RegulonDB RegulonDB 11.1: 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 Lamrabet O, Plumbridge J, Martin M, Lenski RE, Schneider D, Hindré T,2019
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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huerta AM., et al., 2003
[1] Plumbridge J. 1998
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator manXp 1901830 1901851 -92.5 ctttgcaaacGAATGTGACAAGGATATTTTACctttcgaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2], [7]
proximal CRP-cyclic-AMP activator manXp 1901882 1901903 -40.5 cgaaagttaaATTACGGATCTTCATCACATAAaataattttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [1], [2]
[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 manXp 1901965 1901981 40.5 tgtagcccttATCTGAATCGATTCGATtgtggacgac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [8]
[Mlc,-] 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 Mlc repressor manXp 1901843 1901865 -79.0 tgtgacaaggATATTTTACCTTTCGAAATTTCTgctaatcgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [1]
proximal Mlc repressor manXp 1901909 1901931 -13.0 cataaaataaTTTTTTCGATATCTAAAATAAATcgcgaaacgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [1]
[NagC,-] 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 NagC repressor manXp 1901842 1901864 -80.0 atgtgacaagGATATTTTACCTTTCGAAATTTCtgctaatcga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [1], [2]
proximal NagC repressor manXp 1901925 1901947 4.0 cgatatctaaAATAAATCGCGAAACGCAGGGGTttttggttgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [1], [2]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA SgrS manXYZ repressor 1903038 1903052 ACUCAGUUUUCACAC TRANSLATION-BLOCKING, MRNA-DEGRADATION [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP-SITE-MUTATION], [EXP-IPI] [5], [6]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IPI] Inferred from physical interaction


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] 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

 [5] Azam MS., Vanderpool CK., 2020, Translation inhibition from a distance: The small RNA SgrS silences a ribosomal protein S1-dependent enhancer., Mol Microbiol 114(3):391-408

 [6] Rice JB., Balasubramanian D., Vanderpool CK., 2012, Small RNA binding-site multiplicity involved in translational regulation of a polycistronic mRNA., Proc Natl Acad Sci U S A 109(40):E2691-8

 [7] 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

 [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] Azam MS., Vanderpool CK., 2018, Translational regulation by bacterial small RNAs via an unusual Hfq-dependent mechanism., Nucleic Acids Res 46(5):2585-2599

 [10] Rice JB., Vanderpool CK., 2011, The small RNA SgrS controls sugar-phosphate accumulation by regulating multiple PTS genes., Nucleic Acids Res 39(9):3806-19

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