAATTATTTTCATgcacttaaat nd [AIBSCS], [BPP], [SM] [5]
proximal GalR repressor galPp 3088186 3088201 -61.5 ataaatgttaGTGTAAGCGATTACACtgatgtgatt nd [GEA], [BPP], [SM] [3], [5], [6]
remote GalR repressor galPp 3088383 3088398 136.5 cctggatatcGGTGTAATTGCTGGCGcactgccgtt nd [GEA], [BPP], [SM] [3], [5], [6]
[GalS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GalS-D-galactose repressor galPp 3088004 3088019 -243.5 atcatcacaaCTGAAACCGATTACACcaaccacaac nd [AIBSCS], [BPP], [SM] [5]
remote GalS-D-galactose repressor galPp 3088040 3088055 -207.5 agacaaagatTTGTAATATTTTCATAttattattcg nd [BPP] [5]
remote GalS-D-galactose repressor galPp 3088069 3088084 -178.5 ttattcggttTTCACAGTTGTTACATttcttttcag nd [AIBSCS], [BPP], [SM] [5]
remote GalS-D-galactose repressor galPp 3088140 3088155 -107.5 tgatgatataACTCAATTATTTTCATgcacttaaat nd [AIBSCS], [BPP], [SM] [5]
proximal GalS repressor galPp 3088186 3088201 -61.5 ataaatgttaGTGTAAGCGATTACACtgatgtgatt nd [GEA], [BPP], [SM] [3], [5], [6]
remote GalS repressor galPp 3088383 3088398 136.5 cctggatatcGGTGTAATTGCTGGCGcactgccgtt nd [GEA], [BPP], [SM] [3], [5], [6]
[NagC,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NagC repressor galPp 3088245 3088267 2.0 actcacctatCTTAATTCACAATAAAAAATAACcatattggag nd [AIBSCS], [BPP], [SM] [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -8.0 3088203 3088228 gattacactgATGTGATTTGCTTCACATCTTTTTAcgtcgtactc
  anti-terminator -10.6 3088180 3088207 ctaagataaaTGTTAGTGTAAGCGATTACACTGATGTgatttgcttc
  anti-anti-terminator -3.6 3088155 3088190 ttattttcatGCACTTAAATCATAACTAAGATAAATGTTAGTGTAagcgattaca
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    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [NTAS] Non-traceable author statement

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

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

 [BPP] Binding of purified proteins

 [SM] 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] 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.

 [3] Semsey S., Krishna S., Sneppen K., Adhya S., 2007, Signal integration in the galactose network of Escherichia coli., Mol Microbiol 65(2):465-76

 [4] Weickert MJ., Adhya S., 1993, The galactose regulon of Escherichia coli., Mol Microbiol 10(2):245-51

 [5] El Qaidi S., Allemand F., Oberto J., Plumbridge J., 2009, Repression of galP, the galactose transporter in Escherichia coli, requires the specific regulator of N-acetylglucosamine metabolism., Mol Microbiol 71(1):146-57

 [6] Geanacopoulos M., Adhya S., 1997, Functional characterization of roles of GalR and GalS as regulators of the gal regulon., J Bacteriol 179(1):228-34

 [7] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

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