RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: cirA
Synonym(s): OP00019, cir
Gene(s): cirA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PM] Polar mutation
Reference(s): [1] Griggs DW., et al., 1987
Promoter
Name: cirAp1
+1: 2246929
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 160
Sequence: ggatataaaatttaacatttggattgataattgttatcgtttgcattatcgttacgccgcAatcaaaaaaggctgacaaat
                        -35                    -10          +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [1] Griggs DW., et al., 1987
[2] Huerta AM., et al., 2003
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
remote CRP-cAMP1 activator cirAp1 2246801 2246823 118.5 ggacgtgaagAAGATGTGAGCGATAACCCATTTtattttcgta nd [APIORCISFBSCS], [GEA] [8]
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ repressor cirAp1 2246937 2246955 -17.0 ttgataattgTTATCGTTTGCATTATCGTTacgccgcaat nd [AIBSCS], [GEA] [6], [7]
proximal Fur-Fe2+ repressor cirAp1 2246943 2246961 -23.0 tttggattgaTAATTGTTATCGTTTGCATTatcgttacgc nd [APIORCISFBSCS], [BCE] [4]
proximal Fur-Fe2+ repressor cirAp1 2246949 2246967 -29.0 ttaacatttgGATTGATAATTGTTATCGTTtgcattatcg nd [APIORCISFBSCS], [BPP], [GEA] [4], [5], [6], [7]
proximal Fur-Fe2+ repressor cirAp1 2246955 2246973 -35.0 taaaatttaaCATTTGGATTGATAATTGTTatcgtttgca nd [APIORCISFBSCS], [BPP], [GEA] [4], [5], [6], [7]
Note(s): 1Because the CRP DNA-binding site is located downstream of the transcriptional start site of cirA, two options of activation were proposed: (1) a DNA loop is formed in a way that CRP reaches the RNA polymerase; (2) the binding of CRP affects the formation of a regulatory negative secondary DNA structure Griggs DW,1990.5Because the CRP DNA-binding site is located downstream of the transcriptional start site of cirA, two options of activation were proposed: (1) a DNA loop is formed in a way that CRP reaches the RNA polymerase; (2) the binding of CRP affects the formation of a regulatory negative secondary DNA structure Griggs DW,1990.
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA OmrA cirA repressor 2246779 2246804 CCAUGAGGUAACUACGAAAAUAAAAU MRNA-DEGRADATION [SM] [3]
small regulatory RNA OmrB cirA repressor 2246779 2246804 CCAUGAGGUAACUACGAAAAUAAAAU MRNA-DEGRADATION [SM] [3]


Transcription unit          
Name: cirA
Synonym(s): OP00019
Gene(s): cirA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PM] Polar mutation
Reference(s): [1] Griggs DW., et al., 1987
Promoter
Name: cirAp2
+1: 2246942
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 173
Sequence: tgacaaatcatgcggatataaaatttaacatttggattgataattgttatcgtttgcattAtcgttacgccgcaatcaaaa
                         -35                    -10         +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [1] Griggs DW., et al., 1987
[2] Huerta AM., et al., 2003
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
remote CRP-cAMP1 activator cirAp2 2246801 2246823 131.5 ggacgtgaagAAGATGTGAGCGATAACCCATTTtattttcgta nd [APIORCISFBSCS], [GEA] [8]
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ repressor cirAp2 2246937 2246955 -4.0 ttgataattgTTATCGTTTGCATTATCGTTacgccgcaat nd [AIBSCS], [GEA] [6], [7]
proximal Fur-Fe2+ repressor cirAp2 2246949 2246967 -16.0 ttaacatttgGATTGATAATTGTTATCGTTtgcattatcg nd [APIORCISFBSCS], [BPP], [GEA] [5], [6], [7]
proximal Fur-Fe2+ repressor cirAp2 2246955 2246973 -22.0 taaaatttaaCATTTGGATTGATAATTGTTatcgtttgca nd [APIORCISFBSCS], [BPP], [GEA] [5], [7]
Note(s): 1Because the CRP DNA-binding site is located downstream of the transcriptional start site of cirA, two options of activation were proposed: (1) a DNA loop is formed in a way that CRP reaches the RNA polymerase; (2) the binding of CRP affects the formation of a regulatory negative secondary DNA structure Griggs DW,1990.4Because the CRP DNA-binding site is located downstream of the transcriptional start site of cirA, two options of activation were proposed: (1) a DNA loop is formed in a way that CRP reaches the RNA polymerase; (2) the binding of CRP affects the formation of a regulatory negative secondary DNA structure Griggs DW,1990.
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA OmrB cirA repressor 2246779 2246804 CCAUGAGGUAACUACGAAAAUAAAAU MRNA-DEGRADATION [SM] [3]
small regulatory RNA OmrA cirA repressor 2246779 2246804 CCAUGAGGUAACUACGAAAAUAAAAU MRNA-DEGRADATION [SM] [3]


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

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

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [SM] Site mutation


Reference(s)    

 [1] Griggs DW., Tharp BB., Konisky J., 1987, Cloning and promoter identification of the iron-regulated cir gene of Escherichia coli., J Bacteriol 169(12):5343-52

 [2] 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

 [3] Guillier M., Gottesman S., 2008, The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator., Nucleic Acids Res 36(21):6781-94

 [4] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77

 [5] Griggs DW., Konisky J., 1989, Mechanism for iron-regulated transcription of the Escherichia coli cir gene: metal-dependent binding of fur protein to the promoters., J Bacteriol 171(2):1048-54

 [6] Vassinova N., Kozyrev D., 2000, A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli., Microbiology 146 Pt 12:3171-3182

 [7] White-Ziegler CA., Malhowski AJ., Young S., 2007, Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12., J Bacteriol 189(15):5429-40

 [8] Griggs DW., Kafka K., Nau CD., Konisky J., 1990, Activation of expression of the Escherichia coli cir gene by an iron-independent regulatory mechanism involving cyclic AMP-cyclic AMP receptor protein complex., J Bacteriol 172(6):3529-33

 [9] Salvail H., Caron MP., Belanger J., Masse E., 2013, Antagonistic functions between the RNA chaperone Hfq and an sRNA regulate sensitivity to the antibiotic colicin., EMBO J 32(20):2764-78

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