RegulonDB RegulonDB 11.2: Operon Form
   

edd-eda operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: eda
Gene(s): eda   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the eda gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in a mutant of the transcriptional regulator Fur. However, it is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Egan SE., et al., 1992
Promoter
Name: edap3
+1: 1932784
Distance from start of the gene: 28
Sequence: gcgtgaaaaactgtccggtgccgaacagggcgcaacctgtatcactttttaagacgacaaAtttgtaatcaggcgagagaa
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Egan SE., et al., 1992
[2] Murray EL., et al., 2005
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gctacaaaaaTGCCCGATCCTCGATCGGGCAttttgacttt
Reference(s): [1] Egan SE., et al., 1992
TF binding sites (TFBSs)
[PhoB,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PhoB-phosphorylated repressor edap3 1932827 1932848 -53.0 ttattcagcgCCTTGCGTGAAAAACTGTCCGGtgccgaacag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]


Transcription unit       
Name: eda
Gene(s): eda   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the eda gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in a mutant of the transcriptional regulator Fur. However, it is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Egan SE., et al., 1992
Promoter
Name: edap2
+1: 1932799
Distance from start of the gene: 43
Sequence: attattcagcgccttgcgtgaaaaactgtccggtgccgaacagggcgcaacctgtatcacTttttaagacgacaaatttgt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Egan SE., et al., 1992
Terminator(s)
Type: rho-independent
Sequence: gctacaaaaaTGCCCGATCCTCGATCGGGCAttttgacttt
Reference(s): [1] Egan SE., et al., 1992


Transcription unit          
Name: eda
Gene(s): eda   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the eda gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in a mutant of the transcriptional regulator Fur. However, it is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Egan SE., et al., 1992
Promoter
Name: edap1
+1: 1933109
Distance from start of the gene: 353
Sequence: caaaagcgaacggaatgccagaattacataaactcatgccgccacttggtgtattattggAccggtgtttcaaaattgcgt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Egan SE., et al., 1992
[2] Murray EL., et al., 2005
Terminator(s)
Type: rho-independent
Sequence: gctacaaaaaTGCCCGATCCTCGATCGGGCAttttgacttt
Reference(s): [1] Egan SE., et al., 1992
TF binding sites (TFBSs)
[KdgR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal KdgR repressor edap1 1933095 1933115 5.0 cttggtgtatTATTGGACCGGTGTTTCAAAAttgcgttagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]


Transcription unit          
Name: edd-eda
Synonym(s): OP00322
Gene(s): eda, edd   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the operon edd-eda is increased under acidic growth conditions in microaerobiosis Marzan LW,2013
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for edd . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Egan SE., et al., 1992
Promoter
Name: eddp
+1: 1934713
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 109
Sequence: ttttacactttcaggcctcgtgcggattcacccacgaggctttttttattacactgactgAaacgtttttgccctatgagc
                                -35                    -10  +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Egan SE., et al., 1992
[4] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gctacaaaaaTGCCCGATCCTCGATCGGGCAttttgacttt
Reference(s): [1] Egan SE., et al., 1992
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor eddp 1934701 1934718 4.5 ttattacactGACTGAAACGTTTTTGCCctatgagctc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6]
[GntR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GntR repressor eddp 1934576 1934595 128.5 tatgaatccaCAATTGTTACGCGTAACAAAtcgaatcatt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]
remote GntR repressor eddp 1934797 1934816 -93.5 tcctttatggTTATTTTACCGGTAACATGAtcttgcgcag nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]
[KdgR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal KdgR repressor eddp 1934779 1934799 -76.0 accggtaacaTGATCTTGCGCAGATTGTAGAacaattttta nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.4 1934724 1934761 ttacactttcAGGCCTCGTGCGGATTCACCCACGAGGCTTTTTTTATtacactgact
  anti-terminator -6.7 1934749 1934794 taacatgatcTTGCGCAGATTGTAGAACAATTTTTACACTTTCAGGCCTCGTGCGgattcaccca
  anti-anti-terminator -9.5 1934789 1934833 agtaatatctGCGCTTATCCTTTATGGTTATTTTACCGGTAACATGATCTTGCGcagattgtag
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    

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] Egan SE., Fliege R., Tong S., Shibata A., Wolf RE., Conway T., 1992, Molecular characterization of the Entner-Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd-eda operon., J Bacteriol 174(14):4638-46

 [2] Murray EL., Conway T., 2005, Multiple regulators control expression of the Entner-Doudoroff aldolase (Eda) of Escherichia coli., J Bacteriol 187(3):991-1000

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] 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

 [5] Kaleta C., Gohler A., Schuster S., Jahreis K., Guthke R., Nikolajewa S., 2010, Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis., BMC Syst Biol 4:116

 [6] Ramseier TM., Bledig S., Michotey V., Feghali R., Saier MH., 1995, The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli., Mol Microbiol 16(6):1157-69

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