RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: purEK
Synonym(s): OP00112, purE
Gene(s): purK, purE   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Koduri RK., et al., 1980
[2] Meng LM., et al., 1990
[3] Watanabe W., et al., 1989
Promoter
Name: purEp
+1: 553142
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 42
Sequence: gctgatttcacagccacgcaaccgttttccttgctctctttccgtgctattctctgtgccCtctaaagccgagagttgtgc
                               -35                   -10    +1                   
Note(s): 554 promoter regions from Escherichia coli were aligned in order to analyze their sequence similarities. Mitchell et al. (2003) Mitchell JE,2003 focused on conservation, patterns, similarities, and differences between promoters with or without an extended -10 5'-TG-3' element and other conserved elements. They experimentally showed that, for several naturally occurring extended -10 promoters, the 5'-TRTG-3' motif is an important determinant for promoter activity. Eleven promoters were selected for further experimental study. Of those, the seven most active (aroF > ompF > envA > purFp1 > purEF > purMN > gyrA) were investigated for the contribution of the extended -10 motif by changing the 5'-TG-3'. Promoters with poor matches to the -10 and -35 consensus hexamers are more dependent on the 5'-TG-3' motif and this plays a similar role on different promoters. The dinucleotide at -17 and -16 in aroFp results in similar patterns of activity, suggesting that these bases play a similar role on different promoters Mitchell JE,2003.
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [4] He B., et al., 1990
[5] Huerta AM., et al., 2003
[6] Mitchell JE., et al., 2003
[7] Tiedeman AA., et al., 1989
TF binding sites (TFBSs)
[PurR,-] 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 PurR-hypoxanthine repressor purEp 553172 553187 -37.5 tttcacagccACGCAACCGTTTTCCTtgctctcttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [2], [3], [4], [8]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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


Reference(s)    

 [1] Koduri RK., Gots JS., 1980, A DNA-binding protein with specificity for pur genes in Escherichia coli., J Biol Chem 255(20):9594-8

 [2] Meng LM., Kilstrup M., Nygaard P., 1990, Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli., Eur J Biochem 187(2):373-9

 [3] Watanabe W., Sampei G., Aiba A., Mizobuchi K., 1989, Identification and sequence analysis of Escherichia coli purE and purK genes encoding 5'-phosphoribosyl-5-amino-4-imidazole carboxylase for de novo purine biosynthesis., J Bacteriol 171(1):198-204

 [4] He B., Shiau A., Choi KY., Zalkin H., Smith JM., 1990, Genes of the Escherichia coli pur regulon are negatively controlled by a repressor-operator interaction., J Bacteriol 172(8):4555-62

 [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] Mitchell JE., Zheng D., Busby SJ., Minchin SD., 2003, Identification and analysis of 'extended -10' promoters in Escherichia coli., Nucleic Acids Res 31(16):4689-95

 [7] Tiedeman AA., Keyhani J., Kamholz J., Daum HA., Gots JS., Smith JM., 1989, Nucleotide sequence analysis of the purEK operon encoding 5'-phosphoribosyl-5-aminoimidazole carboxylase of Escherichia coli K-12., J Bacteriol 171(1):205-12

 [8] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res 39(15):6456-64

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