RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit       
Name: topA
Gene(s): topA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: topAp5
+1: 1330789
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 259
Sequence: cacgctggtggcaagagcgccttactggcaactttggattttgcatgctaataaagttgcGtatcggattttatcaggtac
                         -35                     -10        +1                   
Note(s): It is likely that topAp5 is recognized by both σ70 and σS, because there is a basal level of topAp5 activity in rpoS::Tn10 strains. This promoter shows a decrease in transcription during heat shock Qi H,1997.
Evidence: [HIPP]
[TIM]
Reference(s): [1] Qi H., et al., 1997


Transcription unit          
Name: topA
Gene(s): topA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: topAp4
+1: 1330818
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 230
Sequence: aactttggattttgcatgctaataaagttgcgtatcggattttatcaggtacagtgtgacGctttcgtcaatctggcaata
                            -35                   -10       +1                   
Note(s): topAp4 shows a decrease in transcription during the stationary phase, probably due to the very small spacing between topAp4 and topAp5, where binding of σS polymerase to promoter topAp5 might block binding of σ70 RNA polymerase. This promoter shows a decrease in transcription during heat shock.
Transcription of promoter topAp4 is negatively regulated under the conditions of oxidative stress and high FIS levels. This repressor overlaps the promoter topAp4 and recruits additional FIS molecules to form multiple complexes in the upstream region of topA Weinstein-Fischer D,2007
Evidence: [AIPP]
[CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[HIPP]
[IMP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Lesley SA., et al., 1990
[1] Qi H., et al., 1997
[3] Salgado H, et al., 2012
[4] Tse-Dinh YC., et al., 1988
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 repressor topAp4 1330717 1330731 -94.0 catggcttgcAGACAAATATACCACgctggtggca nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
proximal Fis repressor topAp4 1330743 1330757 -68.0 ctggtggcaaGAGCGCCTTACTGGCaactttggat nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
proximal Fis repressor topAp4 1330774 1330788 -37.0 ggattttgcaTGCTAATAAAGTTGCgtatcggatt nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
proximal Fis repressor topAp4 1330795 1330809 -16.0 ttgcgtatcgGATTTTATCAGGTACagtgtgacgc nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
proximal Fis repressor topAp4 1330816 1330830 6.0 gtacagtgtgACGCTTTCGTCAATCtggcaataga nd [BPP], [GEA] [5]


Transcription unit       
Name: topA
Gene(s): topA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: topAp3
+1: 1330848
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 200
Sequence: cgtatcggattttatcaggtacagtgtgacgctttcgtcaatctggcaatagatttgcttGacattcgaccaaaattccgt
                          -35                     -10       +1                   
Note(s): Sometimes the activity of topAp3 is not detected.
Evidence: [AIPP]
[HIPP]
[TIM]
Reference(s): [2] Lesley SA., et al., 1990
[4] Tse-Dinh YC., et al., 1988


Transcription unit       
Name: topA
Gene(s): topA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: topAp2
+1: 1330883
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 165
Sequence: cgtcaatctggcaatagatttgcttgacattcgaccaaaattccgtcgtgctatagcgccTgtaggccaagacctgttaac
                        -35                      -10        +1                   
Note(s): topAp2 shows a decrease in transcription during heat shock.
Evidence: [AIPP]
[HIPP]
[TIM]
Reference(s): [2] Lesley SA., et al., 1990
[1] Qi H., et al., 1997
[4] Tse-Dinh YC., et al., 1988


Transcription unit          
Name: topA
Gene(s): topA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: topAp1
+1: 1330980
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 68
Sequence: tcgtgaacagagtcacgacaaggggttgatatccgcagagagcgagtccatatcggtaacTcgttgccagtggaaggttta
                          -35                 -10           +1                   
Note(s): topAp1 is induced by heat shock and by hydrogen peroxide. The first induction is dependent of sigma32 and the last induction is dependent of Fis protein.No auxiliar factors are required for transcription of this promoter by the sigma32 holoenzyme, however this promoter is induced by the Fis protein, maybe this activation is sigma70-dependent, because it also resembles the core promoter recognized by this sigma factor.
The transcription of promoter topAp1 increases when FIS levels are low under the conditions of oxidative stress (hydrogen peroxide) and during the late exponential phase Weinstein-Fischer D,2007. Ochs M,1996 In contrast, high FIS levels of early exponential phase result in its repression. Recently, it had been demonstrated that this transcription factor overlaps the promoter topAp1 in a cooperative process, favoring the binding and the additional recruitment of molecules to form multiple complexes at the promoter topAp1 Weinstein-Fischer D,2007
Evidence: [AIPP]
[HIPP]
[IMP]
[TIM]
Reference(s): [2] Lesley SA., et al., 1990
[6] Nonaka G., et al., 2006
[7] Qi H., et al., 1999
[1] Qi H., et al., 1997
[4] Tse-Dinh YC., et al., 1988
[8] Wade JT., et al., 2006
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 topAp1 1330717 1330731 -256.0 catggcttgcAGACAAATATACCACgctggtggca nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
remote Fis activator topAp1 1330743 1330757 -230.0 ctggtggcaaGAGCGCCTTACTGGCaactttggat nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
remote Fis activator topAp1 1330774 1330788 -199.0 ggattttgcaTGCTAATAAAGTTGCgtatcggatt nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
remote Fis activator topAp1 1330795 1330809 -178.0 ttgcgtatcgGATTTTATCAGGTACagtgtgacgc nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
remote Fis activator topAp1 1330816 1330830 -157.0 gtacagtgtgACGCTTTCGTCAATCtggcaataga nd [BPP], [GEA] [5]
remote Fis activator topAp1 1330844 1330858 -129.0 caatagatttGCTTGACATTCGACCaaaattccgt nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5], [9]
remote Fis activator topAp1 1330879 1330893 -94.0 cgtgctatagCGCCTGTAGGCCAAGacctgttaac nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5], [9]
proximal Fis activator topAp1 1330911 1330925 -62.0 aactcagtcaCCTGAATTTTCGTGAacagagtcac nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5], [9]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor topAp1 1330943 1330957 -30.0 cacgacaaggGGTTGATATCCGCAGagagcgagtc nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
proximal Fis repressor topAp1 1330963 1330977 -10.0 cgcagagagcGAGTCCATATCGGTAactcgttgcc nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]
proximal Fis repressor topAp1 1330992 1331006 20.0 gttgccagtgGAAGGTTTATCAACGtgcgacgcat nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [AIPP] Automated inference of promoter position

 [CV(RS-EPT-CBR/TA)] cross validation(RS-EPT-CBR/TA)

 [CV(TA/TIM)] cross validation(TA/TIM)

 [IMP] Inferred from mutant phenotype

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

 [BPP] Binding of purified proteins

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] Qi H., Menzel R., Tse-Dinh YC., 1997, Regulation of Escherichia coli topA gene transcription: involvement of a sigmaS-dependent promoter., J Mol Biol 267(3):481-9

 [2] Lesley SA., Jovanovich SB., Tse-Dinh YC., Burgess RR., 1990, Identification of a heat shock promoter in the topA gene of Escherichia coli., J Bacteriol 172(12):6871-4

 [3] 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.

 [4] Tse-Dinh YC., Beran RK., 1988, Multiple promoters for transcription of the Escherichia coli DNA topoisomerase I gene and their regulation by DNA supercoiling., J Mol Biol 202(4):735-42

 [5] Weinstein-Fischer D., Altuvia S., 2007, Differential regulation of Escherichia coli topoisomerase I by Fis., Mol Microbiol 63(4):1131-44

 [6] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [7] Qi H., Menzel R., Tse-Dinh YC., 1999, Increased thermosensitivity associated with topoisomerase I deletion and promoter mutations in Escherichia coli., FEMS Microbiol Lett 178(1):141-6

 [8] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [9] Weinstein-Fischer D., Elgrably-Weiss M., Altuvia S., 2000, Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, topoisomerase I and Fis., Mol Microbiol 35(6):1413-20

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