RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: glcDEFGBA
Gene(s): glcA, glcB, glcG, glcF, glcE, glcD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Nunez MF., et al., 2001
Promoter
Name: glcDp
+1: 3128076
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 55
Sequence: ggtctgaccggtagctaaagagatagacgaaaacgaaaagcccgcttaataactgttcacAgaagcagcgcgcaaaaatca
                        -35                    -10          +1                   
Evidence: [HIPP]
[ICWHO]
[IHBCE]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Pellicer MT., et al., 1999
TF binding sites (TFBSs)
[ArcA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-phosphorylated repressor glcDp 3128173 3128187 -104.0 tatgttacatCAATTTAACATTGAGttaaccaaga nd [GEA], [AIBSCS], [AIBSPD], [BPP], [CCE] [3], [4]
remote ArcA-phosphorylated repressor glcDp 3128180 3128194 -111.0 aagtgattatGTTACATCAATTTAAcattgagtta nd [GEA], [AIBSPD], [BPP], [CCE] [3]
[GlcC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GlcC-glycolate activator glcDp 3128245 3128259 -176.0 ccggacctcgTGCACAGGTAGGACCaatttttctg nd [GEA], [BCE], [SM] [3]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator glcDp 3128177 3128189 -107.0 attatgttacATCAATTTAACATtgagttaacc nd [GEA], [BCE] [3]
[PdhR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PdhR repressor glcDp 3128124 3128140 -56.0 gctggaaaaaAAATGGTCTGACCGGTAgctaaagaga nd [GEA], [AIBSCS], [BPP] [5]


Transcription unit       
Name: glcBA
Gene(s): glcA, glcB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Promoter
Name: glcBp
+1: Unknown
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [IEP]
Reference(s): [6] Zaslaver A., et al., 2006


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.3 3121354 3121398 ggtagcaattGCGTTAGCGGCGTACTGTTGCTGTAAAGTATAACGCCTATATTTtacagttcag
  anti-terminator -7.72 3121385 3121417 atatacttgtTATGCCAGAGGTAGCAATTGCGTTAGCGGCGTactgttgctg
  anti-anti-terminator -13.51 3121404 3121463 taacgatactCTGCGTCTGCGTGTGCGGAACAGAAACCCTTACCCGATATACTTGTTATGCCAGAGGTAgcaattgcgt
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

 [IHBCE] Inferred by a human based on computational evidence

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [AIBSPD] Automated inference based on sequence pattern discovery

 [BPP] Binding of purified proteins

 [CCE] ChIP-chip evidence

 [BCE] Binding of cellular extracts

 [SM] Site mutation

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Nunez MF., Pellicer MT., Badia J., Aguilar J., Baldoma L., 2001, The gene yghK linked to the glc operon of Escherichia coli encodes a permease for glycolate that is structurally and functionally similar to L-lactate permease., Microbiology 147(Pt 4):1069-77

 [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] Pellicer MT., Fernandez C., Badia J., Aguilar J., Lin EC., Baldom L., 1999, Cross-induction of glc and ace operons of Escherichia coli attributable to pathway intersection. Characterization of the glc promoter., J Biol Chem 274(3):1745-52

 [4] Liu X., De Wulf P., 2004, Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling., J Biol Chem 279(13):12588-97

 [5] Gohler AK., Kokpinar O., Schmidt-Heck W., Geffers R., Guthke R., Rinas U., Schuster S., Jahreis K., Kaleta C., 2011, More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli., BMC Syst Biol 5(1):197

 [6] 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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