RegulonDB RegulonDB 10.10: 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
                          -35               -10             +1                   
Evidence: [HIPP]
[ICWHO]
[IEP]
[TIM]
Reference(s): [1] Cairrao F., et al., 2001
[2] Huerta AM., et al., 2003
[3] Sommerfeldt N., et al., 2009
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 FliZ repressor pdeRp 1346857 1346905 -37.5 atccaggcagATTTTTTAACTGACTTTCGTTTGAAAACTGGCGTTTTTCCAAAACTGGAttacaaataa nd [GEA], [BPP], [SM] [4], [5]
[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], [BPP] [6]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [7] Merino E, et al., 2005
  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

 [ICWHO] Inferred computationally without human oversight

 [IEP] Inferred from expression pattern

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [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] 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

 [3] Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N., Hengge R., 2009, Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli., Microbiology 155(Pt 4):1318-31

 [4] 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

 [5] 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

 [6] 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

 [7] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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