RegulonDB RegulonDB 11.2: Operon Form
   

thrU-tyrU-glyT-thrT-tufB operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: thrU-tyrU-glyT-thrT-tufB
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: thrU-tyrU-glyT-thrT-tufB
Synonym(s): thrU
Gene(s): thrU, tyrU, glyT, thrT, tufB   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for tufB. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Lee JS., et al., 1981
[2] van Delft JH., et al., 1987
Promoter
Name: thrUp
+1: 4175381
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 7
Sequence: aaaacaaattatgcaattttttagttgcatgaactcgcatgtctccatagaatgcgcgctActtgatgccgacttagctca
                         -35                    -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IMP]
Reference(s): [3] Huerta AM., et al., 2003
[1] Lee JS., et al., 1981
[4] Mizushima-Sugano J., et al., 1985
Terminator(s)
Type: rho-independent
Sequence: caatgcgcacTAAAAGGGCATCATTTGATGCCCTTTTTgcacgctttc
Reference(s): [5] Fournier MJ., et al., 1985
[6] Hudson L., et al., 1981
TF binding sites (TFBSs)
[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 thrUp 4175251 4175265 -123.0 gcacaatgatGTTGAAAAAGTGTGCtaatctgccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [7], [8]
proximal Fis activator thrUp 4175283 4175297 -91.0 ccctccgttcGGCTGTTTCTTCATCgtgtcgcata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [7], [8]
proximal Fis activator thrUp 4175303 4175317 -71.0 tcatcgtgtcGCATAAAATGTGACCaataaaacaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [7], [8], [9]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition thrUp nd   [EXP-IEP]
[EXP-IMP] 		[4]
Evidence: [EXP-IEP] Inferred from expression pattern
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [4] Mizushima-Sugano J., et al., 1985


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IMP] Inferred from mutant phenotype

 [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-CHIP-SEQ] high throughput ChIP-seq evidence

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

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

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence


Reference(s)    

 [1] Lee JS., An G., Friesen JD., Fill NP., 1981, Location of the tufB promoter of E. coli: cotranscription of tufB with four transfer RNA genes., Cell 25(1):251-8

 [2] van Delft JH., Marinon B., Schmidt DS., Bosch L., 1987, Transcription of the tRNA-tufB operon of Escherichia coli: activation, termination and antitermination., Nucleic Acids Res 15(22):9515-30

 [3] 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

 [4] Mizushima-Sugano J., Kaziro Y., 1985, Regulation of the expression of the tufB operon: DNA sequences directly involved in the stringent control., EMBO J 4(4):1053-8

 [5] Fournier MJ., Ozeki H., 1985, Structure and organization of the transfer ribonucleic acid genes of Escherichia coli K-12., Microbiol Rev 49(4):379-97

 [6] Hudson L., Rossi J., Landy A., 1981, Dual function transcripts specifying tRNA and mRNA., Nature 294(5840):422-7

 [7] Nilsson L., Vanet A., Vijgenboom E., Bosch L., 1990, The role of FIS in trans activation of stable RNA operons of E. coli., EMBO J 9(3):727-34

 [8] Verbeek H., Nilsson L., Baliko G., Bosch L., 1990, Potential binding sites of the trans-activator FIS are present upstream of all rRNA operons and of many but not all tRNA operons., Biochim Biophys Acta 1050(1-3):302-6

 [9] Bosch L., Nilsson L., Vijgenboom E., Verbeek H., 1990, FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli., Biochim Biophys Acta 1050(1-3):293-301

RegulonDB