RegulonDB RegulonDB 11.1: 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: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
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)
[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 crpp1 3485883 3485904 -59.5 cgcgcaacggAAGGCGACCTGGGTCATGCTGAagcgagacac 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
remote CRP-cyclic-AMP repressor crpp1 3485983 3486004 41.5 atgtactgcaTGTATGCAAAGGACGTCACATTaccgtgcagt 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], [9]
[Cra,+] 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 Cra activator crpp1 3485900 3485916 -45.5 cctgggtcatGCTGAAGCGAGACACCAggagacacaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8]
[Fis,-] 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 Fis repressor crpp1 3485854 3485868 -92.0 tcctgacagaGTACGCGTACTAACCaaatcgcgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
remote Fis repressor crpp1 3485976 3485990 31.0 tacattgatgTACTGCATGTATGCAaaggacgtca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
remote Fis repressor crpp1 3485994 3486008 49.0 gtatgcaaagGACGTCACATTACCGtgcagtacag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
remote Fis repressor crpp1 3486014 3486028 69.0 taccgtgcagTACAGTTGATAGCCCcttcccaggt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [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: crpp3
+1: 3486025
Distance from start of the gene: 95
Sequence: atacattgatgtactgcatgtatgcaaaggacgtcacattaccgtgcagtacagttgataGccccttcccaggtagcggga
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
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)
[Fis,-] 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
remote Fis repressor crpp3 3485854 3485868 -164.0 tcctgacagaGTACGCGTACTAACCaaatcgcgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal Fis repressor crpp3 3485975 3485989 -43.0 atacattgatGTACTGCATGTATGCaaaggacgtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal Fis repressor crpp3 3485993 3486007 -25.0 tgtatgcaaaGGACGTCACATTACCgtgcagtaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal Fis repressor crpp3 3486013 3486027 -5.0 ttaccgtgcaGTACAGTTGATAGCCccttcccagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [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: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
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)
[Fis,-] 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
remote Fis repressor crpp2 3485854 3485868 -170.0 tcctgacagaGTACGCGTACTAACCaaatcgcgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal Fis repressor crpp2 3485975 3485989 -49.0 atacattgatGTACTGCATGTATGCaaaggacgtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal Fis repressor crpp2 3485993 3486007 -31.0 tgtatgcaaaGGACGTCACATTACCgtgcagtaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal Fis repressor crpp2 3486013 3486027 -11.0 ttaccgtgcaGTACAGTTGATAGCCccttcccagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition crpp2 nd   [EXP-IEP] [10]
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [10] Johansson J., et al., 2000


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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


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] 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

 [10] 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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