RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: adhE
Gene(s): adhE   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for adhE . 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.
Reference(s): [1] Aristarkhov A., et al., 1996
[2] Leonardo MR., et al., 1993
Promoter
Name: adhEp2
+1: 1298309
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 188
Sequence: tttgcaaaaatttgatttggatcacgtaatcagtacccagaagtgagtaatcttgcttacGccacctggaagtgacgcatt
                            -35                      -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [1] Aristarkhov A., et al., 1996
[3] Huerta AM., et al., 2003
[4] Membrillo-Hernandez J., et al., 1999
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator adhEp2 1298345 1298358 -42.5 ttgcaaaaatTTGATTTGGATCACgtaatcagta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [4]
[NarL,-] 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 NarL-phosphorylated repressor adhEp2 1298321 1298327 -15.0 gtacccagaaGTGAGTAatcttgctta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO] S [4]
proximal NarL-phosphorylated repressor adhEp2 1298330 1298336 -24.0 acgtaatcagTACCCAGaagtgagtaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO] S [4]


Transcription unit          
Name: adhE
Synonym(s): OP00278
Gene(s): adhE   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for adhE . 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-TAS] Traceable author statement to experimental support
Reference(s): [1] Aristarkhov A., et al., 1996
[2] Leonardo MR., et al., 1993
Promoter
Name: adhEp
+1: 1298413
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 292
Sequence: ttgttatctagttgtgcaaaacatgctaatgtagccaccaaatcatactacaatttattaActgttagctataatggcgaa
                              -35                     -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [1] Aristarkhov A., et al., 1996
[3] Huerta AM., et al., 2003
[4] Membrillo-Hernandez J., et al., 1999
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
remote Cra repressor adhEp 1298370 1298386 36.5 cgaaaagcgaTGCTGAAAGGTGTCAGCtttgcaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [7], [8], [9]
[Fis,+] 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 Fis activator adhEp 1298448 1298462 -42.0 tgttatctagTTGTGCAAAACATGCtaatgtagcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
proximal Fis activator adhEp 1298474 1298488 -68.0 tacttaaaatTGCTATCATTCGTTAttgttatcta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
remote Fis activator adhEp 1298554 1298568 -148.0 gccggataatGTTAGCCATAAATAAggttgaaaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
[Lrp,-] 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 Lrp repressor adhEp 1298412 1298427 -6.0 accaaatcatACTACAATTTATTAACtgttagctat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [5]
proximal Lrp repressor adhEp 1298472 1298485 -65.0 ttaaaattgcTATCATTCGTTATTgttatctagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [5]
remote Lrp repressor adhEp 1298563 1298578 -157.0 cgaagcaaaaGCCGGATAATGTTAGCcataaataag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [5]
[NarL,-] 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 NarL-phosphorylated repressor adhEp 1298321 1298327 90.0 gtacccagaaGTGAGTAatcttgctta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO] S [4], [10]
remote NarL-phosphorylated repressor adhEp 1298330 1298336 81.0 acgtaatcagTACCCAGaagtgagtaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO] S [4], [10]


Transcription unit          
Name: adhE
Synonym(s): OP00278
Gene(s): adhE   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for adhE . 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-TAS] Traceable author statement to experimental support
Reference(s): [1] Aristarkhov A., et al., 1996
[2] Leonardo MR., et al., 1993
Promoter
Name: adhEp1
+1: 1298413
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 292
Sequence: ttgttatctagttgtgcaaaacatgctaatgtagccaccaaatcatactacaatttattaActgttagctataatggcgaa
                            -35                       -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [1] Aristarkhov A., et al., 1996
[3] Huerta AM., et al., 2003
[4] Membrillo-Hernandez J., et al., 1999
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
remote Cra repressor adhEp1 1298370 1298386 36.5 cgaaaagcgaTGCTGAAAGGTGTCAGCtttgcaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [7], [8], [9]
[Fis,+] 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 Fis activator adhEp1 1298448 1298462 -42.0 tgttatctagTTGTGCAAAACATGCtaatgtagcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
proximal Fis activator adhEp1 1298474 1298488 -68.0 tacttaaaatTGCTATCATTCGTTAttgttatcta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
remote Fis activator adhEp1 1298554 1298568 -148.0 gccggataatGTTAGCCATAAATAAggttgaaaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
[Lrp,-] 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 Lrp repressor adhEp1 1298412 1298427 -6.0 accaaatcatACTACAATTTATTAACtgttagctat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [5]
proximal Lrp repressor adhEp1 1298472 1298485 -65.0 ttaaaattgcTATCATTCGTTATTgttatctagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [5]
remote Lrp repressor adhEp1 1298563 1298578 -157.0 cgaagcaaaaGCCGGATAATGTTAGCcataaataag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [5]
[NarL,-] 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 NarL-phosphorylated repressor adhEp1 1298321 1298327 90.0 gtacccagaaGTGAGTAatcttgctta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO] S [4], [10]
remote NarL-phosphorylated repressor adhEp1 1298330 1298336 81.0 acgtaatcagTACCCAGaagtgagtaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO] S [4], [10]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [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-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IMP] Inferred from mutant phenotype

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

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

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

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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-IMP-SITE-MUTATION] Site mutation

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

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


Reference(s)    

 [1] Aristarkhov A., Mikulskis A., Belasco JG., Lin EC., 1996, Translation of the adhE transcript to produce ethanol dehydrogenase requires RNase III cleavage in Escherichia coli., J Bacteriol 178(14):4327-32

 [2] Leonardo MR., Cunningham PR., Clark DP., 1993, Anaerobic regulation of the adhE gene, encoding the fermentative alcohol dehydrogenase of Escherichia coli., J Bacteriol 175(3):870-8

 [3] 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

 [4] Membrillo-Hernandez J., Lin EC., 1999, Regulation of expression of the adhE gene, encoding ethanol oxidoreductase in Escherichia coli: transcription from a downstream promoter and regulation by fnr and RpoS., J Bacteriol 181(24):7571-9

 [5] Lintner RE., Mishra PK., Srivastava P., Martinez-Vaz BM., Khodursky AB., Blumenthal RM., 2008, Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio., BMC Microbiol 8:60

 [6] Membrillo-Hernandez J., Kwon O., De Wulf P., Finkel SE., Lin EC., 1999, Regulation of adhE (encoding ethanol oxidoreductase) by the Fis protein in Escherichia coli., J Bacteriol 181(23):7390-3

 [7] Kaga N., Umitsuki G., Clark DP., Nagai K., Wachi M., 2002, Extensive overproduction of the AdhE protein by rng mutations depends on mutations in the cra gene or in the Cra-box of the adhE promoter., Biochem Biophys Res Commun 295(1):92-7

 [8] Mikulskis A., Aristarkhov A., Lin EC., 1997, Regulation of expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by catabolite repressor activator protein Cra., J Bacteriol 179(22):7129-34

 [9] Sarkar D., Siddiquee KA., Arauzo-Bravo MJ., Oba T., Shimizu K., 2008, Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli., Arch Microbiol 190(5):559-71

 [10] Chen YM., Lin EC., 1991, Regulation of the adhE gene, which encodes ethanol dehydrogenase in Escherichia coli., J Bacteriol 173(24):8009-13

RegulonDB