RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: metR
Gene(s): metR   Genome Browser M3D Gene expression COLOMBOS
Note(s): In 1989 Urbanowski et al. proposed that, in Salmonella typhimurium, MetR binds to a region of 13 bp (TGAAnnnnnTTCA) 2676984 in the regulatory region located between the divergent genes metE and metR. More recently, Wu et al. showed, in S. typhimurium, that this regulator binds as dimer of dimers in the same region of regulation Lorenz E,1995.
The central positions of the MetR binding sites in Escherichia coli have been assigned according to the consensus sequence obtained for S. typhimurium (TGAAnnnnnTTCA). Using a new methodology based on analysis of orthologous sequences, the curator has identified the consensus sequence of MetR (aTGAAaaattTTCAt) of 15 bp, which is similar to the consensus sequence identified in the RegPrecise database (aTGAAaTcaaTTCAt). According to this information, the curator assigned two possible binding sites for MetR, located at bp 16 and -6 of the transcription start site of metRp2.
Promoter
Name: metRp2
+1: 4012837
Distance from start of the gene: 21
Sequence: ccagatgtttacacatccataattggcggttactgtatattcctcaagcgcaaattattcAtgccgaagtgaaggactttc
Evidence: [TIM]
Reference(s): [1] Cai XY., et al., 1989
TF binding sites (TFBSs)
[MetJ-S-adenosylmethionine,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MetJ-S-adenosylmethionine1 repressor metRp2 4012877 4012892 -47.5 agccgtccagATGTTTACACATCCATAattggcggtt nd [BPP] [1]
remote MetJ-S-adenosylmethionine2 repressor metRp2 4012992 4013007 -162.5 attttgaattTAGGGAAGGCGGCAAGTttattcatcc nd [BPP] [1]
[MetR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MetR-L-homocysteine repressor metRp2 4012815 4012829 16.0 ttcatgccgaAGTGAAGGACTTTCATgatcgaagta nd [APIORCISFBSCS], [BPP], [GEA] [1], [2], [4]
proximal MetR-L-homocysteine repressor metRp2 4012836 4012850 -6.0 atattcctcaAGCGCAAATTATTCATgccgaagtga nd [BPP], [GEA], [BPP], [GEA] [1], [2], [3], [4]
Note(s): 1Both sites of the MetJ regulator in the intergenic region of metE and metR could negatively regulate both the metRp2 and metRp1 promoters.
2Both sites of the MetJ regulator in the intergenic region of metE and metR could negatively regulate both the metRp2 and metRp1 promoters.1Both sites of the MetJ regulator in the intergenic region of metE and metR could negatively regulate both the metRp2 and metRp1 promoters.
2Both sites of the MetJ regulator in the intergenic region of metE and metR could negatively regulate both the metRp2 and metRp1 promoters.


Transcription unit          
Name: metR
Gene(s): metR   Genome Browser M3D Gene expression COLOMBOS
Note(s): In 1989 Urbanowski et al. proposed that, in Salmonella typhimurium, MetR binds to a region of 13 bp (TGAAnnnnnTTCA) 2676984 in the regulatory region located between the divergent genes metE and metR. More recently, Wu et al. showed, in S. typhimurium, that this regulator binds as dimer of dimers in the same region of regulation Lorenz E,1995.
The central positions of the MetR binding sites in Escherichia coli have been assigned according to the consensus sequence obtained for S. typhimurium (TGAAnnnnnTTCA). Using a new methodology based on analysis of orthologous sequences, the curator has identified the consensus sequence of MetR (aTGAAaaattTTCAt) of 15 bp, which is similar to the consensus sequence identified in the RegPrecise database (aTGAAaTcaaTTCAt). According to this information, the curator assigned two possible binding sites for MetR, located at bp 13 and 34 of the transcription start site of metRp1.
Promoter
Name: metRp1
+1: 4012855
Distance from start of the gene: 39
Sequence: acgaaggattttagccgtccagatgtttacacatccataattggcggttactgtatattcCtcaagcgcaaattattcatg
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [1] Cai XY., et al., 1989
[5] Salgado H, et al., 2012
TF binding sites (TFBSs)
[MetJ-S-adenosylmethionine,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MetJ-S-adenosylmethionine1 repressor metRp1 4012877 4012892 -29.5 agccgtccagATGTTTACACATCCATAattggcggtt nd [BPP] [1]
remote MetJ-S-adenosylmethionine2 repressor metRp1 4012992 4013007 -144.5 attttgaattTAGGGAAGGCGGCAAGTttattcatcc nd [BPP] [1]
[MetR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote MetR-L-homocysteine repressor metRp1 4012815 4012829 34.0 ttcatgccgaAGTGAAGGACTTTCATgatcgaagta nd [APIORCISFBSCS], [BPP], [GEA] [1], [2], [4]
proximal MetR-L-homocysteine repressor metRp1 4012836 4012850 13.0 atattcctcaAGCGCAAATTATTCATgccgaagtga nd [BPP], [GEA], [BPP], [GEA] [1], [2], [3], [4]
[OxyR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR activator metRp1 4012852 4012868 -5.0 ataattggcgGTTACTGTATATTCCTCAagcgcaaatt nd [CEEUMA], [IHBCE], [RSE] [6]
Note(s): 1Both sites of the MetJ regulator in the intergenic region of metE and metR could negatively regulate both promoters metRp2 and metRp1.
2Both sites of the MetJ regulator in the intergenic region of metE and metR could negatively regulate both promoters metRp2 and metRp1.1Both sites of the MetJ regulator in the intergenic region of metE and metR could negatively regulate both promoters metRp2 and metRp1.
2Both sites of the MetJ regulator in the intergenic region of metE and metR could negatively regulate both promoters metRp2 and metRp1.


Evidence    

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

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

 [GEA] Gene expression analysis

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

 [CEEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [RSE] RNA-seq evidence


Reference(s)    

 [1] Cai XY., Maxon ME., Redfield B., Glass R., Brot N., Weissbach H., 1989, Methionine synthesis in Escherichia coli: effect of the MetR protein on metE and metH expression., Proc Natl Acad Sci U S A 86(12):4407-11

 [2] Cai XY., Redfield B., Maxon M., Weissbach H., Brot N., 1989, The effect of homocysteine on MetR regulation of metE, metR and metH expression in vitro., Biochem Biophys Res Commun 163(1):79-83

 [3] Jafri S., Urbanowski ML., Stauffer GV., 1995, A mutation in the rpoA gene encoding the alpha subunit of RNA polymerase that affects metE-metR transcription in Escherichia coli., J Bacteriol 177(3):524-9

 [4] Maxon ME., Redfield B., Cai XY., Shoeman R., Fujita K., Fisher W., Stauffer G., Weissbach H., Brot N., 1989, Regulation of methionine synthesis in Escherichia coli: effect of the MetR protein on the expression of the metE and metR genes., Proc Natl Acad Sci U S A 86(1):85-9

 [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] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

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