RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: trg
Gene(s): trg   Genome Browser M3D Gene expression COLOMBOS
Note(s): The trgp1 and aerp promoters are the only Escherichia coli σ28 promoters that are activated by CRP Hollands K,2010
Evidence: [IC] Inferred by curator
Promoter
Name: trgp
+1: 1492439
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 31
Sequence: tgtgacgcaaagaggtttttggtcataagtaattaccgtcaagtgccgatgactttctatCaggagtaaacctggacgaga
                          -35                -10            +1                   
Note(s): The trg promoter is the only Escherichia coli σ28 promoter that is activated by CRP Hollands K,2010
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [1] Helmann JD., et al., 1987
[2] Hollands K., et al., 2010
[3] Mendoza-Vargas A., et al., 2009
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 activator trgp 1492376 1492397 -52.5 attgttgtaaAAATGTGACGCAAAGAGGTTTTtggtcataag nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [5]
[Fis,+] 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 Fis activator trgp 1492283 1492297 -149.0 gtgctgttttCCAGAATTTTTCGTCattcgggtta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4]
proximal Fis activator trgp 1492372 1492386 -60.0 aataattgttGTAAAAATGTGACGCaaagaggttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4]


Evidence    

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

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

 [EXP-IDA] Inferred from direct assay

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

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


Reference(s)    

 [1] Helmann JD., Chamberlin MJ., 1987, DNA sequence analysis suggests that expression of flagellar and chemotaxis genes in Escherichia coli and Salmonella typhimurium is controlled by an alternative sigma factor., Proc Natl Acad Sci U S A 84(18):6422-4

 [2] Hollands K., Lee DJ., Lloyd GS., Busby SJ., 2010, Activation of sigma 28-dependent transcription in Escherichia coli by the cyclic AMP receptor protein requires an unusual promoter organization., Mol Microbiol 75(5):1098-111

 [3] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [4] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [5] Robison K., McGuire AM., Church GM., 1998, A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome., J Mol Biol 284(2):241-54

RegulonDB