RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: trxA
Gene(s): trxA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Matsumoto Y., et al., 1986
Promoter
Name: trxAp1
+1: 3965647
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 114
Sequence: gcgaagtcggaaaacttctgttctgttaaatgtgttttgctcatagtgtggtagaatatcAgcttactattgctttacgaa
                       -10-35                               +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Aldea M., et al., 1988
[1] Matsumoto Y., et al., 1986
Terminator(s)
Type: rho-independent
Sequence: atttcatgttCGGGTGCCCCGTCGCTAAAAACTGGACGCCCGgcgtgagtca
Reference(s): [1] Matsumoto Y., et al., 1986
TF binding sites (TFBSs)
[CRP,-] 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 CRP-cyclic-AMP repressor trxAp1 3965613 3965634 -23.5 tctgttctgtTAAATGTGTTTTGCTCATAGTGtggtagaata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation trxAp1 nd   [EXP-IMP] [4]
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [4] Lim CJ., et al., 2000


Transcription unit       
Name: trxA
Gene(s): trxA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Matsumoto Y., et al., 1986
Promoter
Name: trxAp3
+1: 3965650
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 111
Sequence: aagtcggaaaacttctgttctgttaaatgtgttttgctcatagtgtggtagaatatcagcTtactattgctttacgaaagc
                       -35                       -10        +1                   
Note(s): This promoter was not identified in the analysis of transcription initiation mapping of trxA done by Matsumoto et al. Matsumoto Y,1986.
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [5] Horn M., et al., 1985
[6] MacLean DB. 1985
[1] Matsumoto Y., et al., 1986
[7] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: atttcatgttCGGGTGCCCCGTCGCTAAAAACTGGACGCCCGgcgtgagtca
Reference(s): [1] Matsumoto Y., et al., 1986


Transcription unit       
Name: trxA
Gene(s): trxA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Matsumoto Y., et al., 1986
Promoter
Name: trxAp2
+1: 3965687
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 74
Sequence: tcatagtgtggtagaatatcagcttactattgctttacgaaagcgtatccggtgaaataaAgtcaacctttagttggttaa
                              -35                    -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Aldea M., et al., 1988
[8] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: atttcatgttCGGGTGCCCCGTCGCTAAAAACTGGACGCCCGgcgtgagtca
Reference(s): [1] Matsumoto Y., et al., 1986
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation trxAp2 nd   [EXP-IMP] [4]
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [4] Lim CJ., et al., 2000


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

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

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


Reference(s)    

 [1] Matsumoto Y., Shigesada K., Hirano M., Imai M., 1986, Autogenous regulation of the gene for transcription termination factor rho in Escherichia coli: localization and function of its attenuators., J Bacteriol 166(3):945-58

 [2] Aldea M., Claverie-Martin F., Diaz-Torres MR., Kushner SR., 1988, Transcript mapping using [35S]DNA probes, trichloroacetate solvent and dideoxy sequencing ladders: a rapid method for identification of transcriptional start points., Gene 65(1):101-10

 [3] Sa JH., Namgung MA., Lim CJ., Fuchs JA., 1997, Expression of the Escherichia coli thioredoxin gene is negatively regulated by cyclic AMP., Biochem Biophys Res Commun 234(3):564-7

 [4] Lim CJ., Daws T., Gerami-Nejad M., Fuchs JA., 2000, Growth-phase regulation of the Escherichia coli thioredoxin gene., Biochim Biophys Acta 1491(1-3):1-6

 [5] Horn M., Witztum K., Neveu C., Perkins G., Walsh B., 1985, Krypton-81m imaging of the right ventricle., J Nucl Med 26(1):33-6

 [6] MacLean DB., 1985, Abrogation of peripheral cholecystokinin-satiety in the capsaicin treated rat., Regul Pept 11(4):321-33

 [7] 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.

 [8] 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

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