RegulonDB RegulonDB 11.2: Operon Form
   

dnaAN-recF operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: recF
Gene(s): recF   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: recFp1
+1: 3881841
Distance from start of the gene: 620
Sequence: gcgacccagttttctatggcgcatcaggacgttcgctattacttaaatggtatgctgtttGaaaccgaaggtgaagaactg
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Armengod ME., et al., 1986
[2] Salgado H, et al., 2012


Transcription unit       
Name: recF
Gene(s): recF   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: recFp2
+1: 3881861
Distance from start of the gene: 640
Sequence: cgatgaagcgtctgattgaagcgacccagttttctatggcgcatcaggacgttcgctattActtaaatggtatgctgtttg
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Armengod ME., et al., 1986


Transcription unit       
Name: dnaN-recF
Gene(s): recF, dnaN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [3] Villarroya M., et al., 1998
Promoter
Name: dnaNp4
+1: 3882348
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: gccgtaagatcgagcagttgcgtgaagagagccacgatatcaaagaagatttttcaaattTaatcagaacattgtcatcgt
                           -35                       -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [4] Armengod ME., et al., 1988
[5] Huerta AM., et al., 2003
[3] Villarroya M., et al., 1998


Transcription unit       
Name: dnaN-recF
Gene(s): recF, dnaN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [3] Villarroya M., et al., 1998
Promoter
Name: dnaNp5
+1: 3882348
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 27
Sequence: gccgtaagatcgagcagttgcgtgaagagagccacgatatcaaagaagatttttcaaattTaatcagaacattgtcatcgt
                                    -35                     +10                  
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [4] Armengod ME., et al., 1988
[5] Huerta AM., et al., 2003
[3] Villarroya M., et al., 1998


Transcription unit       
Name: dnaN-recF
Gene(s): recF, dnaN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [3] Villarroya M., et al., 1998
Promoter
Name: dnaNp3
+1: 3882562
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 241
Sequence: caggaaaaactggtcaccatcgacaatattcagaagacggtggcggagtactacaagatcAaagtcgcggatctcctttcc
                                  -35                    -10+1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Armengod ME., et al., 1988
[5] Huerta AM., et al., 2003
[3] Villarroya M., et al., 1998


Transcription unit       
Name: dnaN-recF
Gene(s): recF, dnaN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [3] Villarroya M., et al., 1998
Promoter
Name: dnaNp6
+1: 3882590
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 269
Sequence: tgaggcgctgcgcgacttgctggcattgcaggaaaaactggtcaccatcgacaatattcaGaagacggtggcggagtacta
                               -35                     -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [4] Armengod ME., et al., 1988
[5] Huerta AM., et al., 2003
[3] Villarroya M., et al., 1998


Transcription unit       
Name: dnaN-recF
Gene(s): recF, dnaN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [3] Villarroya M., et al., 1998
Promoter
Name: dnaNp2
+1: 3882590
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 269
Sequence: tgaggcgctgcgcgacttgctggcattgcaggaaaaactggtcaccatcgacaatattcaGaagacggtggcggagtacta
                               -35                        -1+1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [4] Armengod ME., et al., 1988
[5] Huerta AM., et al., 2003
[3] Villarroya M., et al., 1998


Transcription unit       
Name: dnaN-recF
Gene(s): recF, dnaN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [3] Villarroya M., et al., 1998
Promoter
Name: dnaNp
+1: 3882733
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 412
Sequence: aacgacattcgtttgccgggcgaagtggcgttctttatcgccaagcgtctacgatctaacGtacgtgagctggaaggggcg
                              -35                      -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [4] Armengod ME., et al., 1988
[5] Huerta AM., et al., 2003
[3] Villarroya M., et al., 1998


Transcription unit       
Name: dnaN-recF
Gene(s): recF, dnaN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [3] Villarroya M., et al., 1998
Promoter
Name: dnaNp1
+1: 3882733
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 412
Sequence: aacgacattcgtttgccgggcgaagtggcgttctttatcgccaagcgtctacgatctaacGtacgtgagctggaaggggcg
                              -35                      -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [4] Armengod ME., et al., 1988
[5] Huerta AM., et al., 2003
[3] Villarroya M., et al., 1998


Transcription unit          
Name: dnaAN-recF
Gene(s): recF, dnaN, dnaA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The autoregulation of dnaA is growth temperature dependent Saggioro C,2013
Reference(s): [6] Macian F., et al., 1994
[7] Perez-Roger I., et al., 1991
Promoter
Name: dnaAp2
+1: 3883882
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 153
Sequence: ataaatcgggaaaatctgtgagaaacagaagatctcttgcgcagtttaggctatgatccgCggtcccgatcgttttgcagg
                                   -35                   -10+1                   
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [8] Hansen FG., et al., 1982
[9] Saggioro C., et al., 2013
TF binding sites (TFBSs)
[DnaA,+] 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 DnaA-ATP activator dnaAp2 3883918 3883927 -40.0 tcgggaaaatCTGTGAGAAAcagaagatct nd [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9]
proximal DnaA-ATP activator dnaAp2 3883929 3883938 -51.0 ctgtggataaATCGGGAAAAtctgtgagaa nd [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [9]
proximal DnaA-ATP activator dnaAp2 3883939 3883948 -61.0 ctggaaagtcCTGTGGATAAatcgggaaaa nd [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9]
proximal DnaA-ATP activator dnaAp2 3883951 3883960 -73.0 acttagcgagTTCTGGAAAGtcctgtggat nd [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [9]
[DnaA,-] 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 DnaA-ATP repressor dnaAp2 3883918 3883927 -40.0 tcgggaaaatCTGTGAGAAAcagaagatct nd [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9]
proximal DnaA-ATP repressor dnaAp2 3883929 3883938 -51.0 ctgtggataaATCGGGAAAAtctgtgagaa nd [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [9]
proximal DnaA-ATP repressor dnaAp2 3883935 3883943 -57.0 aagtcctgtgGATAAATCGggaaaatctg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10], [11]
proximal DnaA-ATP repressor dnaAp2 3883939 3883948 -61.0 ctggaaagtcCTGTGGATAAatcgggaaaa nd [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9]
proximal DnaA-ATP repressor dnaAp2 3883951 3883960 -73.0 acttagcgagTTCTGGAAAGtcctgtggat nd [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [9]
[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 dnaAp2 3883901 3883915 -26.0 gtgagaaacaGAAGATCTCTTGCGCagtttaggct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [12]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition dnaAp2 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [13]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [13] Chiaramello AE., et al., 1990


Transcription unit          
Name: dnaAN-recF
Gene(s): recF, dnaN, dnaA   Genome Browser M3D Gene expression COLOMBOS
Note(s): In 1997 Lee et al. showed that ArgP binds to two regions in the intergenic region of the gene dnaA, acts as a dimer of dimers upstream of the transcription start site Lee Y,1997, and binds as a dimer near the Shine-Dalgarno sequence of the gene dnaA Lee YS,1996. Despite strong experimental evidence, those authors did not identify the center positions of the binding sites. According to this evidence, the curator has assigned three possible binding sites of 20 bp for ArgP, located at bp -69.5, -49.5, and 219.5 relative to the transcription start site of lysP. The curator identified the consensus sequence of ArgP and assigned the possible central position of these binding sites, based on similarity to consensus sequences.
Reference(s): [6] Macian F., et al., 1994
[7] Perez-Roger I., et al., 1991
Promoter
Name: dnaAp1
+1: 3883961
Distance from start of the gene: 232
Sequence:
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [8] Hansen FG., et al., 1982
[14] Ohmori H., et al., 1984
[9] Saggioro C., et al., 2013
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[ArgP,+] 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 ArgP activator dnaAp1 3883733 3883752 219.5 tcattatcgaCTTTTGTTCGAGTGGAGTCCgccgtgtcac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [10], [11], [15], [16]
proximal ArgP activator dnaAp1 3884001 3884020 -49.5 gtcattaaatTTTCCAATATGCGGCGTAAAtcgtgcccgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [10], [11], [15], [16]
proximal ArgP activator dnaAp1 3884021 3884040 -69.5 taagccaattTTTGTCTATGGTCATTAAATtttccaatat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [10], [11], [15], [16]
[DnaA,-] 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 DnaA-ATP repressor dnaAp1 3883935 3883943 23.0 aagtcctgtgGATAAATCGggaaaatctg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10], [11]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition dnaAp1 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [13]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [13] Chiaramello AE., et al., 1990


Evidence    

 [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-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IMP] Inferred from mutant phenotype

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [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-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [IC] Inferred by curator


Reference(s)    

 [1] Armengod ME., Lambies E., 1986, Overlapping arrangement of the recF and dnaN operons of Escherichia coli; positive and negative control sequences., Gene 43(3):183-96

 [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] Villarroya M., Perez-Roger I., Macian F., Armengod ME., 1998, Stationary phase induction of dnaN and recF, two genes of Escherichia coli involved in DNA replication and repair., EMBO J 17(6):1829-37

 [4] Armengod ME., Garcia-Sogo M., Lambies E., 1988, Transcriptional organization of the dnaN and recF genes of Escherichia coli K-12., J Biol Chem 263(24):12109-14

 [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] Macian F., Perez-Roger I., Armengod ME., 1994, An improved vector system for constructing transcriptional lacZ fusions: analysis of regulation of the dnaA, dnaN, recF and gyrB genes of Escherichia coli., Gene 145(1):17-24

 [7] Perez-Roger I., Garcia-Sogo M., Navarro-Avino JP., Lopez-Acedo C., Macian F., Armengod ME., 1991, Positive and negative regulatory elements in the dnaA-dnaN-recF operon of Escherichia coli., Biochimie 73(2-3):329-34

 [8] Hansen FG., Hansen EB., Atlung T., 1982, The nucleotide sequence of the dnaA gene promoter and of the adjacent rpmH gene, coding for the ribosomal protein L34, of Escherichia coli., EMBO J 1(9):1043-8

 [9] Saggioro C., Olliver A., Sclavi B., 2013, Temperature-dependence of the DnaA-DNA interaction and its effect on the autoregulation of dnaA expression., Biochem J 449(2):333-41

 [10] Lee Y., Lee H., Yim J., Hwang D., 1997, The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P., Nucleic Acids Res 25(17):3486-9

 [11] Lee YS., Kim H., Hwang DS., 1996, Transcriptional activation of the dnaA gene encoding the initiator for oriC replication by IciA protein, an inhibitor of in vitro oriC replication in Escherichia coli., Mol Microbiol 19(2):389-96

 [12] Froelich JM., Phuong TK., Zyskind JW., 1996, Fis binding in the dnaA operon promoter region., J Bacteriol 178(20):6006-12

 [13] Chiaramello AE., Zyskind JW., 1990, Coupling of DNA replication to growth rate in Escherichia coli: a possible role for guanosine tetraphosphate., J Bacteriol 172(4):2013-9

 [14] Ohmori H., Kimura M., Nagata T., Sakakibara Y., 1984, Structural analysis of the dnaA and dnaN genes of Escherichia coli., Gene 28(2):159-70

 [15] Lee YS., Hwang DS., 1997, Occlusion of RNA polymerase by oligomerization of DnaA protein over the dnaA promoter of Escherichia coli., J Biol Chem 272(1):83-8

 [16] Marbaniang CN., Gowrishankar J., 2011, Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli., J Bacteriol 193(21):5985-96

RegulonDB