RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: trpR
Gene(s): trpR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the trpR gene is repressed threefold by the TrpR protein. This protein binds around the transcriptional start site of trpR. Therefore, TrpR could minimally block the transcription initiation because the RNA polymerase could not bind to the promoterKlig LS,1988
The trpLEDCBA, aroH, and trpR operons are coordinately regulated by the TrpR transcriptional repressor in response to intracellular levels of L-tryptophan (Kumamoto AA,1987and references therein). TrpR acts differently at each operator and binds to multiple helically stacked sites Kumamoto AA,1987
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gunsalus RP., et al., 1980
Promoter
Name: trpRp
+1: 4632704
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 56
Sequence: gccacggaatggggacgtcgttactgatccgcacgtttatgatatgctatcgtactctttAgcgagtacaaccgggggagg
                     -35                        -10         +1                   
Note(s): trpRp is regulated over a four- to fivefold range by TrpR Kumamoto AA,1987and references therein|.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Gunsalus RP., et al., 1980
[2] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: taagacgtggCGCATCAGGCATCGTGCACCGAATGCCGGATGCGgcgtgaacgc
Reference(s): [1] Gunsalus RP., et al., 1980
TF binding sites (TFBSs)
[TrpR,-] 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 TrpR-L-tryptophan repressor trpRp 4632695 4632712 -0.5 atatgctatcGTACTCTTTAGCGAGTACaaccggggga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3], [4], [5], [6], [7]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

 [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


Reference(s)    

 [1] Gunsalus RP., Yanofsky C., 1980, Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor., Proc Natl Acad Sci U S A 77(12):7117-21

 [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] Jeeves M., Evans PD., Parslow RA., Jaseja M., Hyde EI., 1999, Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences., Eur J Biochem 265(3):919-28

 [4] Klig LS., Carey J., Yanofsky C., 1988, trp repressor interactions with the trp aroH and trpR operators. Comparison of repressor binding in vitro and repression in vivo., J Mol Biol 202(4):769-77

 [5] Kumamoto AA., Miller WG., Gunsalus RP., 1987, Escherichia coli tryptophan repressor binds multiple sites within the aroH and trp operators., Genes Dev 1(6):556-64

 [6] Shimamoto N., Toda M., Nara S., Komatsuzaki T., Kamagata K., Kinebuchi T., Tomizawa JI., 2020, Dependence of DNA length on binding affinity between TrpR and trpO of DNA., Sci Rep 10(1):15624

 [7] Yang J., Gunasekera A., Lavoie TA., Jin L., Lewis DE., Carey J., 1996, In vivo and in vitro studies of TrpR-DNA interactions., J Mol Biol 258(1):37-52

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