RegulonDB RegulonDB 11.1: Operon Form
   

tyrTV-tpr operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: tyrTV-tpr
Synonym(s): tyrT
Gene(s): tpr, tyrV, tyrT   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] Ow MC., et al., 2002
Promoter
Name: tyrTp
+1: 1287665
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 43
Sequence: cagttcatttttctcaacgtaacactttacagcggcgcgtcatttgatatgatgcgccccGcttcccgataagggagcagg
                               -35                   -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Auner H., et al., 2003
[3] Huerta AM., et al., 2003
[4] Lazarus LR., et al., 1993
[5] Maciag A., et al., 2011
[6] Muskhelishvili G., et al., 1997
[7] Pemberton IK., et al., 2002
Terminator(s)
Type: rho-dependent
Sequence: ccttccccgcATGGGCAGAATATTTGATTGCGGATtcgcttgaga
Reference(s): [8] Rossi J., 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
proximal Fis activator tyrTp 1287736 1287750 -78.0 tacctttaatCCGTTACGGATGAAAattacgcaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [4], [9], [10]
remote Fis activator tyrTp 1287756 1287770 -98.0 cgccagcaaaAATAACTGGTTACCTttaatccgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [4], [9], [10]
remote Fis activator tyrTp 1287787 1287801 -129.0 gtttacggtaATCGAACGATTATTCtttaatcgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [4], [9], [10]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition tyrTp nd   [EXP-IEP] [11]
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [11] Travers AA., et al., 1983


Transcription unit       
Name: tyrV-tpr
Gene(s): tpr, tyrV   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: tyrVp
+1: Unknown
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [EXP-IEP]
Reference(s): [12] Zaslaver A., et al., 2006
Terminator(s)
Type: rho-dependent
Sequence: ccttccccgcATGGGCAGAATATTTGATTGCGGATtcgcttgaga
Reference(s): [8] Rossi J., et al., 1981


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

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

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

 [EXP-IMP] Inferred from mutant phenotype

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

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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

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

 [EXP-IEP] Inferred from expression pattern


Reference(s)    

 [1] Ow MC., Kushner SR., 2002, Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli., Genes Dev 16(9):1102-15

 [2] Auner H., Buckle M., Deufel A., Kutateladze T., Lazarus L., Mavathur R., Muskhelishvili G., Pemberton I., Schneider R., Travers A., 2003, Mechanism of transcriptional activation by FIS: role of core promoter structure and DNA topology., J Mol Biol 331(2):331-44

 [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] Lazarus LR., Travers AA., 1993, The Escherichia coli FIS protein is not required for the activation of tyrT transcription on entry into exponential growth., EMBO J 12(6):2483-94

 [5] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [6] Muskhelishvili G., Buckle M., Heumann H., Kahmann R., Travers AA., 1997, FIS activates sequential steps during transcription initiation at a stable RNA promoter., EMBO J 16(12):3655-65

 [7] Pemberton IK., Muskhelishvili G., Travers AA., Buckle M., 2002, FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter., J Mol Biol 318(3):651-63

 [8] Rossi J., Egan J., Hudson L., Landy A., 1981, The tyrT locus: termination and processing of a complex transcript., Cell 26(3 Pt 1):305-14

 [9] Li S., Waters R., 1997, Induction and repair of cyclobutane pyrimidine dimers in the Escherichia coli tRNA gene tyrT: Fis protein affects dimer induction in the control region and suppresses preferential repair in the coding region of the transcribed strand, except in a short region near the transcription start site., J Mol Biol 271(1):31-46

 [10] Travers A., Schneider R., Muskhelishvili G., 2001, DNA supercoiling and transcription in Escherichia coli: The FIS connection., Biochimie 83(2):213-7

 [11] Travers AA., Lamond AI., Mace HA., Berman ML., 1983, RNA polymerase interactions with the upstream region of the E. coli tyrT promoter., Cell 35(1):265-73

 [12] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

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