RegulonDB RegulonDB 11.2: Operon Form
   

mutY-yggX-mltC-nupG operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: mutY-yggX-mltC-nupG
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: mutY-yggX-mltC
Gene(s): mutY, yggX, mltC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: mutYp2
+1: 3102911
Distance from start of the gene: 102
Sequence: ataaaggtttagtcgcttgtgaaagtgttctgaaaacgggcattatccaaagttagttgcCggatgcaagcatgataaggc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Gifford CM., et al., 1999


Transcription unit       
Name: mutY-yggX-mltC-nupG
Gene(s): mutY, yggX, mltC, nupG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: mutYp2
+1: 3102911
Distance from start of the gene: 102
Sequence: ataaaggtttagtcgcttgtgaaagtgttctgaaaacgggcattatccaaagttagttgcCggatgcaagcatgataaggc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Gifford CM., et al., 1999


Transcription unit       
Name: mutY-yggX
Gene(s): mutY, yggX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: mutYp2
+1: 3102911
Distance from start of the gene: 102
Sequence: ataaaggtttagtcgcttgtgaaagtgttctgaaaacgggcattatccaaagttagttgcCggatgcaagcatgataaggc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Gifford CM., et al., 1999


Transcription unit       
Name: mutY-yggX
Gene(s): mutY, yggX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: mutYp1
+1: 3102988
Distance from start of the gene: 25
Sequence: aggccgtggctgcggaaagttccggtttacaccctgccgtcgctgtgctgcaatcttgccCccaacaacagtgaattcggt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Gifford CM., et al., 1999
[2] Salgado H, et al., 2012


Transcription unit       
Name: mutY-yggX-mltC-nupG
Gene(s): mutY, yggX, mltC, nupG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: mutYp1
+1: 3102988
Distance from start of the gene: 25
Sequence: aggccgtggctgcggaaagttccggtttacaccctgccgtcgctgtgctgcaatcttgccCccaacaacagtgaattcggt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Gifford CM., et al., 1999
[2] Salgado H, et al., 2012


Transcription unit       
Name: mutY-yggX-mltC
Gene(s): mutY, yggX, mltC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: mutYp1
+1: 3102988
Distance from start of the gene: 25
Sequence: aggccgtggctgcggaaagttccggtttacaccctgccgtcgctgtgctgcaatcttgccCccaacaacagtgaattcggt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Gifford CM., et al., 1999
[2] Salgado H, et al., 2012


Transcription unit       
Name: yggX
Gene(s): yggX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: yggXp
+1: 3103993
Distance from start of the gene: 100
Sequence: cgtgtcgtcattcaccggctgcatggatgaaggcaatgcgctctggtataacttagcgcaAccgccgtcagttggcctagc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Gifford CM., et al., 1999


Transcription unit       
Name: yggX-mltC
Gene(s): yggX, mltC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: yggXp
+1: 3103993
Distance from start of the gene: 100
Sequence: cgtgtcgtcattcaccggctgcatggatgaaggcaatgcgctctggtataacttagcgcaAccgccgtcagttggcctagc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Gifford CM., et al., 1999


Transcription unit       
Name: yggX-mltC-nupG
Gene(s): yggX, mltC, nupG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Gifford CM., et al., 1999
Promoter
Name: yggXp
+1: 3103993
Distance from start of the gene: 100
Sequence: cgtgtcgtcattcaccggctgcatggatgaaggcaatgcgctctggtataacttagcgcaAccgccgtcagttggcctagc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Gifford CM., et al., 1999


Transcription unit          
Name: nupG
Synonym(s): OP00172
Gene(s): nupG   Genome Browser M3D Gene expression COLOMBOS
Note(s): Gavigan et al. (1999) and Perini et al. (1996) showed that CytR binds in tandem in the regulated intergenic region Gavigan SA,1999. Perini LT,1996 On the other hand, in 1997, Pedersen and Valentin-Hanses showed that CytR binds to octamer repeats, GTTGCATT in either the direct or inverted orientation and preferably separated by 2 or 3 bp Pedersen H,1997. Jorgensen CI,1998. For this reason the length of the CytR DNA-binding site is variable.
However, footprinting analyses showed that the dimers of CytR are flanked or sandwiched by two dimers of CRP Pedersen H,1995 Thus, the binding sites of CytR located in this region were assigned by the curator in agreement based on similarity to the consensus sequence and on the data from the footprinting assays and mutational evidence Pedersen H,1995. Holst B,1992. Holt AK,2010. Pedersen H,1997. Sogaard-Andersen L,1990. Zolotukhina MA,2002
The repressor CytR and the activator CRP, two dimeric proteins, interact to form a complex repressor nucleoprotein in the intergenic region. When only CRP is bound to this promoter, it functions as an activator, and then, when CytR binds to DNA and to CRP, the activation is repressed because CytR masks an activating region of CRP that otherwise would contact the RNA polymerase to activate transcription Pedersen H,1995. Valentin-Hansen P, Søgaard-Andersen L, Pedersen H,1996. Meibom KL, Kallipolitis BH, Ebright RH, Valentin-Hansen P,2000 The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP Pedersen H,1995. Sogaard-Andersen L,1990. Sogaard-Andersen L,1990. Sogaard-Andersen L,1991 At times CytR also repositions CRP to alternative DNA-binding sites that are not functional for activation Valentin-Hansen P, Søgaard-Andersen L, Pedersen H,1996
The transcript of nupG is decreased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Reference(s): [3] Li J., et al., 1994
[4] Pedersen H., et al., 1995
Promoter
Name: nupGp
+1: 3105651
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 63
Sequence: tttgcaattatttgccacaggtaacaaaaaaccagtccgcgaagttgatagaatcccatcAtctcgcacggtcaaatgtgc
                      -35                        -10        +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Gifford CM., et al., 1999
[5] Huerta AM., et al., 2003
[4] Pedersen H., et al., 1995
[2] Salgado H, et al., 2012
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 nupGp 3105548 3105569 -92.5 tcaggggcaaAAATGTTATCCACATCACAATTtcgttttgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [6], [7]
proximal CRP-cyclic-AMP activator nupGp 3105598 3105619 -42.5 atgtttgcaaTTATTTGCCACAGGTAACAAAAaaccagtccg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
remote CRP-cyclic-AMP activator nupGp 3105696 3105717 56.5 atccgcatcaCGATGTGAGGAAATTAACATGAatcttaagct nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
[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 repressor nupGp 3105548 3105569 -92.5 tcaggggcaaAAATGTTATCCACATCACAATTtcgttttgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [6], [7]
proximal CRP-cyclic-AMP repressor nupGp 3105600 3105621 -40.5 gtttgcaattATTTGCCACAGGTAACAAAAAAccagtccgcg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
remote CRP-cyclic-AMP repressor nupGp 3105696 3105717 56.5 atccgcatcaCGATGTGAGGAAATTAACATGAatcttaagct nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
[CytR,-] 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 CytR repressor nupGp 3105568 3105582 -76.5 cacatcacaaTTTCGTTTTGCAAATtgggaatgtt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
proximal CytR repressor nupGp 3105581 3105599 -61.0 cgttttgcaaATTGGGAATGTTTGCAATTatttgccaca nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
proximal CytR repressor nupGp 3105589 3105608 -53.0 aaattgggaaTGTTTGCAATTATTTGCCACaggtaacaaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
[DeoR,-] 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
nd DeoR repressor nupGp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.1 3105575 3105603 aatttcgtttTGCAAATTGGGAATGTTTGCAATTATTTgccacaggta
  anti-terminator -7.7 3105537 3105586 ctgacgatgcTCAGGGGCAAAAATGTTATCCACATCACAATTTCGTTTTGCAAATTGGGaatgtttgca
  anti-anti-terminator -17.4 3105508 3105557 accgccgccgATAATTCCATTAACCGCCCCTGACGATGCTCAGGGGCAAAAATGTTATCcacatcacaa
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"


Evidence    

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

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

 [COMP-AINF] Inferred computationally without human oversight

 [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-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

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


Reference(s)    

 [1] Gifford CM., Wallace SS., 1999, The genes encoding formamidopyrimidine and MutY DNA glycosylases in Escherichia coli are transcribed as part of complex operons., J Bacteriol 181(14):4223-36

 [2] 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.

 [3] Li J., Kustu S., Stewart V., 1994, In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12., J Mol Biol 241(2):150-65

 [4] Pedersen H., Dall J., Dandanell G., Valentin-Hansen P., 1995, Gene-regulatory modules in Escherichia coli: nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promoter., Mol Microbiol 17(5):843-53

 [5] 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

 [6] Munch-Petersen A., Jensen N., 1990, Analysis of the regulatory region of the Escherichia coli nupG gene, encoding a nucleoside-transport protein., Eur J Biochem 190(3):547-51

 [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

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