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
ECOLIHUB:	topB
OU-MICROARRAY:	b1763
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:

ECOLIHUB:

OU-MICROARRAY:

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	nd	[ICWHO]	[17]
promoter	ynjIp4	1844902	reverse	nd	[ICWHO]	[17]
promoter	ynjIp1	1845011	reverse	nd	[ICWHO]	[17]
promoter	TSS_2071	1847772	reverse	nd	[RS-EPT-CBR]	[18]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

ynjIp5

1844886

reverse

[ICWHO]

[17]

promoter

ynjIp4

1844902

reverse

[ICWHO]

[17]

promoter

ynjIp1

1845011

reverse

[ICWHO]

[17]

promoter

TSS_2071

1847772

reverse

[RS-EPT-CBR]

[18]

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] Bichara M., Pelet S., Lambert IB., 2021, Recombinational repair in the absence of holliday junction resolvases in E. coli., Mutat Res 822:111740
[4] DiGate RJ., 1999, Overexpression and purification of Escherichia coli DNA topoisomerase III., Methods Mol Biol 94:153-62
[5] Gomez-Eichelmann MC., Camacho-Carranza R., 1995, [DNA supercoiling and topoisomerases in Escherichia coli]., Rev Latinoam Microbiol 37(3):291-304
[6] 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
[7] 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
[8] Martel M., Balleydier A., Brochu J., Drolet M., 2018, Detection of oriC-Independent Replication in Escherichia coli Cells., Methods Mol Biol 1703:131-138
[9] 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
[10] Rydberg B., 1978, Bromouracil mutagenesis and mismatch repair in mutator strains of Escherichia coli., Mutat Res 52(1):11-24
[11] Santos ME., Drake JW., 1994, Rates of spontaneous mutation in bacteriophage T4 are independent of host fidelity determinants., Genetics 138(3):553-64
[12] Stockum A., Lloyd RG., Rudolph CJ., 2012, On the viability of Escherichia coli cells lacking DNA topoisomerase I., BMC Microbiol 12:26
[13] 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
[14] 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
[15] 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
[16] 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
[17] 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
[18] 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] Bichara M., Pelet S., Lambert IB., 2021, Recombinational repair in the absence of holliday junction resolvases in E. coli., Mutat Res 822:111740

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

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

[6] 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

[7] 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

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

[9] 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

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

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

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

[13] 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

[14] 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

[15] 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

[16] 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

[17] 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

[18] 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.