RegulonDB RegulonDB 11.1: Operon Form
   

murQP-yfeW operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: murQP
Gene(s): murQ, murP   Genome Browser M3D Gene expression COLOMBOS
Note(s): murR and murQ are divergently orientated and expressed from nonoverlapping face-to-face (convergent) promoters, and their transcripts are complementary at the 5' end. CRP controls positively murQP expression and it also may affect murR transcription as a consequence of this unusual promoter arrangement (face-to-face) Jaeger T,2008
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Jaeger T., et al., 2008
Promoter
Name: murQp
+1: 2545733
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 40
Sequence: tgcgagtgtagactcaatgattcctttaagcctgtcaattcgggatatatgattccatacAtctgcaattatttgatcgta
                          -35                 -10           +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[1] Jaeger T., et al., 2008
[3] Maciag A., et al., 2011
[4] 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 murQp 2545651 2545672 -71.5 ccgcttaagtTCTTATGACGCTCTTCACACTCtgcgagtgta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
[MurR,-] 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 MurR repressor murQp 2545682 2545697 -44.0 ctgcgagtgtAGACTCAATGATTCCTttaagcctgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
proximal MurR repressor murQp 2545714 2545729 -12.0 ctgtcaattcGGGATATATGATTCCAtacatctgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]


Transcription unit          
Name: murQP
Gene(s): murQ, murP   Genome Browser M3D Gene expression COLOMBOS
Note(s): murR and murQ are divergently orientated and expressed from nonoverlapping face-to-face (convergent) promoters, and their transcripts are complementary at the 5' end. CRP controls positively murQP expression and it also may affect murR transcription as a consequence of this unusual promoter arrangement (face-to-face) Jaeger T,2008
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Jaeger T., et al., 2008
Promoter
Name: murQp1
+1: 2545733
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 40
Sequence: tgcgagtgtagactcaatgattcctttaagcctgtcaattcgggatatatgattccatacAtctgcaattatttgatcgta
                         -35                    -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[1] Jaeger T., et al., 2008
[3] Maciag A., et al., 2011
[4] 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 murQp1 2545651 2545672 -71.5 ccgcttaagtTCTTATGACGCTCTTCACACTCtgcgagtgta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
[MurR,-] 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 MurR repressor murQp1 2545682 2545697 -44.0 ctgcgagtgtAGACTCAATGATTCCTttaagcctgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
proximal MurR repressor murQp1 2545714 2545729 -12.0 ctgtcaattcGGGATATATGATTCCAtacatctgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]


Transcription unit          
Name: murQP
Gene(s): murQ, murP   Genome Browser M3D Gene expression COLOMBOS
Note(s): murR and murQ are divergently orientated and expressed from nonoverlapping face-to-face (convergent) promoters, and their transcripts are complementary at the 5' end. CRP controls positively murQP expression and it also may affect murR transcription as a consequence of this unusual promoter arrangement (face-to-face) Jaeger T,2008
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Jaeger T., et al., 2008
Promoter
Name: murQp2
+1: 2545741
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 32
Sequence: tagactcaatgattcctttaagcctgtcaattcgggatatatgattccatacatctgcaaTtatttgatcgtaaatagtaa
                        -35                     -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Jaeger T., et al., 2008
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 murQp2 2545651 2545672 -79.5 ccgcttaagtTCTTATGACGCTCTTCACACTCtgcgagtgta nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1]
[MurR,-] 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 MurR repressor murQp2 2545682 2545697 -52.0 ctgcgagtgtAGACTCAATGATTCCTttaagcctgt nd [COMP-AINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1]
proximal MurR repressor murQp2 2545714 2545729 -20.0 ctgtcaattcGGGATATATGATTCCAtacatctgca nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1]


Transcription unit       
Name: murQP-yfeW
Gene(s): murQ, murP, yfeW   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [3] Maciag A., et al., 2011


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational 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

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

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Jaeger T., Mayer C., 2008, The transcriptional factors MurR and catabolite activator protein regulate N-acetylmuramic acid catabolism in Escherichia coli., J Bacteriol 190(20):6598-608

 [2] 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

 [3] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [4] 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.

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