RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: crp
Synonym(s): OP00160
Gene(s): crp   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the crp gene was decreased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, the gene expression was increased in the Fur, cyoA, and cydB mutants. Kumar R,2011
The expression of the gene crp is decreased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The decreased expression appears to be caused by the transcription factor PhoB, and also could be caused by the increased glucose concentration observed under acidic conditions Marzan LW,2013
It is unknown if the effects of the transcriptional regulators act directly on the gene expression; also, it is unknown which of the three promoters that transcribe the gene could be regulated by the regulators and by acidic and nitrogen-rich growth conditions.
Reference(s): [1] Hanamura A., et al., 1991
[2] Ishizuka H., et al., 1994
Promoter
Name: crpp1
+1: 3485953
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 167
Sequence: gggtcatgctgaagcgagacaccaggagacacaaagcgaaagctatgctaaaacagtcagGatgctacagtaatacattga
                 -35                        -10             +1                   
Evidence: [ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Aiba H., et al., 1982
[4] Gonzalez-Gil G., et al., 1998
[5] Huerta AM., et al., 2003
[6] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: taatcccgtcGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTgtttcccccg
Reference(s): [7] Cossart P., et al., 1982
TF binding sites (TFBSs)
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 crpp1 3485883 3485904 -59.5 cgcgcaacggAAGGCGACCTGGGTCATGCTGAAgcgagacacc nd [APIORCISFBSCS], [BPP], [SM] [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP1 repressor crpp1 3485983 3486004 41.5 atgtactgcaTGTATGCAAAGGACGTCACATTAccgtgcagta nd [AIBSCS], [APIORCISFBSCS], [BPP], [GEA], [SM] [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra activator crpp1 3485900 3485916 -45.5 cctgggtcatGCTGAAGCGAGACACCAggagacacaa nd [BPP], [GEA], [SM] [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor crpp1 3485854 3485868 -92.0 tcctgacagaGTACGCGTACTAACCAaatcgcgcaa nd [APIORCISFBSCS], [BPP], [GEA] [4]
remote Fis repressor crpp1 3485976 3485990 31.0 tacattgatgTACTGCATGTATGCAAaggacgtcac nd [APIORCISFBSCS], [BPP], [GEA] [4]
remote Fis repressor crpp1 3485994 3486008 49.0 gtatgcaaagGACGTCACATTACCGTgcagtacagt nd [APIORCISFBSCS], [BPP], [GEA] [4]
remote Fis repressor crpp1 3486014 3486028 69.0 taccgtgcagTACAGTTGATAGCCCCttcccaggta nd [APIORCISFBSCS], [BPP], [GEA] [4]
Note(s): 1This site essentially eliminates the effect of glucose.1Glucose lowers the level of crp mRNA without affecting its stability.2This site essentially eliminates the effect of glucose.
5Glucose lowers the level of crp mRNA without affecting its stability.


Transcription unit          
Name: crp
Gene(s): crp   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the crp gene was decreased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, the gene expression was increased in the Fur, cyoA, and cydB mutants. Kumar R,2011
The expression of the gene crp is decreased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The decreased expression appears to be caused by the transcription factor PhoB, and also could be caused by the increased glucose concentration observed under acidic conditions Marzan LW,2013
It is unknown if the effects of the transcriptional regulators act directly on the gene expression; also, it is unknown which of the three promoters that transcribe the gene could be regulated by the regulators and by acidic and nitrogen-rich growth conditions.
Promoter
Name: crpp3
+1: 3486025
Distance from start of the gene: 95
Sequence: atacattgatgtactgcatgtatgcaaaggacgtcacattaccgtgcagtacagttgataGccccttcccaggtagcggga
Evidence: [TIM]
Reference(s): [4] Gonzalez-Gil G., et al., 1998
Terminator(s)
Type: rho-independent
Sequence: taatcccgtcGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTgtttcccccg
Reference(s): [7] Cossart P., et al., 1982
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis repressor crpp3 3485854 3485868 -164.0 tcctgacagaGTACGCGTACTAACCAaatcgcgcaa nd [APIORCISFBSCS], [BPP], [GEA] [4]
proximal Fis repressor crpp3 3485975 3485989 -43.0 atacattgatGTACTGCATGTATGCAaaggacgtca nd [APIORCISFBSCS], [BPP], [GEA] [4]
proximal Fis repressor crpp3 3485993 3486007 -25.0 tgtatgcaaaGGACGTCACATTACCGtgcagtacag nd [APIORCISFBSCS], [BPP], [GEA] [4]
proximal Fis repressor crpp3 3486013 3486027 -5.0 ttaccgtgcaGTACAGTTGATAGCCCcttcccaggt nd [APIORCISFBSCS], [BPP], [GEA] [4]


Transcription unit          
Name: crp
Gene(s): crp   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the crp gene was decreased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, the gene expression was increased in the Fur, cyoA, and cydB mutants. Kumar R,2011
The expression of the gene crp is decreased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The decreased expression appears to be caused by the transcription factor PhoB, and also could be caused by the increased glucose concentration observed under acidic conditions Marzan LW,2013
It is unknown if the effects of the transcriptional regulators act directly on the gene expression; also, it is unknown which of the three promoters that transcribe the gene could be regulated by the regulators and by acidic and nitrogen-rich growth conditions.
Promoter
Name: crpp2
+1: 3486031
Distance from start of the gene: 89
Sequence: tgatgtactgcatgtatgcaaaggacgtcacattaccgtgcagtacagttgatagcccctTcccaggtagcgggaagcata
Evidence: [TIM]
Reference(s): [4] Gonzalez-Gil G., et al., 1998
Terminator(s)
Type: rho-independent
Sequence: taatcccgtcGGAGTGGCGCGTTACCTGGTAGCGCGCCATTTTgtttcccccg
Reference(s): [7] Cossart P., et al., 1982
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis repressor crpp2 3485854 3485868 -170.0 tcctgacagaGTACGCGTACTAACCAaatcgcgcaa nd [APIORCISFBSCS], [BPP], [GEA] [4]
proximal Fis repressor crpp2 3485975 3485989 -49.0 atacattgatGTACTGCATGTATGCAaaggacgtca nd [APIORCISFBSCS], [BPP], [GEA] [4]
proximal Fis repressor crpp2 3485993 3486007 -31.0 tgtatgcaaaGGACGTCACATTACCGtgcagtacag nd [APIORCISFBSCS], [BPP], [GEA] [4]
proximal Fis repressor crpp2 3486013 3486027 -11.0 ttaccgtgcaGTACAGTTGATAGCCCcttcccaggt nd [APIORCISFBSCS], [BPP], [GEA] [4]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition crpp2 nd   [IEP] [9]
Evidence: [IEP] Inferred from expression pattern
Reference(s): [9] Johansson J., et al., 2000




Reference(s)    

 [1] Hanamura A., Aiba H., 1991, Molecular mechanism of negative autoregulation of Escherichia coli crp gene., Nucleic Acids Res 19(16):4413-9

 [2] Ishizuka H., Hanamura A., Inada T., Aiba H., 1994, Mechanism of the down-regulation of cAMP receptor protein by glucose in Escherichia coli: role of autoregulation of the crp gene., EMBO J 13(13):3077-82

 [3] Aiba H., Fujimoto S., Ozaki N., 1982, Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein., Nucleic Acids Res 10(4):1345-61

 [4] Gonzalez-Gil G., Kahmann R., Muskhelishvili G., 1998, Regulation of crp transcription by oscillation between distinct nucleoprotein complexes., EMBO J 17(10):2877-85

 [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] 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.

 [7] Cossart P., Gicquel-Sanzey B., 1982, Cloning and sequence of the crp gene of Escherichia coli K 12., Nucleic Acids Res 10(4):1363-78

 [8] Zhang Z., Aboulwafa M., Saier MH., 2014, Regulation of crp Gene Expression by the Catabolite Repressor/Activator, Cra, in Escherichia coli., J Mol Microbiol Biotechnol 24(3):135-41

 [9] Johansson J., Balsalobre C., Wang SY., Urbonaviciene J., Jin DJ., Sonden B., Uhlin BE., 2000, Nucleoid proteins stimulate stringently controlled bacterial promoters: a link between the cAMP-CRP and the (p)ppGpp regulons in Escherichia coli., Cell 102(4):475-85


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