RegulonDB

Gene
Name:	topB
Synonym(s):	ECK1761, EG11014, b1763, mutR
Genome position(nucleotides):	1844999 <-- 1846960 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	55.15
External database links:

ASAP:	ABE-0005869
CGSC:	29988
CGSC:	36749
ECHOBASE:	EB1007
OU-MICROARRAY:	b1763
PortEco:	topB
STRING:	511145.b1763
COLOMBOS:	topB

Gene

Name:

topB

Synonym(s):

ECK1761, EG11014, b1763, mutR

Genome position(nucleotides):

1844999 <-- 1846960 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

55.15

External database links:

ASAP:

CGSC:

CGSC:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

194 -> 199

SVGRVQ

3 -> 135

LFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLIN

1 -> 134

MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLI

158 -> 593

LCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQ

Type

Positions

Sequence

194 -> 199

SVGRVQ

3 -> 135

LFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLIN

1 -> 134

MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLI

158 -> 593

Multifun Terms (GenProtEC)

2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication

2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related

Gene Ontology Terms (GO)

cellular_component

GO:0005829 - cytosol
GO:0043597 - cytoplasmic replication fork

molecular_function

GO:0098847 - sequence-specific single stranded DNA binding
GO:0003677 - DNA binding
GO:0003916 - DNA topoisomerase activity
GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0046872 - metal ion binding
GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity
GO:0000287 - magnesium ion binding

biological_process

GO:0006261 - DNA-dependent DNA replication
GO:0006310 - DNA recombination
GO:0006265 - DNA topological change
GO:0051304 - chromosome separation

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	ynjIp5	1844886	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.378. P-value: 9.445e-6 Read more >	[ICWHO]	[16]
promoter	ynjIp4	1844902	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.063. P-value: 7.139e-6 Read more >	[ICWHO]	[16]
promoter	ynjIp1	1845011	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 2.376. P-value: 8.028e-5 Read more >	[ICWHO]	[16]
promoter	TSS_2071	1847772	reverse	nd	[RS-EPT-CBR]	[17]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

ynjIp5

1844886

reverse

Similarity to the consensus
Read more >

[ICWHO]

[16]

promoter

ynjIp4

1844902

reverse

Similarity to the consensus
Read more >

[ICWHO]

[16]

promoter

ynjIp1

1845011

reverse

Similarity to the consensus
Read more >

[ICWHO]

[16]

promoter

TSS_2071

1847772

reverse

[RS-EPT-CBR]

[17]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[ICWHO] Inferred computationally without human oversight

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

Reference(s)
[1] Bebenek K., Janion C., 1983, Involvement of the mismatch repair system in base analogue-induced mutagenesis., Mol Gen Genet 191(2):276-81
[2] Bernstein DA., Zittel MC., Keck JL., 2003, High-resolution structure of the E.coli RecQ helicase catalytic core., EMBO J 22(19):4910-21
[3] DiGate RJ., 1999, Overexpression and purification of Escherichia coli DNA topoisomerase III., Methods Mol Biol 94:153-62
[4] Gomez-Eichelmann MC., Camacho-Carranza R., 1995, [DNA supercoiling and topoisomerases in Escherichia coli]., Rev Latinoam Microbiol 37(3):291-304
[5] Hiasa H., Marians KJ., 1994, Topoisomerase III, but not topoisomerase I, can support nascent chain elongation during theta-type DNA replication., J Biol Chem 269(51):32655-9
[6] Jarukanont D., Coimbra JT., Bauerhenne B., Fernandes PA., Patel S., Ramos MJ., Garcia ME., 2014, Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase., Phys Chem Chem Phys 16(39):21768-77
[7] Martel M., Balleydier A., Brochu J., Drolet M., 2018, Detection of oriC-Independent Replication in Escherichia coli Cells., Methods Mol Biol 1703:131-138
[8] Martel M., Balleydier A., Sauriol A., Drolet M., 2015, Constitutive stable DNA replication in Escherichia coli cells lacking type 1A topoisomerase activity., DNA Repair (Amst) 35:37-47
[9] Rydberg B., 1978, Bromouracil mutagenesis and mismatch repair in mutator strains of Escherichia coli., Mutat Res 52(1):11-24
[10] Santos ME., Drake JW., 1994, Rates of spontaneous mutation in bacteriophage T4 are independent of host fidelity determinants., Genetics 138(3):553-64
[11] Stockum A., Lloyd RG., Rudolph CJ., 2012, On the viability of Escherichia coli cells lacking DNA topoisomerase I., BMC Microbiol 12:26
[12] Uematsu N., Eda S., Yamamoto K., 1997, An Escherichia coli topB mutant increases deletion and frameshift mutations in the supF target gene., Mutat Res 383(3):223-30
[13] Usongo V., Martel M., Balleydier A., Drolet M., 2016, Mutations reducing replication from R-loops suppress the defects of growth, chromosome segregation and DNA supercoiling in cells lacking topoisomerase I and RNase HI activity., DNA Repair (Amst) 40:1-17
[14] Usongo V., Nolent F., Sanscartier P., Tanguay C., Broccoli S., Baaklini I., Drlica K., Drolet M., 2008, Depletion of RNase HI activity in Escherichia coli lacking DNA topoisomerase I leads to defects in DNA supercoiling and segregation., Mol Microbiol 69(4):968-81
[15] Zhang HL., DiGate RJ., 1995, The carboxyl-terminal residues of Escherichia coli DNA topoisomerase III are involved in substrate binding., J Biol Chem 270(35):20870
[16] 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
[17] 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.

Reference(s)

[1] Bebenek K., Janion C., 1983, Involvement of the mismatch repair system in base analogue-induced mutagenesis., Mol Gen Genet 191(2):276-81

[2] Bernstein DA., Zittel MC., Keck JL., 2003, High-resolution structure of the E.coli RecQ helicase catalytic core., EMBO J 22(19):4910-21

[3] DiGate RJ., 1999, Overexpression and purification of Escherichia coli DNA topoisomerase III., Methods Mol Biol 94:153-62

[4] Gomez-Eichelmann MC., Camacho-Carranza R., 1995, [DNA supercoiling and topoisomerases in Escherichia coli]., Rev Latinoam Microbiol 37(3):291-304

[5] Hiasa H., Marians KJ., 1994, Topoisomerase III, but not topoisomerase I, can support nascent chain elongation during theta-type DNA replication., J Biol Chem 269(51):32655-9

[6] Jarukanont D., Coimbra JT., Bauerhenne B., Fernandes PA., Patel S., Ramos MJ., Garcia ME., 2014, Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase., Phys Chem Chem Phys 16(39):21768-77

[7] Martel M., Balleydier A., Brochu J., Drolet M., 2018, Detection of oriC-Independent Replication in Escherichia coli Cells., Methods Mol Biol 1703:131-138

[8] Martel M., Balleydier A., Sauriol A., Drolet M., 2015, Constitutive stable DNA replication in Escherichia coli cells lacking type 1A topoisomerase activity., DNA Repair (Amst) 35:37-47

[9] Rydberg B., 1978, Bromouracil mutagenesis and mismatch repair in mutator strains of Escherichia coli., Mutat Res 52(1):11-24

[10] Santos ME., Drake JW., 1994, Rates of spontaneous mutation in bacteriophage T4 are independent of host fidelity determinants., Genetics 138(3):553-64

[11] Stockum A., Lloyd RG., Rudolph CJ., 2012, On the viability of Escherichia coli cells lacking DNA topoisomerase I., BMC Microbiol 12:26

[12] Uematsu N., Eda S., Yamamoto K., 1997, An Escherichia coli topB mutant increases deletion and frameshift mutations in the supF target gene., Mutat Res 383(3):223-30

[13] Usongo V., Martel M., Balleydier A., Drolet M., 2016, Mutations reducing replication from R-loops suppress the defects of growth, chromosome segregation and DNA supercoiling in cells lacking topoisomerase I and RNase HI activity., DNA Repair (Amst) 40:1-17

[14] Usongo V., Nolent F., Sanscartier P., Tanguay C., Broccoli S., Baaklini I., Drlica K., Drolet M., 2008, Depletion of RNase HI activity in Escherichia coli lacking DNA topoisomerase I leads to defects in DNA supercoiling and segregation., Mol Microbiol 69(4):968-81

[15] Zhang HL., DiGate RJ., 1995, The carboxyl-terminal residues of Escherichia coli DNA topoisomerase III are involved in substrate binding., J Biol Chem 270(35):20870

[16] 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

[17] 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.