RegulonDB RegulonDB 10.8: 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 31964733.
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                   
Note(s): The upstream promoter region acts as a silencer of this promoter. The actual existence of this promoter and the ability of Fnr to activate the anaerobic expression of this 5' truncated promoter suggest that under certain conditions the silencer effect of the upstream promoter region can be lifted to allow significant transcription at this promoter.
Evidence: [HIPP]
[TIM]
Reference(s): [1] Aristarkhov A., et al., 1996
[3] Membrillo-Hernandez J., et al., 1999
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 activator adhEp2 1298345 1298358 -42.5 ttgcaaaaatTTGATTTGGATCACgtaatcagta nd [APIORCISFBSCS], [CV(GEA)], [GEA] [3]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated repressor adhEp2 1298316 1298331 -15.0 atcagtacccAGAAGTGAGTAATCTTgcttacgcca nd [APIORCISFBSCS], [CV(GEA)], [GEA] [3]
proximal NarL-Phosphorylated repressor adhEp2 1298325 1298340 -24.0 gatcacgtaaTCAGTACCCAGAAGTGagtaatcttg nd [APIORCISFBSCS], [CV(GEA)], [GEA] [3]
Note(s): 1Fnr can regulate adhE expression from the adhEp2 promoter only in the physical absence of the upstream promoter region.1Fnr can regulate adhE expression from the adhEp2 promoter only in the physical absence of the upstream promoter region.


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 31964733.
Evidence: [TASES] 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: Sigma38, Sigma70
Distance from start of the gene: 292
Sequence: ttgttatctagttgtgcaaaacatgctaatgtagccaccaaatcatactacaatttattaActgttagctataatggcgaa
                         -35                -10             +1                   
Evidence: [IMP]
[TIM]
Reference(s): [1] Aristarkhov A., et al., 1996
[3] Membrillo-Hernandez J., et al., 1999
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra1 repressor adhEp1 1298370 1298386 36.5 cgaaaagcgaTGCTGAAAGGTGTCAGCtttgcaaaaa nd [BCE], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [ICWHO], [SM] [6], [7], [8]
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator adhEp1 1298448 1298462 -42.0 tgttatctagTTGTGCAAAACATGCtaatgtagcc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [5]
proximal Fis activator adhEp1 1298474 1298488 -68.0 tacttaaaatTGCTATCATTCGTTAttgttatcta nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [5]
remote Fis activator adhEp1 1298554 1298568 -148.0 gccggataatGTTAGCCATAAATAAggttgaaaag nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [5]
[Lrp,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Lrp repressor adhEp1 1298412 1298427 -6.0 accaaatcatACTACAATTTATTAACtgttagctat nd [AIBSCS], [CV(GEA)], [GEA] [4]
proximal Lrp repressor adhEp1 1298472 1298485 -65.0 ttaaaattgcTATCATTCGTTATTgttatctagt nd [AIBSCS], [CV(GEA)], [GEA] [4]
remote Lrp repressor adhEp1 1298563 1298578 -157.0 cgaagcaaaaGCCGGATAATGTTAGCcataaataag nd [AIBSCS], [CV(GEA)], [GEA] [4]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NarL-Phosphorylated repressor adhEp1 1298316 1298331 90.0 atcagtacccAGAAGTGAGTAATCTTgcttacgcca nd [APIORCISFBSCS], [CV(GEA)], [GEA] [3], [9]
remote NarL-Phosphorylated repressor adhEp1 1298325 1298340 81.0 gatcacgtaaTCAGTACCCAGAAGTGagtaatcttg nd [APIORCISFBSCS], [CV(GEA)], [GEA] [3], [9]
Note(s): 1The effect of FruR repression of the adhE gene was studied under aerobic and anaerobic growth conditions, and stronger repression was observed during aerobic growth. Neither respiratory condition implies direct regulation, but they may reflect a difference of fructose or fructose-1,6-diphosphate levels Mikulskis A,1997. Later, the FruR site was localized downstream of the promoter, and it has been proposed as a repressor site Kaga N,2002 (as it has been observed that other FruR repressor sites are overlapping or downstream of the promoter) (see 8655535).7The effect of FruR repression of the adhE gene was studied under aerobic and anaerobic growth conditions, and stronger repression was observed during aerobic growth. Neither respiratory condition implies direct regulation, but they may reflect a difference of fructose or fructose-1,6-diphosphate levels Mikulskis A,1997. Later, the FruR site was localized downstream of the promoter, and it has been proposed as a repressor site Kaga N,2002 (as it has been observed that other FruR repressor sites are overlapping or downstream of the promoter) (see 8655535).


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gcvB unknown unknown activator       [IMP] [10]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [IMP] Inferred from mutant phenotype

 [BCE] Binding of cellular extracts

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(SM)] cross validation(SM)

 [ICWHO] Inferred computationally without human oversight

 [SM] Site mutation

 [BPP] Binding of purified proteins

 [AIBSCS] 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] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] 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

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

 [10] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14

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