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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	soxR
Gene Synonym(s)	ECK4055, b4063, JW4024^[1], JW4024, marC
Product Desc.	SoxR transcriptional dual regulator^[2]^[3] Redox-sensitive transcriptional activator for soxS; superoxide response; AraC family^[4]
Product Synonyms(s)	DNA-binding transcriptional dual regulator, Fe-S center for redox-sensing^[1], B4063^[2]^[1], SoxR^[2]^[1], redox-sensing activator of soxS^[2]^[1] , ECK4055, JW4024, marC, b4063
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): soxR^[2]
Regulation/Activity
Quick Links
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Notes

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SoxR responds to superoxide and activates the SoxS global regulator in a regulatory cascade; reduced by RseC and RsxABCDGE.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	soxR
Mnemonic	Superoxide
Synonyms	ECK4055, b4063, JW4024^[1], JW4024, marC
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	92.15 minutes	MG1655: 4275492..4275956 <gbrowseImage> name=NC_000913:4275492..4275956 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4256402..4256866 <gbrowseImage> name=NC_012967:4256402..4256866 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4214337..4214801 <gbrowseImage> name=NC_012759:4214337..4214801 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4281059..4281523 <gbrowseImage> name=NC_007779:4281059..4281523 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4375188..4375652 <gbrowseImage> name=NC_010473:4375188..4375652 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔsoxR (Keio:JW4024)	deletion	deletion			PMID:16738554	Shigen CGSC10892^[5]
soxRR20C		R20C		(in soxR102; constitutively activated allele)			Strain variation; seeded from UniProt:P0ACS2
ΔsoxR::kan	deletion		Biolog:respiration	unable to respire D-Mannose	PMID:16095938
soxR101(Const,mdR, [CmR])					PMID:1696718 PMID:7679383	CGSC:64033	overexpresses the micF RNA
soxR102(Const,mdR, [CmR])					PMID:1696718	CGSC:70386
soxR103(Const,mdR, [CmR])					PMID:1696718 PMID:8065907	CGSC:70388
soxR104(Const,mdR, [CmR])					PMID:1696718 PMID:8065907	CGSC:70390
soxR105(Const,mdR, [CmR])			Resistant to	provides increased resistance to ampicillin and tetracycline	PMID:1696718 PMID:8065907 PMID:7679383	CGSC:70392
ΔsoxR757::kan					PMID:16738554	CGSC:102990
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW4024	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGAAAAGAAATTACCCCGCAT Primer 2:CCGTTTTGTTCATCTTCCAGCAA
12D1	Kohara Phage	Genobase	PMID:3038334
3F12	Kohara Phage	Genobase	PMID:3038334
malF3089::Tn10	Linked marker	CAG12164 = CGSC7476^[5]	est. P1 cotransduction: 24% ^[6]
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 31% ^[6]
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10957	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10957	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000946	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948566	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0950	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013316	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	SoxR
Synonyms	DNA-binding transcriptional dual regulator, Fe-S center for redox-sensing^[1], B4063^[2]^[1], SoxR^[2]^[1], redox-sensing activator of soxS^[2]^[1] , ECK4055, JW4024, marC, b4063
Product description	SoxR transcriptional dual regulator^[2]^[3] Redox-sensitive transcriptional activator for soxS; superoxide response; AraC family^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0000166	nucleotide binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009061	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010211	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000551	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010211	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005506	iron ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010211	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000551	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010211	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006979	response to oxidative stress	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010211	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0411	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051537	2 iron, 2 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0001	F	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1147374
Protein	yfgI	PMID:16606699	Experiment(s):EBI-1147374
Protein	alkA	PMID:16606699	Experiment(s):EBI-1147374
Protein	rplB	PMID:16606699	Experiment(s):EBI-1147374
Protein	yciH	PMID:16606699	Experiment(s):EBI-1147374
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MEKKLPRIKA LLTPGEVAKR SGVAVSALHF YESKGLITSI RNSGNQRRYK RDVLRYVAII KIAQRIGIPL ATIGEAFGVL PEGHTLSAKE WKQLSSQWRE ELDRRIHTLV ALRDELDGCI GCGCLSRSDC PLRNPGDRLG EEGTGARLLE DEQN
Length	154
Mol. Wt	17.149 kDa
pI	9.3 (calculated)
Extinction coefficient	15,470 - 15,970 (calc based on 3 Y, 2 W, and 4 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	References
Domain	13..49	PF00376 MerR family regulatory protein	PMID:19920124
Domain	54..119	PF09278 MerR, DNA binding	PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=soxR taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16131889	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948566	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013316	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACS2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10957	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10957	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948566	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000946	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0950	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	206	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	74	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	259	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
soxR
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:4275472..4275512 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b4063 (EcoliWiki Page)	NCBI GEO profiles for soxR
microarray	GenExpDB:b4063 (EcoliWiki Page)	Summary of data for soxR from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to soxR Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10957	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0950	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4063
EcoGene	EcoGene:EG10957	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000946	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013316	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Shigella flexneri	SOXR	From SHIGELLACYC
E. coli O157	SOXR	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00376 MerR family regulatory protein
Superfamily (EcoliWiki Page)	SUPERFAMILY:46955
Pfam (EcoliWiki Page)	PF09278 MerR, DNA binding
PFAM (EcoliWiki Page)	PFAM:PF00376
EcoCyc	EcoCyc:EG10957	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10957	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000946	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0950	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013316	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

soxR:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to soxR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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