RegulonDB RegulonDB 10.6.3: Operon Form
   

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




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


Transcription unit          
Name: pdeR
Synonym(s): gmr
Gene(s): pdeR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pdeRp
+1: 1346843
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 101
Sequence: tttttaactgactttcgtttgaaaactggcgtttttccaaaactggattacaaataaataTataaaaaaaacaatgcgttt
                          -10               -35             +1                   
Note(s): There were identified two 5' ends of the gmr gene, one of them corresponds to this promoter but there is no a reasonable promoter sequence upstream of the other 5' end.
Evidence: [HIPP]
[TIM]
Reference(s): [1] Cairrao F., et al., 2001
TF binding sites (TFBSs)
[FliZ,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FliZ1 repressor pdeRp 1346857 1346905 -37.5 atccaggcagATTTTTTAACTGACTTTCGTTTGAAAACTGGCGTTTTTCCAAAACTGGAttacaaataa nd [BPP], [GEA], [SM] [2], [3]
[RutR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RutR repressor pdeRp nd nd nd nd nd [GEA] [4]
Note(s): 1No DNA consensus sequence that is recognized by FliZ has been established. Therefore, for this DNA-binding site we added the complete region, determined by footprinting analysis Pesavento C,2012 to which FliZ binds.1No DNA consensus sequence that is recognized by FliZ has been established. Therefore, for this DNA-binding site we added the complete region, determined by footprinting analysis Pesavento C,2012 to which FliZ binds.


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [5] null null
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.9 1346936 1346968 atctcctttcACGGCCCATTCCTCATGGATGGGCCGTTTATTtccccgctct
  anti-terminator -12.69 1346957 1347014 aagtccgcatGGAAACCCGCAGCATTATTGCGCGCCCGGTCGCGTAATCTCCTTTCACGGCCCATTCctcatggatg
  anti-anti-terminator -8.9 1347014 1347043 gactgacgttATTGACGTCACTATTGCCGAAGTCCGCATggaaacccgc
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    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [1] Cairrao F., Chora A., Zilhao R., Carpousis AJ., Arraiano CM., 2001, RNase II levels change according to the growth conditions: characterization of gmr, a new Escherichia coli gene involved in the modulation of RNase II., Mol Microbiol 39(6):1550-61

 [2] Pesavento C., Becker G., Sommerfeldt N., Possling A., Tschowri N., Mehlis A., Hengge R., 2008, Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli., Genes Dev 22(17):2434-46

 [3] Pesavento C., Hengge R., 2012, The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity., Nucleic Acids Res 40(11):4783-93

 [4] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol 66(3):744-57

 [5] null, null, null, null


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