RegulonDB RegulonDB 11.1: 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) Urbanowski ML, Stauffer GV,1989 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: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Cai XY., et al., 1989
TF binding sites (TFBSs)
[MetJ,-] 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 MetJ-S-adenosyl-L-methionine repressor metRp2 4012877 4012892 -47.5 gccgtccagaTGTTTACACATCCATAattggcggtt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]
remote MetJ-S-adenosyl-L-methionine repressor metRp2 4012992 4013007 -162.5 ttttgaatttAGGGAAGGCGGCAAGTttattcatcc nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]
[MetR,-] 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 MetR-L-homocysteine repressor metRp2 4012815 4012829 16.0 tcatgccgaaGTGAAGGACTTTCATgatcgaagta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [2], [3], [4]
proximal MetR-L-homocysteine repressor metRp2 4012836 4012850 -6.0 tattcctcaaGCGCAAATTATTCATgccgaagtga nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [3], [4]


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) Urbanowski ML, Stauffer GV,1989 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: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Cai XY., et al., 1989
[5] Salgado H, et al., 2012
TF binding sites (TFBSs)
[MetJ,-] 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 MetJ-S-adenosyl-L-methionine repressor metRp1 4012877 4012892 -29.5 gccgtccagaTGTTTACACATCCATAattggcggtt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]
remote MetJ-S-adenosyl-L-methionine repressor metRp1 4012992 4013007 -144.5 ttttgaatttAGGGAAGGCGGCAAGTttattcatcc nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]
[MetR,-] 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 MetR-L-homocysteine repressor metRp1 4012815 4012829 34.0 tcatgccgaaGTGAAGGACTTTCATgatcgaagta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [2], [3], [4]
proximal MetR-L-homocysteine repressor metRp1 4012836 4012850 13.0 tattcctcaaGCGCAAATTATTCATgccgaagtga nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [3], [4]
[OxyR,+] 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 OxyR activator metRp1 4012852 4012868 -5.0 taattggcggTTACTGTATATTCCTCAagcgcaaatt nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [6]


Evidence    

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

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

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

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

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

 [EXP-IEP-RNA-SEQ] RNA-seq evidence

 [COMP-HINF] Inferred by a human based on computational evidence

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


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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