RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: melAB
Synonym(s): OP00174
Gene(s): melA, melB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The binding targets for MelR consist of repeated sequences 18 nucleotides long that possess conserved motifs. Each monomer binds to one of these conserved sequences Wade JT,2000. Belyaeva TA,2000. Wade JT,2001. Howard VJ,2002MelR binds to five target sites, R(-238.5), 1' (-120.5), 1 (-100.5), 2 (-62.5), and 2' (-42.5), in the melAB promoter, where the less-conserved site 2' (7 of 18 bases) binds MelR most weakly Belyaeva TA,2000 MelR binding to site 2' (-42.5) occurs only in the presence of melibiose and is absolutely required for expression of melAB Howard VJ,2002 Improvement of the base sequence of site 2' removes the requirement for sites 1 and 1' and for melobiose Tamai E,2000. Belyaeva TA,2000Binding of MelR to a fifth site (R) that overlaps the melR promoter has been shown to downregulate expression from the melR promoter Wade JT,2000. Belyaeva TA,2000. Kahramanoglou C,2006
In the presence of melibiose, MelR binds in tandem to four inverted repeated sequences along the melAB-melR intergenic region and activates the transcription overlapping the -35 box of promoter melAp Howard VJ,2002. Wade JT,2000. Tamai E,2000. Caswell R, Webster C, Busby S,1992. Belyaeva TA,2000
In the absence of melibiose, MelR is unable to activate the melAB promoter but autoregulates its own expression by repressing the melR promoter Wade JT,2000 Melibiose triggers MelR-dependent activation of the melAB promoter and relieves MelR-dependent repression of the melR promoter Howard VJ,2002. Wade JT,2000. Tamai E,2000. Caswell R, Webster C, Busby S,1992. Belyaeva TA,2000br>MelR regulates the melAB operon in both the absence and presence of the inducer melibiose Grainger DC, Overton TW, Reppas N, Wade JT, Tamai E, Hobman JL, Constantinidou C, Struhl K, Church G, Busby SJ,2004. Belyaeva TA,2000. On the other hand, RNAP is recruited to the melA promoter only in the presence of inducer Grainger DC, Overton TW, Reppas N, Wade JT, Tamai E, Hobman JL, Constantinidou C, Struhl K, Church G, Busby SJ,2004. MelR activates transcription of the melAB operon by direct interaction with the RNAP subunit via residue D261 Grainger DC, Belyaeva TA, Lee DJ, Hyde EI, Busby SJ,2004.
The melAB operon can be induced by β-thiogalactosides, such as TMG (methyl-β-D-thiogalactopyranoside) and IPTG (isopropyl-β-D-thiogalactopyranoside), and β-galactosides, such as lactose [β-D-galactopyranosyl-(14)-D-glucose] Narang A, Oehler S,2017.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Bourgerie SJ., et al., 1997
[2] Hanatani M., et al., 1984
Promoter
Name: melAp
+1: 4341887
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 24
Sequence: tgggaatgctcaacctggaagccggaggttttctgcagattcgcctgccatgatgaagttAttcaagcaagccaggagatc
                            -35                  -10        +1                   
Note(s): During stationary phase, the σ70 factor remains bound to the RNA polymerase in the transcription elongation complex of the melAB operon. In contrast, this σ factor is not observed in the complex during stationary phase Wade JT, Struhl K,2004.
Evidence: [ICWHO]
[IMP]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[4] Keen J., et al., 1996
[5] Shimamoto T., et al., 1984
[6] Webster C., et al., 1987
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator melAp 4341681 4341702 -195.5 gagggaggatGACTGCGAGTGGGAGCACGGTTttcaccctct nd [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] [7], [8], [9], [10]
proximal CRP-cyclic-AMP activator melAp 4341795 4341816 -81.5 taaactcagaTTTACTGCTGCTTCACGCAGGAtctgagttta nd [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] [8], [9], [11]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote MelR-melibiose activator melAp 4341758 4341775 -120.5 aggccgaaaaCTCTGCTTTTCAGGTAATttattcccat nd [GEA], [APIORCISFBSCS], [BPP] [7], [9], [11]
remote MelR-melibiose activator melAp 4341778 4341795 -100.5 caggtaatttATTCCCATAAACTCAGATttactgctgc nd [GEA], [APIORCISFBSCS], [BPP] [7], [9], [11]
proximal MelR-melibiose activator melAp 4341816 4341833 -62.5 ttcacgcaggATCTGAGTTTATGGGAATgctcaacctg nd [GEA], [BPP] [7], [8], [9], [12], [13]
proximal MelR-melibiose activator melAp 4341836 4341853 -42.5 atgggaatgcTCAACCTGGAAGCCGGAGgttttctgca nd [GEA], [BPP], [SM] [7], [8], [9], [12], [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote MelR repressor melAp 4341640 4341657 -238.5 gatggctctcTTTCCTGGAATATCAGAAttatggcagg nd [GEA], [APIORCISFBSCS], [BPP], [SM] [7], [8]
proximal MelR repressor melAp 4341816 4341833 -62.5 ttcacgcaggATCTGAGTTTATGGGAATgctcaacctg nd [GEA], [BPP] [7], [8], [9], [12], [13]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.3 4343336 4343368 aataacagaaGGCGGGCGTTGGTAACAGCGACCCGATACCCTatgagcattt
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"




Reference(s)    

 [1] Bourgerie SJ., Michan CM., Thomas MS., Busby SJ., Hyde EI., 1997, DNA binding and DNA bending by the MelR transcription activator protein from Escherichia coli., Nucleic Acids Res 25(9):1685-93

 [2] Hanatani M., Yazyu H., Shiota-Niiya S., Moriyama Y., Kanazawa H., Futai M., Tsuchiya T., 1984, Physical and genetic characterization of the melibiose operon and identification of the gene products in Escherichia coli., J Biol Chem 259(3):1807-12

 [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] Keen J., Williams J., Busby S., 1996, Location of essential sequence elements at the Escherichia coli melAB promoter., Biochem J 318 ( Pt 2):443-9

 [5] Shimamoto T., Yazyu H., Futai M., Tsuchiya T., 1984, Nucleotide sequence of the promoter region of the melibiose operon of Escherichia coli., Biochem Biophys Res Commun 121(1):41-6

 [6] Webster C., Kempsell K., Booth I., Busby S., 1987, Organisation of the regulatory region of the Escherichia coli melibiose operon., Gene 59(2-3):253-63

 [7] Belyaeva TA., Wade JT., Webster CL., Howard VJ., Thomas MS., Hyde EI., Busby SJ., 2000, Transcription activation at the Escherichia coli melAB promoter: the role of MelR and the cyclic AMP receptor protein., Mol Microbiol 36(1):211-22

 [8] Kahramanoglou C., Webster CL., El-Robh MS., Belyaeva TA., Busby SJ., 2006, Mutational analysis of the Escherichia coli melR gene suggests a two-state concerted model to explain transcriptional activation and repression in the melibiose operon., J Bacteriol 188(9):3199-207

 [9] Wade JT., Belyaeva TA., Hyde EI., Busby SJ., 2000, Repression of the Escherichia coli melR promoter by MelR: evidence that efficient repression requires the formation of a repression loop., Mol Microbiol 36(1):223-9

 [10] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [11] Wade JT., Belyaeva TA., Hyde EI., Busby SJ., 2001, A simple mechanism for co-dependence on two activators at an Escherichia coli promoter., EMBO J 20(24):7160-7

 [12] Grainger DC., Belyaeva TA., Lee DJ., Hyde EI., Busby SJ., 2003, Binding of the Escherichia coli MelR protein to the melAB promoter: orientation of MelR subunits and investigation of MelR-DNA contacts., Mol Microbiol 48(2):335-48

 [13] Tamai E., Belyaeva TA., Busby SJ., Tsuchiya T., 2000, Mutations that increase the activity of the promoter of the Escherichia coli melibiose operon improve the binding of MelR, a transcription activator triggered by melibiose., J Biol Chem 275(22):17058-63


RegulonDB