RegulonDB RegulonDB 10.9: Operon Form
   

nagBAC-umpH operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: umpH
Synonym(s): nagD
Gene(s): umpH   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Plumbridge JA. 1989
Promoter
Name: umpHp
+1: 700352
Distance from start of the gene: 26
Sequence: ctcaacggtattttgctccagcatttgctggaaaattaatgtgcttttatagtggcgcttAttgttgtcaatattctgggt
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [1] Plumbridge JA. 1989
[2] Salgado H, et al., 2012


Transcription unit       
Name: nagC
Gene(s): nagC   Genome Browser M3D Gene expression COLOMBOS
Note(s): Two promoters localized within the nagA gene sequence are responsible for most of the nagC expression. Although mutational and S1 mapping analyses have been carried out by Plumbridge J.,1996 they did not point out the transcriptional start of nagCp1 and nagCp2, and they only mentioned the putative boxes for σ70-type promoters. Therefore, a putative transcriptional start site to these promoters was assigned based on the observation that the majority of the promoters with experimentally determined transcriptional start sites present a distance of 6 nucleotides between the transcriptional start site and the -10 box 3550697
Promoter
Name: nagCp1
+1: 701865
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 271
Sequence: cgccagcaggtgccaacattgaacagttcatttttgcgggtaaaacaatatactaccgtaAcggactttgtgtggatgaga
                           -35                   -10        +1                   
Evidence: [HIPP]
[ICWHO]
[IMP]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[4] Plumbridge J. 1996
[2] Salgado H, et al., 2012


Transcription unit       
Name: nagC
Gene(s): nagC   Genome Browser M3D Gene expression COLOMBOS
Note(s): Two promoters localized within the nagA gene sequence are responsible for most of the nagC expression. Although mutational and S1 mapping analyses have been carried out by Plumbridge J.,1996 they did not point out the transcriptional start of nagCp1 and nagCp2, and they only mentioned the putative boxes for σ70-type promoters. Therefore, a putative transcriptional start site to these promoters was assigned based on the observation that the majority of the promoters with experimentally determined transcriptional start sites present a distance of 6 nucleotides between the transcriptional start site and the -10 box 3550697
Promoter
Name: nagCp2
+1: 702008
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 414
Sequence: acctggcctggcgggcgcgatcctcgacgaagctgacatttattgcggtattattgctgaTggcctgcatgttgattacgc
                       -35                       -10        +1                   
Evidence: [HIPP]
[ICWHO]
[IMP]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[4] Plumbridge J. 1996


Transcription unit          
Name: nagA
Gene(s): nagA   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: nagAp
+1: 703175
Distance from start of the gene: 424
Sequence: gttcttacggaaaaattcatctgtttatgggcggtgtaggtaacgacggtcatattgcatTtaacgaaccggcgtcttctc
Evidence: [TIM]
Reference(s): [5] Minagawa S., et al., 2003
TF binding sites (TFBSs)
[PhoP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PhoP-Phosphorylated activator nagAp 703198 703214 -31.0 aaaaattcatCTGTTTATGGGCGGTGTAggtaacgacg nd [APIORCISFBSCS], [BPP], [GEA] [5]


Transcription unit          
Name: nagBACD
Synonym(s): OP00058, nagB
Gene(s): umpH, nagC, nagA, nagB   Genome Browser M3D Gene expression COLOMBOS
Note(s): CAP and NagC can bind simultaneously and produce a more stable complex than the binary NagC-DNA complex.
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [6] Plumbridge J., et al., 1991
[7] Plumbridge JA. 1991
[1] Plumbridge JA. 1989
[8] Rogers MJ., et al., 1988
[9] Vogler AP., et al., 1989
Promoter
Name: nagBp
+1: 703708
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 97
Sequence: atatcgttattatcactcccttttactggctaaaccagaaaacttattttatcattcaaaAaatcaggtcggattgacgcc
                       -35                        -10       +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[6] Plumbridge J., et al., 1991
[10] Plumbridge J., et al., 1993
[11] Plumbridge J., et al., 1998
[8] Rogers MJ., et al., 1988
[9] Vogler AP., et al., 1989
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 nagBp 703768 703789 -70.5 aaacgcgtgtCTTTTGTGAGTTTTGTCACCAAAtatcgttatt nd [APIORCISFBSCS], [BCE], [BPP], [GEA] [6], [10], [11]
remote CRP-cAMP2 activator nagBp 703802 703823 -104.5 agagtgtgtgAAAATTTAATTCGTATCGCAAATtaaacgcgtg nd [APIORCISFBSCS], [BPP] [6]
[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 repressor nagBp 703768 703789 -70.5 aaacgcgtgtCTTTTGTGAGTTTTGTCACCAAAtatcgttatt nd [APIORCISFBSCS], [BCE], [BPP], [GEA] [6], [10], [11]
remote CRP-cAMP2 repressor nagBp 703802 703823 -104.5 agagtgtgtgAAAATTTAATTCGTATCGCAAATtaaacgcgtg nd [APIORCISFBSCS], [BPP] [6]
[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 nagBp 703704 703726 -7.0 aaaccagaaaACTTATTTTATCATTCAAAAAATCaggtcggatt nd [BPP], [GEA], [SM] [6], [10], [11], [12]
remote NagC2 repressor nagBp 703798 703820 -101.0 gtgtgtgaaaATTTAATTCGTATCGCAAATTAAAcgcgtgtctt nd [BPP], [GEA], [SM] [6], [10], [11], [12]
Note(s): 1CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.
2CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex. This is a weak CAP binding site.1CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.
2CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex. This is a weak CAP binding site.1CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.
2CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.1CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex. This is a weak CAP binding site.
2CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex. This is a weak CAP binding site.
3CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.
4CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.
5CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.
6CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [13] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -15.1 702767 702800 ttgttatcccTGCCCTGGCTCCTTGCTCAGGGCAATATTTTTTaaaatcgggg
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    

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

 [TIM] Transcription initiation mapping

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IMP] Inferred from mutant phenotype

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

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [BCE] Binding of cellular extracts

 [SM] Site mutation


Reference(s)    

 [1] Plumbridge JA., 1989, Sequence of the nagBACD operon in Escherichia coli K12 and pattern of transcription within the nag regulon., Mol Microbiol 3(4):505-15

 [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] 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] Plumbridge J., 1996, How to achieve constitutive expression of a gene within an inducible operon: the example of the nagC gene of Escherichia coli., J Bacteriol 178(9):2629-36

 [5] Minagawa S., Ogasawara H., Kato A., Yamamoto K., Eguchi Y., Oshima T., Mori H., Ishihama A., Utsumi R., 2003, Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli., J Bacteriol 185(13):3696-702

 [6] 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

 [7] Plumbridge JA., 1991, Repression and induction of the nag regulon of Escherichia coli K-12: the roles of nagC and nagA in maintenance of the uninduced state., Mol Microbiol 5(8):2053-62

 [8] Rogers MJ., Ohgi T., Plumbridge J., Soll D., 1988, Nucleotide sequences of the Escherichia coli nagE and nagB genes: the structural genes for the N-acetylglucosamine transport protein of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and for glucosamine-6-phosphate deaminase., Gene 62(2):197-207

 [9] Vogler AP., Lengeler JW., 1989, Analysis of the nag regulon from Escherichia coli K12 and Klebsiella pneumoniae and of its regulation., Mol Gen Genet 219(1-2):97-105

 [10] Plumbridge J., Kolb A., 1993, DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo., Mol Microbiol 10(5):973-81

 [11] Plumbridge J., Kolb A., 1998, DNA bending and expression of the divergent nagE-B operons., Nucleic Acids Res 26(5):1254-60

 [12] 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

 [13] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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