RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: treR
Gene(s): treR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Horlacher R., et al., 1997
Promoter
Name: treRp1
+1: 4467271
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 25
Sequence: aacgataaaccagactttacccattgctgaatgcacgggtaacgttaggctcaaataattAaacaacacgttacaggacaa
                                -35                        -+1                   
Note(s): This promoter has other transcription start sites, but position -25 is the strongest.
A σ32-dependent promoter was suggested to be located upstream of treR Wade JT,2006, but it is unknown whether one of the four promoters transcribing the gene (treRp1, treRp2, treRp3, and treRp4) is the same as the σ32 promoter. An overlapping of σ factors, σ32/σ70, has been observed in some promoters Wade JT,2006.
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Horlacher R., et al., 1997
[2] Huerta AM., et al., 2003
[3] Yamamoto K., et al., 2002
Terminator(s)
Type: rho-independent
Sequence: tcacaatttaTCGTTCAGGAAACGAtcaggacagg
Reference(s): [1] Horlacher R., et al., 1997


Transcription unit       
Name: treR
Gene(s): treR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Horlacher R., et al., 1997
Promoter
Name: treRp2
+1: 4467275
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: aaccaacgataaaccagactttacccattgctgaatgcacgggtaacgttaggctcaaatAattaaacaacacgttacagg
                                 -35                   -10  +1                   
Note(s): A σ32-dependent promoter was suggested to be located upstream of treR Wade JT,2006, but it is unknown whether one of the four promoters transcribing the gene (treRp1, treRp2, treRp3, and treRp4) is the same as the σ32 promoter. An overlapping of sigma factors, σ32/σ70, was observed in some promoters Wade JT,2006.
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Horlacher R., et al., 1997
[2] Huerta AM., et al., 2003
[3] Yamamoto K., et al., 2002
Terminator(s)
Type: rho-independent
Sequence: tcacaatttaTCGTTCAGGAAACGAtcaggacagg
Reference(s): [1] Horlacher R., et al., 1997


Transcription unit          
Name: treR
Gene(s): treR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Horlacher R., et al., 1997
Promoter
Name: treRp3
+1: 4467279
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 33
Sequence: actaaaccaacgataaaccagactttacccattgctgaatgcacgggtaacgttaggctcAaataattaaacaacacgtta
Note(s): A σ32-dependent promoter was suggested to be located upstream of treR Wade JT,2006, but it is unknown whether one of the four promoters transcribing the gene (treRp1, treRp2, treRp3, and treRp4) is the same as the σ32 promoter. An overlapping of sigma factors, σ32/σ70, has been observed in some promoters Wade JT,2006.
Evidence: [EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Horlacher R., et al., 1997
[3] Yamamoto K., et al., 2002
Terminator(s)
Type: rho-independent
Sequence: tcacaatttaTCGTTCAGGAAACGAtcaggacagg
Reference(s): [1] Horlacher R., et al., 1997
TF binding sites (TFBSs)
[PhoP,-] 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 PhoP-phosphorylated repressor treRp3 4467321 4467337 -50.0 tgctgacaacTAAACCAACGATAAACCagactttacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [4]


Transcription unit          
Name: treR
Gene(s): treR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Horlacher R., et al., 1997
Promoter
Name: treRp4
+1: 4467347
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 101
Sequence: gcgccgcaaataataaggagaatccaataatattcgtagcatctatggcgatataataccTgctgacaactaaaccaacga
                                -35                      -10+1                   
Note(s): A σ32-dependent promoter was suggested to be located upstream of treR Wade JT,2006, but it is unknown whether one of the four promoters transcribing the gene (treRp1, treRp2, treRp3, or treRp4) is the same as the σ32 promoter. An overlapping of sigma factors, σ32/σ70, has been observed in some promoters Wade JT,2006.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Huerta AM., et al., 2003
[3] Yamamoto K., et al., 2002
Terminator(s)
Type: rho-independent
Sequence: tcacaatttaTCGTTCAGGAAACGAtcaggacagg
Reference(s): [1] Horlacher R., et al., 1997
TF binding sites (TFBSs)
[PhoP,-] 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 PhoP-phosphorylated repressor treRp4 4467321 4467337 19.0 tgctgacaacTAAACCAACGATAAACCagactttacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA] Inferred from direct assay

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

 [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.

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IMP] Inferred from mutant phenotype


Reference(s)    

 [1] Horlacher R., Boos W., 1997, Characterization of TreR, the major regulator of the Escherichia coli trehalose system., J Biol Chem 272(20):13026-32

 [2] 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

 [3] Yamamoto K., Ogasawara H., Fujita N., Utsumi R., Ishihama A., 2002, Novel mode of transcription regulation of divergently overlapping promoters by PhoP, the regulator of two-component system sensing external magnesium availability., Mol Microbiol 45(2):423-38

 [4] Minagawa S., Ogasawara H., Kato A., Yamamoto K., Eguchi Y., Oshima T., Mori H., Ishihama A., Utsumi R., 2003, Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli., J Bacteriol 185(13):3696-702

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