RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: manXYZ
Synonym(s): OP00275, ptsX
Gene(s): manX, manY, manZ   Genome Browser M3D Gene expression COLOMBOS
Note(s): The plasticity of the promoter regions was demonstrated for two CRP target genes, ptsG and manX. Four genetically different strains with the crp gene deleted were propagated in a glucose minimal medium, the crp gene. This deletion led to deleterious effects on growth in the four strains, but most of the populations quickly evolved compensatory changes that restored fast growth and were specific to the glucose environment in which they evolved. The adaptation involved plasticity of the promoter regions of two CRP target genes involved in glucose transport, ptsG and manX 30825312
Reference(s): [1] Plumbridge J. 1998
[2] Plumbridge J., et al., 1991
[3] Plumbridge J., et al., 1995
Promoter
Name: manXp
+1: 1901933
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 115
Sequence: gaaagttaaattacggatcttcatcacataaaataattttttcgatatctaaaataaatcGcgaaacgcaggggtttttgg
                       -35                        -10       +1                   
Note(s): The homology with the consensus -35 sequences is poor, but it has been noted that the lack of a good -35 sequences is a characteristic of positively regulated genes Plumbridge J.,1998.
Evidence: [HIPP]
[TIM]
Reference(s): [1] Plumbridge J. 1998
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-cAMP1 activator manXp 1901830 1901851 -92.5 ctttgcaaacGAATGTGACAAGGATATTTTACctttcgaaat nd [AIBSCS], [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [2], [4]
proximal CRP-cAMP2 activator manXp 1901882 1901903 -40.5 cgaaagttaaATTACGGATCTTCATCACATAAaataattttt nd [APIORCISFBSCS], [BCE], [CV(GEA/ROMA)], [GEA] [1], [2]
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor manXp 1901965 1901981 40.5 tgtagcccttATCTGAATCGATTCGATtgtggacgac nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [7]
[Mlc,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Mlc1 repressor manXp 1901843 1901865 -79.0 tgtgacaaggATATTTTACCTTTCGAAATTTCTgctaatcgaa nd [BCE], [CV(GEA/ROMA)], [GEA] [1]
proximal Mlc2 repressor manXp 1901909 1901931 -13.0 cataaaataaTTTTTTCGATATCTAAAATAAATcgcgaaacgc nd [BCE], [CV(GEA/ROMA)], [GEA] [1]
[NagC,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NagC1 repressor manXp 1901842 1901864 -80.0 atgtgacaagGATATTTTACCTTTCGAAATTTCtgctaatcga nd [AIBSCS], [APIORCISFBSCS], [BCE], [CV(GEA/ROMA)], [GEA] [1], [2], [5], [6]
proximal NagC2 repressor manXp 1901925 1901947 4.0 cgatatctaaAATAAATCGCGAAACGCAGGGGTttttggttgt nd [BCE], [CV(GEA/ROMA)], [GEA] [1], [2]
Note(s): 1This second very weak CAP site upstream from manX in the region -80 to -100 is detected only at very high CAP concentrations Plumbridge J,1991. Zheng D,2004.
2A Class II promoter. CAP and NagC can bind simultaneously and produce a complex more stable than the binary NagC-DNA complex Plumbridge J.,1998.1A mutation in the mlc gene, encoding a homolog of nagC, results in a threefold derepression of manX expression, suggesting that this protein is a more important regulator of maX expression than NagC. The Mlc protein binds to the NagC operators, binding preferentially to the promoter-proximal operator. Plasmids overproducing either the NagC protein or the Mlc protein repress the expression of manX, but the effect with the Mlc protein is stronger. Mcl weakly protects this operator. The manX operator is only partially occupied under physiological concentrations of the Mlc protein. CAP and NagC can bind simultaneously and produce a complex more stable than the binary NagC-DNA complex Plumbridge J.,1998.
2A mutation in the mlc gene, encoding a homolog of nagC, results in a threefold derepression of manX expression, suggesting that this protein is a more important regulator of maX expression than NagC. The Mlc protein binds to the NagC operators, binding preferentially to the promoter-proximal operator. Plasmids overproducing either the NagC protein or the mlc protein repress the expression of manX, but the effect to the Mlc protein is stronger. Mcl weakly protects this operator. The manX operator is only partially occupied under physiological concentrations of the Mlc protein. CAP and NagC can bind simultaneously and produce a complex more stable than the binary NagC-DNA complex Plumbridge J.,1998.1Previously, two binding sites for the NagC repressor were detected upstream from manX, but a mutation in nagC had very little effect on manX expression. Plasmids overproducing either the NagC protein or the Mlc protein repress the expression of manX, but the effect on the Mlc protein is stronger. NagC binds more tightly to the -79 position than to the -13 position Plumbridge J,1991. Plumbridge J.,1998.
2Previously, two binding sites for the NagC repressor were detected upstream of manX, but a mutation in nagC has very little effect on manX expression. Plasmids overproducing either the NagC protein or the Mlc protein repress the expression of manX, but the effect of the Mlc protein is stronger Plumbridge J.,1998. Plumbridge J,1991.1This second very weak CAP site upstream from manX in the region -80 to -100 is detected only at very high CAP concentrations Plumbridge J,1991. Zheng D,2004.
2Previously, two binding sites for the NagC repressor were detected upstream from manX, but a mutation in nagC had very little effect on manX expression. Plasmids overproducing either the NagC protein or the Mlc protein repress the expression of manX, but the effect on the Mlc protein is stronger. NagC binds more tightly to the -79 position than to the -13 position Plumbridge J,1991. Plumbridge J.,1998.
3A mutation in the mlc gene, encoding a homolog of nagC, results in a threefold derepression of manX expression, suggesting that this protein is a more important regulator of maX expression than NagC. The Mlc protein binds to the NagC operators, binding preferentially to the promoter-proximal operator. Plasmids overproducing either the NagC protein or the Mlc protein repress the expression of manX, but the effect with the Mlc protein is stronger. Mcl weakly protects this operator. The manX operator is only partially occupied under physiological concentrations of the Mlc protein. CAP and NagC can bind simultaneously and produce a complex more stable than the binary NagC-DNA complex Plumbridge J.,1998.
4A Class II promoter. CAP and NagC can bind simultaneously and produce a complex more stable than the binary NagC-DNA complex Plumbridge J.,1998.
5A mutation in the mlc gene, encoding a homolog of nagC, results in a threefold derepression of manX expression, suggesting that this protein is a more important regulator of maX expression than NagC. The Mlc protein binds to the NagC operators, binding preferentially to the promoter-proximal operator. Plasmids overproducing either the NagC protein or the mlc protein repress the expression of manX, but the effect to the Mlc protein is stronger. Mcl weakly protects this operator. The manX operator is only partially occupied under physiological concentrations of the Mlc protein. CAP and NagC can bind simultaneously and produce a complex more stable than the binary NagC-DNA complex Plumbridge J.,1998.
6Previously, two binding sites for the NagC repressor were detected upstream of manX, but a mutation in nagC has very little effect on manX expression. Plasmids overproducing either the NagC protein or the Mlc protein repress the expression of manX, but the effect of the Mlc protein is stronger Plumbridge J.,1998. Plumbridge J,1991.


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

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

 [GEA] Gene expression analysis

 [BCE] Binding of cellular extracts


Reference(s)    

 [1] Plumbridge J., 1998, Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS., Mol Microbiol 27(2):369-80

 [2] Plumbridge J., Kolb A., 1991, CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli., J Mol Biol 217(4):661-79

 [3] Plumbridge J., Kolb A., 1995, Nag repressor-operator interactions: protein-DNA contacts cover more than two turns of the DNA helix., J Mol Biol 249(5):890-902

 [4] 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

 [5] Oberto J., 2010, FITBAR: a web tool for the robust prediction of prokaryotic regulons., BMC Bioinformatics 11:554

 [6] Plumbridge J., 2001, DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli., Nucleic Acids Res 29(2):506-14

 [7] 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

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