RegulonDB RegulonDB 11.1: Operon Form
   

upp-uraA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: upp-uraA
Gene(s): uraA, upp   Genome Browser M3D Gene expression COLOMBOS
Note(s): This operon is regulated by pyrimidine-mediated reiterative transcription. There is a putative internal terminator between upp and uraA.
The intergenic region of upp-purMN protects against bacterial cell death via both type I and type II covalent topoisomerase-DNA cleavage complexes Liu IF,2011 Deletion of the binding site for FNR and PurR from the intergenic region of upp-purMN decreases the protective effect, inducing lethality via titration Liu IF,2011
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Andersen PS., et al., 1995
[2] Tu AH., et al., 1997
Promoter
Name: uppp
+1: 2620909
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 37
Sequence: ttttgactaaagtcaacgaaaagaatattgccgccttgaagaaaggaggtataatccgtcGattttttttgtggctgcccc
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Andersen PS., et al., 1992
[4] Cheng Y., et al., 2001
[5] Huerta AM., et al., 2003
[6] Imashimizu M., et al., 2020
[2] Tu AH., et al., 1997
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator uppp 2620964 2620977 -61.5 tatctcaaacCGTTATCATTTTGActaaagtcaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA] Inferred from direct assay

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

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

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


Reference(s)    

 [1] Andersen PS., Frees D., Fast R., Mygind B., 1995, Uracil uptake in Escherichia coli K-12: isolation of uraA mutants and cloning of the gene., J Bacteriol 177(8):2008-13

 [2] Tu AH., Turnbough CL., 1997, Regulation of upp expression in Escherichia coli by UTP-sensitive selection of transcriptional start sites coupled with UTP-dependent reiterative transcription., J Bacteriol 179(21):6665-73

 [3] Andersen PS., Smith JM., Mygind B., 1992, Characterization of the upp gene encoding uracil phosphoribosyltransferase of Escherichia coli K12., Eur J Biochem 204(1):51-6

 [4] Cheng Y., Dylla SM., Turnbough CL., 2001, A long T. A tract in the upp initially transcribed region is required for regulation of upp expression by UTP-dependent reiterative transcription in Escherichia coli., J Bacteriol 183(1):221-8

 [5] 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

 [6] Imashimizu M., Tokunaga Y., Afek A., Takahashi H., Shimamoto N., Lukatsky DB., 2020, Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences., Biomolecules 10(9)

 [7] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

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