RegulonDB RegulonDB 10.7: Operon Form
   

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




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


Transcription unit       
Name: idnR
Gene(s): idnR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The idnR gene is the last of the idnDOTR operon. The whole operon is transcribed from a single promoter. However, most of the expression of idnR comes from its own internal promoter, idnRp, which is constitutive.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bausch C., et al., 2004
[2] Tsunedomi R., et al., 2003
Promoter
Name: idnRp
+1: 4491182
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 43
Sequence: gctgggcgtgttagccattaacgccgtattgcactgaaagaataaaatattgtgatgtagTttcgggggaagattgaagat
                             -35                   -10      +1                   
Note(s): A possible promoter, TTGCACX16TGTGAT, corresponding to -35 and -10 sequences, exists at position
48 upstream of the initiation codon (Tsunedomi Y, 2003).
Evidence: [AIPP]
Reference(s): [2] Tsunedomi R., et al., 2003


Transcription unit          
Name: idnDOTR
Synonym(s): idnD
Gene(s): idnR, idnT, idnO, idnD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The idnR gene is the last of the idnDOTR operon. The whole operon is transcribed from a single promoter. However, most of the expression of idnR comes from its own internal promoter, idnRp, which is constitutive.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bausch C., et al., 2004
Promoter
Name: idnDp
+1: 4494435
Distance from start of the gene: 29
Sequence: caattttctgacgtgatcttcatcacaaataatgacagttaaaaccgcttaaatgcttccGaggtgtctacctgaccagtg
Evidence: [TIM]
Reference(s): [1] Bausch C., et al., 2004
[3] Tsunedomi R., et al., 2003
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator idnDp 4494466 4494488 -41.5 taacaattttCTGACGTGATCTTCATCACAAATaatgacagtt nd [AIBSCS], [APIORCISFBSCS], [GEA] [1], [3], [5], [7]
proximal CRP-cAMP activator idnDp 4494516 4494537 -91.5 tactgataagAATTACAAGGCACATCACGTTAtgcgtaacat nd [APIORCISFBSCS], [GEA] [1], [3], [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GntR repressor idnDp 4494484 4494503 -58.5 cgtaacatagTAATGTAACAATTTTCTGACgtgatcttca nd [APIORCISFBSCS], [GEA] [3]
proximal GntR repressor idnDp 4494504 4494523 -78.5 acaaggcacaTCACGTTATGCGTAACATAGtaatgtaaca nd [AIBSCS], [APIORCISFBSCS], [GEA] [3], [4], [5]
remote GntR repressor idnDp 4494534 4494553 -108.5 cacgttttttTATTTCTACTGATAAGAATTacaaggcaca nd [AIBSCS], [APIORCISFBSCS], [GEA] [3], [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IdnR-5-ketogluconate activator idnDp 4494506 4494521 -78.5 aaggcacatcACGTTATGCGTAACATagtaatgtaa nd [AIBSCS], [GEA] [1], [3], [6]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [8] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.4 4492549 4492572 ccccctacgtGCAGCGCGAAAGCGCTGCTTTTCtggcactaat
  terminator -16.1 4491149 4491185 tattgtgatgTAGTTTCGGGGGAAGATTGAAGATTCCCCCGACGTTgggagaagtt
  anti-terminator -18.2 4492565 4492611 tgtttgttgaTGGCGGCATGTTAGTGGCTGTTTAACAGCCCCCCTACGTGCAGCGCgaaagcgctg
  anti-anti-terminator -19.71 4492588 4492636 tctgatttcgTAAACGGCCACCTGTTGTTTGTTGATGGCGGCATGTTAGTGGCTGTTTaacagccccc
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"




Reference(s)    

 [1] Bausch C., Ramsey M., Conway T., 2004, Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli., J Bacteriol 186(5):1388-97

 [2] Tsunedomi R., Izu H., Kawai T., Matsushita K., Ferenci T., Yamada M., 2003, The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli., J Bacteriol 185(6):1783-95

 [3] Tsunedomi R., Izu H., Kawai T., Yamada M., 2003, Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli., J Mol Microbiol Biotechnol 6(1):41-56

 [4] Suvorova IA., Korostelev YD., Gelfand MS., 2015, GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution., PLoS One 10(7):e0132618

 [5] Rodionov DA., Mironov AA., Rakhmaninova AB., Gelfand MS., 2000, Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria., Mol Microbiol 38(4):673-83

 [6] Bausch C., Peekhaus N., Utz C., Blais T., Murray E., Lowary T., Conway T., 1998, Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli., J Bacteriol 180(14):3704-10

 [7] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

 [8] 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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