RegulonDB

Gene
Name:	sbcB
Synonym(s):	ECK2005, EG10926, b2011, cpeA, exoI, rmuA, xonA
Genome position(nucleotides):	2082756 --> 2084183 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.07
External database links:

ASAP:	ABE-0006686
CGSC:	178
ECHOBASE:	EB0919
OU-MICROARRAY:	b2011
PortEco:	sbcB
STRING:	511145.b2011
COLOMBOS:	sbcB

Gene

Name:

sbcB

Synonym(s):

ECK2005, EG10926, b2011, cpeA, exoI, rmuA, xonA

Genome position(nucleotides):

2082756 --> 2084183 Genome Browser

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

50.07

External database links:

ASAP:

CGSC:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

225 -> 225

316 -> 316

327 -> 327

311 -> 311

212 -> 472

RNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAE

Type

Positions

Sequence

225 -> 225

316 -> 316

327 -> 327

311 -> 311

212 -> 472

318 -> 318

338 -> 338

150 -> 150

181 -> 181

207 -> 207

148 -> 148

319 -> 319

452 -> 452

475 -> 475

202 -> 355

PRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAE

448 -> 448

13 -> 192

FHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHSNAHDAMADVYATIA

343 -> 343

358 -> 475

TPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAEEIV

210 -> 218

THRNKHKLM

227 -> 227

331 -> 331

Multifun Terms (GenProtEC)

1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.2 - DNA

2 - information transfer --> 2.1 - DNA related --> 2.1.5 - DNA degradation

Gene Ontology Terms (GO)

cellular_component

GO:0005829 - cytosol

molecular_function

GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0003697 - single-stranded DNA binding
GO:0004518 - nuclease activity
GO:0004527 - exonuclease activity
GO:0004529 - exodeoxyribonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0000175 - 3'-5'-exoribonuclease activity
GO:0008852 - exodeoxyribonuclease I activity
GO:0000287 - magnesium ion binding
GO:0008310 - single-stranded DNA 3'-5' exodeoxyribonuclease activity
GO:0051575 - 5'-deoxyribose-5-phosphate lyase activity

biological_process

GO:0006308 - DNA catabolic process
GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0006274 - DNA replication termination
GO:0000738 - DNA catabolic process, exonucleolytic
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_2317	2081705	reverse	nd	[RS-EPT-CBR]	[12]
promoter	TSS_2318	2082732	forward	nd	[RS-EPT-CBR]	[12]
promoter	TSS_2319	2083283	forward	nd	[RS-EPT-CBR]	[12]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_2317

2081705

reverse

[RS-EPT-CBR]

[12]

promoter

TSS_2318

2082732

forward

[RS-EPT-CBR]

[12]

promoter

TSS_2319

2083283

forward

[RS-EPT-CBR]

[12]

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

Evidence

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

Reference(s)
[1] Allgood ND., Silhavy TJ., 1991, Escherichia coli xonA (sbcB) mutants enhance illegitimate recombination., Genetics 127(4):671-80
[2] Gopalakrishna K., Bhattacharjee SK., 1976, Role of Rec pathways on sensitivity of Escherichia coli to near-ultraviolet and visible light., J Bacteriol 127(2):1022-3
[3] Jayashree P., Gowrishankar J., 1995, A new phenotype for sbcB mutations in Escherichia coli: RecA-dependent increase in plasmid-borne gene expression., Mol Gen Genet 246(5):648-56
[4] Lehman IR., Nussbaum AL., 1964, The deoxyribonucleases of Escherichia coli. V. On the specificity of exonuclease I (phosphodiesterase)., J Biol Chem 239:2628-36
[5] Phillips GJ., Prasher DC., Kushner SR., 1988, Physical and biochemical characterization of cloned sbcB and xonA mutations from Escherichia coli K-12., J Bacteriol 170(5):2089-94
[6] Prasher D., Kasunic DA., Kushner SR., 1983, Physical and genetic characterization of the cloned sbcB (exonuclease I) region of the Escherichia coli genome., J Bacteriol 153(2):903-8
[7] Prasher DC., Conarro L., Kushner SR., 1983, Amplification and purification of exonuclease I from Escherichia coli K12., J Biol Chem 258(10):6340-3
[8] Sandigursky M., Franklin WA., 1992, DNA deoxyribophosphodiesterase of Escherichia coli is associated with exonuclease I., Nucleic Acids Res 20(18):4699-703
[9] Wang TC., Smith KC., 1985, Mechanism of sbcB-suppression of the recBC-deficiency in postreplication repair in UV-irradiated Escherichia coli K-12., Mol Gen Genet 201(2):186-91
[10] Wendel BM., Courcelle CT., Courcelle J., 2014, Completion of DNA replication in Escherichia coli., Proc Natl Acad Sci U S A 111(46):16454-9
[11] Yamaguchi H., Hanada K., Asami Y., Kato JI., Ikeda H., 2000, Control of genetic stability in Escherichia coli: the SbcB 3'-5' exonuclease suppresses illegitimate recombination promoted by the RecE 5'-3' exonuclease., Genes Cells 5(2):101-9
[12] 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] Allgood ND., Silhavy TJ., 1991, Escherichia coli xonA (sbcB) mutants enhance illegitimate recombination., Genetics 127(4):671-80

[2] Gopalakrishna K., Bhattacharjee SK., 1976, Role of Rec pathways on sensitivity of Escherichia coli to near-ultraviolet and visible light., J Bacteriol 127(2):1022-3

[3] Jayashree P., Gowrishankar J., 1995, A new phenotype for sbcB mutations in Escherichia coli: RecA-dependent increase in plasmid-borne gene expression., Mol Gen Genet 246(5):648-56

[4] Lehman IR., Nussbaum AL., 1964, The deoxyribonucleases of Escherichia coli. V. On the specificity of exonuclease I (phosphodiesterase)., J Biol Chem 239:2628-36

[5] Phillips GJ., Prasher DC., Kushner SR., 1988, Physical and biochemical characterization of cloned sbcB and xonA mutations from Escherichia coli K-12., J Bacteriol 170(5):2089-94

[6] Prasher D., Kasunic DA., Kushner SR., 1983, Physical and genetic characterization of the cloned sbcB (exonuclease I) region of the Escherichia coli genome., J Bacteriol 153(2):903-8

[7] Prasher DC., Conarro L., Kushner SR., 1983, Amplification and purification of exonuclease I from Escherichia coli K12., J Biol Chem 258(10):6340-3

[8] Sandigursky M., Franklin WA., 1992, DNA deoxyribophosphodiesterase of Escherichia coli is associated with exonuclease I., Nucleic Acids Res 20(18):4699-703

[9] Wang TC., Smith KC., 1985, Mechanism of sbcB-suppression of the recBC-deficiency in postreplication repair in UV-irradiated Escherichia coli K-12., Mol Gen Genet 201(2):186-91

[10] Wendel BM., Courcelle CT., Courcelle J., 2014, Completion of DNA replication in Escherichia coli., Proc Natl Acad Sci U S A 111(46):16454-9

[11] Yamaguchi H., Hanada K., Asami Y., Kato JI., Ikeda H., 2000, Control of genetic stability in Escherichia coli: the SbcB 3'-5' exonuclease suppresses illegitimate recombination promoted by the RecE 5'-3' exonuclease., Genes Cells 5(2):101-9

[12] 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.