RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: carAB
Synonym(s): OP00150, pyrA
Gene(s): carA, carB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The carAB operon is repressed in response to arginine, pyrimidine, and purine levels. Arginine regulation is exerted by ArgR at P2; pyrimidine regulation is exerted by IHF and PepA at P1; purine regulation is exerted by PurR. In particular, the IHF and PepA effects are sequence-structure and spacing dependent, as Devroede N,2004has demonstrated. In addition, it has been suggested that the UMP kinase, PyrH, is the pyrimidine sensor of the regulatory system and that it can interact with PepA and possibly bind to the DNA Devroede N,2004 Further studies will complete the evidence. A recent study showed that PepA specifically inhibits the activity of the carAB operon promoter P1 by itself; additionally, the interaction of PepA with the carAB promoter region induced a positive supercoiling in this region Nguyen Le Minh P, Nadal M, Charlier D,2016
The carAB operon is regulted by UTP-sensitive reiterative transcription in the transcription start site and between the -10 region and the transcription start Han X, Turnbough CL,2014
carAB operon expression is downregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020.
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Crabeel M., et al., 1980
[2] Gigot D., et al., 1980
[3] Shimada T., et al., 2007
Promoter
Name: carAp1
+1: 29551
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 100
Sequence: taatataaaaaatcccgccattaagttgacttttagcgcccatatctccagaatgccgccGtttgccagaaattcgtcggt
                          -35                    -10        +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [4] Bouvier J., et al., 1984
[5] Charlier D., et al., 1995
[6] Charlier D., et al., 1995
[7] Charlier D., et al., 1988
[8] Huerta AM., et al., 2003
[3] Shimada T., et al., 2007
Terminator(s)
Type: rho-independent
Sequence: atcgaataacTAATACGGTTCTCTGATGAGGACCGTTTTTTTTTgcccattaag
Reference(s): [4] Bouvier J., et al., 1984
[9] Nyunoya H., et al., 1983
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis activator carAp1 29386 29405 -156.0 ttttttctgcTCGTTTTTATTTCATGCAATcttcttgctg nd [GEA], [AIBSCS] [15]
remote Fis activator carAp1 29439 29458 -103.0 cagaacaggtTAGATGATCTTTTTGTCGCTtaatgcctgt nd [GEA], [AIBSCS] [15]
proximal Fis activator carAp1 29461 29480 -81.0 ttgtcgcttaATGCCTGTAAAACATGCATGagccacaaaa nd [GEA], [AIBSCS] [15]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator carAp1 29240 29252 -305.0 atttaatttaTTGATTATAAAGGgctttaattt nd [GEA], [APIORCISFBSCS], [BCE], [BPP], [SM] [10], [11], [12]
[IHF,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF repressor carAp1 29240 29252 -305.0 atttaatttaTTGATTATAAAGGgctttaattt nd [GEA], [APIORCISFBSCS], [BCE], [BPP], [SM] [10], [11], [12]
[PurR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PurR-hypoxanthine repressor carAp1 29415 29430 -128.5 tcttcttgctGCGCAAGCGTTTTCCAgaacaggtta nd [GEA], [AIBSCS], [BPP] [12], [14], [16]
[RutR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote RutR activator carAp1 29359 29375 -184.0 aatgtaaattTTGACCATTTGGTCCACttttttctgc nd [GEA], [AIBSCS], [BPP], [SM] [3], [13]
[aminopeptidase A/I,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PepA repressor carAp1 29365 29391 -173.0 aattttgaccATTTGGTCCACTTTTTTCTGCTCGTTTttatttcatg nd [GEA], [IMP], [BPP] [12], [14]
proximal PepA repressor carAp1 29459 29485 -79.0 ttttgtcgctTAATGCCTGTAAAACATGCATGAGCCAcaaaataata nd [GEA], [BPP] [12], [14]


Transcription unit          
Name: carAB
Synonym(s): OP00150
Gene(s): carA, carB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The carAB operon is repressed in response to arginine, pyrimidine, and purine levels. Arginine regulation is exerted by ArgR at P2; pyrimidine regulation is exerted by IHF and PepA at P1; purine regulation is exerted by PurR. In particular, the IHF and PepA effects are sequence-structure and spacing dependent, as Devroede N,2004has demonstrated. In addition, it has been suggested that the UMP kinase, PyrH, is the pyrimidine sensor of the regulatory system and that it can interact with PepA and possibly bind to the DNA Devroede N,2004 Further studies will complete the evidence.
The carAB operon is regulted by UTP-sensitive reiterative transcription in the transcription start site and between the -10 region and the transcription start Han X, Turnbough CL,2014
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Crabeel M., et al., 1980
[2] Gigot D., et al., 1980
[3] Shimada T., et al., 2007
Promoter
Name: carAp2
+1: 29619
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 32
Sequence: gaaattcgtcggtaagcagatttgcattgatttacgtcatcattgtgaattaatatgcaaAtaaagtgagtgaatattctc
                           -35                     -10      +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [4] Bouvier J., et al., 1984
[5] Charlier D., et al., 1995
[6] Charlier D., et al., 1995
[7] Charlier D., et al., 1988
[8] Huerta AM., et al., 2003
[3] Shimada T., et al., 2007
Terminator(s)
Type: rho-independent
Sequence: atcgaataacTAATACGGTTCTCTGATGAGGACCGTTTTTTTTTgcccattaag
Reference(s): [4] Bouvier J., et al., 1984
[9] Nyunoya H., et al., 1983
TF binding sites (TFBSs)
[ArgR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArgR-L-arginine repressor carAp2 29602 29619 -8.5 acgtcatcatTGTGAATTAATATGCAAAtaaagtgagt nd [GEA], [AIBSCS], [APIORCISFBSCS], [BPP], [SM] [7], [17], [18]
proximal ArgR-L-arginine repressor carAp2 29623 29640 13.5 atgcaaataaAGTGAGTGAATATTCTCTggagggtgtt nd [EME], [GEA], [AIBSCS], [AIBSPD], [APIORCISFBSCS], [BPP], [CEE], [SM] [7], [17], [18]


Transcription unit       
Name: carB
Gene(s): carB   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: carBp
+1: 30775
Distance from start of the gene: 42
Sequence: agccagccctggtccacacgacgccgcgccgttgttcgaccactttatcgagttaattgaGcagtaccgtaaaaccgctaa
Evidence: [TAS]
Reference(s): [9] Nyunoya H., et al., 1983


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [IMP] Inferred from mutant phenotype

 [EME] Expression microarray evidence

 [AIBSPD] Automated inference based on sequence pattern discovery

 [CEE] ChIP-exo evidence

 [TAS] Traceable author statement


Reference(s)    

 [1] Crabeel M., Charlier D., Weyens G., Feller A., Pierard A., Glansdorff N., 1980, Use of gene cloning to determine polarity of an operon: genes carAB of Escherichia coli., J Bacteriol 143(2):921-5

 [2] Gigot D., Crabeel M., Feller A., Charlier D., Lissens W., Glansdorff N., Pierard A., 1980, Patterns of polarity in the Escherichia coli car AB gene cluster., J Bacteriol 143(2):914-20

 [3] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol 66(3):744-57

 [4] Bouvier J., Patte JC., Stragier P., 1984, Multiple regulatory signals in the control region of the Escherichia coli carAB operon., Proc Natl Acad Sci U S A 81(13):4139-43

 [5] Charlier D., Gigot D., Huysveld N., Roovers M., Pierard A., Glansdorff N., 1995, Pyrimidine regulation of the Escherichia coli and Salmonella typhimurium carAB operons: CarP and integration host factor (IHF) modulate the methylation status of a GATC site present in the control region., J Mol Biol 250(4):383-91

 [6] Charlier D., Hassanzadeh G., Kholti A., Gigot D., Pierard A., Glansdorff N., 1995, carP, involved in pyrimidine regulation of the Escherichia coli carbamoylphosphate synthetase operon encodes a sequence-specific DNA-binding protein identical to XerB and PepA, also required for resolution of ColEI multimers., J Mol Biol 250(4):392-406

 [7] Charlier D., Weyens G., Roovers M., Piette J., Bocquet C., Pierard A., Glansdorff N., 1988, Molecular interactions in the control region of the carAB operon encoding Escherichia coli carbamoylphosphate synthetase., J Mol Biol 204(4):867-77

 [8] 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

 [9] Nyunoya H., Lusty CJ., 1983, The carB gene of Escherichia coli: a duplicated gene coding for the large subunit of carbamoyl-phosphate synthetase., Proc Natl Acad Sci U S A 80(15):4629-33

 [10] Charlier D., Huysveld N., Roovers M., Glansdorff N., 1994, On the role of the Escherichia coli integration host factor (IHF) in repression at a distance of the pyrimidine specific promoter P1 of the carAB operon., Biochimie 76(10-11):1041-51

 [11] Charlier D., Roovers M., Gigot D., Huysveld N., Pierard A., Glansdorff N., 1993, Integration host factor (IHF) modulates the expression of the pyrimidine-specific promoter of the carAB operons of Escherichia coli K12 and Salmonella typhimurium LT2., Mol Gen Genet 237(1-2):273-86

 [12] Devroede N., Huysveld N., Charlier D., 2006, Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase., J Bacteriol 188(9):3236-45

 [13] Shimada T., Ishihama A., Busby SJ., Grainger DC., 2008, The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions., Nucleic Acids Res 36(12):3950-5

 [14] Devroede N., Thia-Toong TL., Gigot D., Maes D., Charlier D., 2004, Purine and pyrimidine-specific repression of the Escherichia coli carAB operon are functionally and structurally coupled., J Mol Biol 336(1):25-42

 [15] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [16] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res 39(15):6456-64

 [17] Caldara M., Charlier D., Cunin R., 2006, The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation., Microbiology 152(Pt 11):3343-54

 [18] Charlier D., Roovers M., Van Vliet F., Boyen A., Cunin R., Nakamura Y., Glansdorff N., Pierard A., 1992, Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression., J Mol Biol 226(2):367-86

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