RegulonDB RegulonDB 10.10: Operon Form
   

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

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


Transcription unit          
Name: malEFGH
Synonym(s): OP00047, malE
Gene(s): malH, malG, malF, malE   Genome Browser M3D Gene expression COLOMBOS
Note(s): malEFGH, among other genes involved in carbon source transport and metabolism, were downregulated in two MG1655 lysogens carrying closely related Stx2a phages O104 and PA8 Berger P,2019.
The mdtEF-tolC, malEFG, gadBC, treBC, entCEBA-ybdB, hdeAB-yhiD, and alaE operons were differentially regulated after induction of the nonnative organic acid citramalate Webb J,2019.
A transcript that contains malF and malG is decreased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Evidence: [ITCR] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
Reference(s): [1] Francoz E., et al., 1988
Promoter
Name: malEp
+1: 4246464
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 45
Sequence: cggtggggcgtaggggcaaggaggatggaaagaggttgccgtataaagaaactagagtccGtttaggtgttttcacgagca
                          -35                        -10    +1                   
Evidence: [ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Bedouelle H. 1983
[3] Huerta AM., et al., 2003
[4] Richet E. 1996
[5] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: agaaaaaaagGCGCTCCGTGGAGCGCCgaataacagt
Reference(s): [1] Francoz E., et al., 1988
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator malEp 4246530 4246551 -76.5 ttaccgccaaTTCTGTAACAGAGATCACACAAagcgacggtg nd [APIORCISFBSCS], [BPP], [SM] [7], [9], [10]
remote CRP-cyclic-AMP activator malEp 4246559 4246580 -105.5 cgtggcgattTTATGTGCGCATCTCCACATTAccgccaattc nd [AIBSCS], [APIORCISFBSCS], [BPP], [SM] [6], [9], [10]
remote CRP-cyclic-AMP activator malEp 4246593 4246614 -139.5 atgtaaggaaTTTCGTGATGTTGCTTGCAAAAatcgtggcga nd [APIORCISFBSCS], [BPP], [SM] [7], [9], [10]
remote CRP-cyclic-AMP activator malEp 4246625 4246646 -171.5 agaacacggcTTCTGTGAACTAAACCGAGGTCatgtaaggaa nd [AIBSCS], [BPP], [SM] [7], [9]
[CreB,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CreB-phosphorylated repressor malEp 4246438 4246456 18.5 ccgtttaggtGTTTTCACGAGCACTTCACcaacaaggac nd [GEA], [AIBSCS] [12]
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis activator malEp 4246404 4246423 52.0 aaggaccataGATTATGAAAATAAAAACAGgtgcacgcat nd [GEA], [AIBSCS] [11]
remote Fis activator malEp 4246571 4246590 -116.0 ttgcaaaaatCGTGGCGATTTTATGTGCGCatctccacat nd [GEA], [AIBSCS] [11]
[H-NS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS activator malEp nd nd nd nd nd [GEA], [BPP] [13]
[MalT,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MalT-maltotriose-ATP activator malEp 4246501 4246510 -41.5 ggggcgtaggGGCAAGGAGGatggaaagag nd [APIORCISFBSCS], [BPP], [SM] [4], [7], [8]
proximal MalT-maltotriose-ATP activator malEp 4246511 4246520 -51.5 aagcgacggtGGGGCGTAGGggcaaggagg nd [AIBSCS], [APIORCISFBSCS], [BPP], [SM] [6]
remote MalT-maltotriose-ATP activator malEp 4246657 4246666 -197.5 ggggaggaggCGGGAGGATGagaacacggc nd [AIBSCS], [BPP], [SM] [4], [7], [8]
remote MalT-maltotriose-ATP activator malEp 4246667 4246676 -207.5 cttttttatgGGGGAGGAGGcgggaggatg nd [APIORCISFBSCS], [BPP], [SM] [6], [7]
remote MalT-maltotriose-ATP activator malEp 4246691 4246700 -231.5 tggcttaaatCCTCCACCCCctggcttttt nd [APIORCISFBSCS], [BPP], [SM] [6], [7]
[StpA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd StpA activator malEp nd nd nd nd nd [GEA], [BPP] [13]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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

 [TIM] Transcription initiation mapping

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

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis


Reference(s)    

 [1] Francoz E., Dassa E., 1988, 3' end of the malEFG operon in E.coli: localization of the transcription termination site., Nucleic Acids Res 16(9):4097-109

 [2] Bedouelle H., 1983, Mutations in the promoter regions of the malEFG and malK-lamB operons of Escherichia coli K12., J Mol Biol 170(4):861-82

 [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] Richet E., 1996, On the role of the multiple regulatory elements involved in the activation of the Escherichia coli malEp promoter., J Mol Biol 264(5):852-62

 [5] 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.

 [6] Raibaud O., 1989, Nucleoprotein structures at positively regulated bacterial promoters: homology with replication origins and some hypotheses on the quaternary structure of the activator proteins in these complexes., Mol Microbiol 3(3):455-8

 [7] Raibaud O., Vidal-Ingigliardi D., Richet E., 1989, A complex nucleoprotein structure involved in activation of transcription of two divergent Escherichia coli promoters., J Mol Biol 205(3):471-85

 [8] Richet E., Raibaud O., 1991, Supercoiling is essential for the formation and stability of the initiation complex at the divergent malEp and malKp promoters., J Mol Biol 218(3):529-42

 [9] Vidal-Ingigliardi D., Raibaud O., 1991, Three adjacent binding sites for cAMP receptor protein are involved in the activation of the divergent malEp-malKp promoters., Proc Natl Acad Sci U S A 88(1):229-33

 [10] Richet E., 2000, Synergistic transcription activation: a dual role for CRP in the activation of an Escherichia coli promoter depending on MalT and CRP., EMBO J 19(19):5222-32

 [11] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [12] Avison MB., Horton RE., Walsh TR., Bennett PM., 2001, Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media., J Biol Chem 276(29):26955-61

 [13] Sun D., Mao X., Fei M., Chen Z., Zhu T., Qiu J., 2020, Histone-like Nucleoid-Structuring Protein (H-NS) Paralogue StpA Activates the Type I-E CRISPR-Cas System against Natural Transformation in Escherichia coli., Appl Environ Microbiol 86(14)

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