RegulonDB RegulonDB 10.10: Operon Form
   

cvpA-purF-ubiX operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: cvpA-purF-ubiX
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: cvpA-purF-ubiX
Gene(s): ubiX, purF, cvpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PM] Polar mutation
Reference(s): [1] Makaroff CA., et al., 1985
Promoter
Name: cvpAp2
+1: 2430770
Distance from start of the gene: 7
Sequence:
Evidence: [HTTIM]
[TIM]
Reference(s): [2] Maciag A., et al., 2011
[1] Makaroff CA., et al., 1985
Terminator(s)
Type: rho-independent
Sequence: ggttgcaaaaTTGCCCTGAAACAGGGCAAcagcggagtt
Reference(s): [3] Nonet ML., et al., 1987


Transcription unit          
Name: cvpA-purF-ubiX
Gene(s): ubiX, purF, cvpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [4] Meng LM., et al., 1990
Promoter
Name: cvpAp1
+1: 2430800
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 37
Sequence: attgatgcgcgggaaggaaatccctacgcaaacgttttctttttctgttagaatgcgcccCgaacaggatgacagggcgta
                        -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 about 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: [HIPP]
[HTTIM]
[ICWHO]
[IHBCE]
[TIM]
Reference(s): [5] Huerta AM., et al., 2003
[2] Maciag A., et al., 2011
[1] Makaroff CA., et al., 1985
[3] Nonet ML., et al., 1987
Terminator(s)
Type: rho-independent
Sequence: ggttgcaaaaTTGCCCTGAAACAGGGCAAcagcggagtt
Reference(s): [3] Nonet ML., et al., 1987
TF binding sites (TFBSs)
[PurR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PurR-hypoxanthine repressor cvpAp1 2430821 2430836 -28.5 aggaaatcccTACGCAAACGTTTTCTttttctgtta nd [GEA], [APIORCISFBSCS], [BCE], [BPP], [SM] [4], [6], [7], [8], [9]


Transcription unit       
Name: ubiX
Gene(s): ubiX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [10] Zaslaver A., et al., 2006
Promoter
Name: ubiXp
+1: Unknown
Evidence: [IEP]
Reference(s): [10] Zaslaver A., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: ggttgcaaaaTTGCCCTGAAACAGGGCAAcagcggagtt
Reference(s): [3] Nonet ML., et al., 1987


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.3 2430858 2430893 ataaaaagtcGATGGCGTTGAATATTTTTTCAGCGCCATTTTTATtgatgcgcgg
  terminator -7.6 2428631 2428659 aatcctgcaaAGTCTGCCTGCAAGTCTGACAGGGCAACtatttatgaa
  anti-terminator -10.7 2430887 2430927 gcatccgacaCGCATTGCCCGATGCCGCAAAGGCATAAAAAGTCGATGGCgttgaatatt
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [HTTIM] High-throughput transcription initiation mapping

 [TIM] Transcription initiation mapping

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IHBCE] Inferred by a human based on computational evidence

 [GEA] Gene expression analysis

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Makaroff CA., Zalkin H., 1985, Regulation of Escherichia coli purF. Analysis of the control region of a pur regulon gene., J Biol Chem 260(18):10378-87

 [2] 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

 [3] Nonet ML., Marvel CC., Tolan DR., 1987, The hisT-purF region of the Escherichia coli K-12 chromosome. Identification of additional genes of the hisT and purF operons., J Biol Chem 262(25):12209-17

 [4] 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

 [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] 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

 [7] 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

 [8] Rolfes RJ., Zalkin H., 1988, Regulation of Escherichia coli purF. Mutations that define the promoter, operator, and purine repressor gene., J Biol Chem 263(36):19649-52

 [9] Rolfes RJ., Zalkin H., 1988, Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator., J Biol Chem 263(36):19653-61

 [10] 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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