RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: nupC
Synonym(s): OP00198
Gene(s): nupC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The nupC gene is regulated by Nac, CRP, and CytR. Two CRP-binding sites have been identified at -40.5 and -89.5 bp upstream of the transcriptional start site. Since no CytR-binding site has been identifed, it was suggested that the CytR protein could bind to a region between the two sites of CRP, such as in the regulatory regions of the deo and cdd operons Craig JE,1994.
Reference(s): [1] Craig JE., et al., 1994
Promoter
Name: nupCp
+1: 2513009
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 33
Sequence: acgtcattatagtgtgtgtcagatctcgttttccttaaccatgttacatagaatgtgcacGgaaatttaacctgcctcata
                       -35                       -10        +1                   
Note(s): The -10 and -35 regions of the nupCp promoter have been identified with the sequences TAGAAT and TCTCGT, respectively. There is a CRP-binding site overlapping the -35 region Craig JE,1994.
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Craig JE., et al., 1994
[2] Salgado H, et al., 2012
[3] Valentin-Hansen P., et al., 1991
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-cAMP activator nupCp 2512909 2512930 -89.5 aacatagcagAAATGTATGACAGATCACTATTtttgaagcct nd [APIORCISFBSCS], [CV(GEA)], [GEA] [1], [4]
proximal CRP-cAMP activator nupCp 2512958 2512980 -40.5 gacgtcattaTAGTGTGTGTCAGATCTCGTTTTccttaaccat nd [AIBSCS], [APIORCISFBSCS], [CV(GEA)], [GEA] [1], [3], [4], [5]
[CytR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd CytR1 repressor nupCp nd nd nd nd nd [TAS] [1]
[Nac,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Nac activator nupCp nd nd nd nd nd [GEA] [6]
Note(s): 1Although no CytR-binding sites have been identified, it was suggested that the CytR protein could bind cooperatively to a region between the two CRP-binding sites, as in the regulatory regions of the deo and cdd operons Craig JE,1994.4Although no CytR-binding sites have been identified, it was suggested that the CytR protein could bind cooperatively to a region between the two CRP-binding sites, as in the regulatory regions of the deo and cdd operons Craig JE,1994.


Evidence    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [CV(TIM)] cross validation(TIM)

 [HIPP] Human inference of promoter position

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

 [TIM] Transcription initiation mapping

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

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [TAS] Traceable author statement


Reference(s)    

 [1] Craig JE., Zhang Y., Gallagher MP., 1994, Cloning of the nupC gene of Escherichia coli encoding a nucleoside transport system, and identification of an adjacent insertion element, IS 186., Mol Microbiol 11(6):1159-68

 [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] Valentin-Hansen P., Holst B., Sogaard-Andersen L., Martinussen J., Nesvera J., Douthwaite SR., 1991, Design of cAMP-CRP-activated promoters in Escherichia coli., Mol Microbiol 5(2):433-7

 [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] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

 [6] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9

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