RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: purMN
Synonym(s): OP00080, purM
Gene(s): purM, purN   Genome Browser M3D Gene expression COLOMBOS
Note(s): 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
Based on DNA microarray analysis, the mechanism of bacterial inactivation by carvacrol and citral was studied Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. Treatment by both compounds caused membrane damage and activated metabolism through the production of nucleotides required for DNA and RNA synthesis and metabolic processes Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. A total of 76 and 156 genes demonstrated significant transcriptional differences by carvacrol and citral, respectively. Genes upregulated by carvacrol treatment included the multidrug efflux pump genes acrA and mdtM, genes related to the phage shock response, pspA, pspB, pspC, pspD, pspF, and pspG, and genes whose products are important for biosynthesis of arginine (argC, argG, artJ) and purine nucleotides (purC, purM). Genes upregulated by citral treatment included purH, pyrB, and pyrI. On the other hand, mutations in several differentially expressed genes confirmed the roles of ygaV, yjbO, pspC, sdhA, yejG, and ygaV in mechanisms of inactivation by carvacrol and citral Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017.
Reference(s): [1] Andersen PS., et al., 1992
[2] Smith JM., et al., 1987
[3] Watanabe W., et al., 1989
Promoter
Name: purMp
+1: 2621153
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 44
Sequence: tgcaaaaaggttgtgtaaagcagtctcgcaaacgtttgctttccctgttagaattgcgccGaattttatttttctaccgca
                         -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 ?-6 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]
Reference(s): [4] He B., et al., 1990
[5] Huerta AM., et al., 2003
[6] Smith JM., et al., 1986
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
remote FNR repressor purMp 2620954 2620967 -192.5 attcttttcgTTGACTTTAGTCAAaatgataacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [7], [8]
[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 purMp 2621118 2621134 -27.5 taaagcagtcTCGCAAACGTTTGCTTTccctgttaga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IMP-SITE-MUTATION] C [6], [7], [9], [10]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [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

 [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-IMP-SITE-MUTATION] Site mutation

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


Reference(s)    

 [1] 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

 [2] Smith JM., Daum HA., 1987, Identification and nucleotide sequence of a gene encoding 5'-phosphoribosylglycinamide transformylase in Escherichia coli K12., J Biol Chem 262(22):10565-9

 [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] Smith JM., Daum HA., 1986, Nucleotide sequence of the purM gene encoding 5'-phosphoribosyl-5-aminoimidazole synthetase of Escherichia coli K12., J Biol Chem 261(23):10632-6

 [7] Liu IF., Aedo S., Tse-Dinh YC., 2011, Resistance to topoisomerase cleavage complex induced lethality in Escherichia coli via titration of transcription regulators PurR and FNR., BMC Microbiol 11:261

 [8] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [9] 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

 [10] 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

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