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Expression|

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Standard Name	sdiA
Gene Synonym(s)	ECK1915, b1916, JW1901, uvrX^[1], uvrX
Product Desc.	SdiA transcriptional activator^[2]; SdiA transcriptional dual regulator^[3] Quorum-sensing ftsQAZ-P2, acrABCDE transcriptional activator; fluoroquinolone resistance; overproduction confers drug resistance by stimulating the acr genes; SdiA senses exogenous N-acyl homoserine lactones^[4]
Product Synonyms(s)	DNA-binding transcriptional activator^[1], B1916^[2]^[1], SdiA^[2]^[1] , ECK1915, JW1901, uvrX, b1916
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): sdiA^[2]
Regulation/Activity
Quick Links
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Notes

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Suppresses inhibitory effect of the MinC/MinD division inhibitor. N-acyl homoserine lactones act as folding switches for SdiA. LuxR family. SdiA has other global transcription targets such as uvrY, csrB, recN and nei. E. coli makes an unknown weak auto-inducer when grown in rich media. Most phenotypic effects require overproduction of SdiA. sdiA mutants are more sensitive to fluoroquinolones and have reduced AcrB protein, but are not defective in cell division. An sdiA ydiV double mutant has twofold reduced cAMP levels than inhibits quorum sensing system 2 (Zhou, 2008).^[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	sdiA
Mnemonic	Suppress division inhibitors
Synonyms	ECK1915, b1916, JW1901, uvrX^[1], uvrX
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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	42.98 minutes	MG1655: 1994856..1994134 <gbrowseImage> name=NC_000913:1994134..1994856 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 1886617..1887339 <gbrowseImage> name=NC_012759:1886617..1887339 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1998969..1998247 <gbrowseImage> name=NC_007779:1998247..1998969 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2085864..2085142 <gbrowseImage> name=NC_010473:2085142..2085864 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
sdiA(del) (Keio:JW1901)	deletion	deletion			PMID:16738554	Shigen CGSC9582^[5]
sdiA(del)::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
sdiA(del)::kan	deletion		Biolog:respiration	unable to respire Bromosuccinate	PMID:16095938
sdiA(del)::kan	deletion		Biolog:respiration	unable to respire L-Asparagine	PMID:16095938
sdiA(del)::kan	deletion		Biolog:respiration	unable to respire L-Aspartate	PMID:16095938
sdiA762(del)::kan					PMID:16738554	CGSC:102900
sdiA1E11	truncation at C-terminus		Growth Phenotype	biofilm formation is reduced from wild type due to increased indole concentration, 2A 2B.	PMID:19168658
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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
JW1901	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAGGATAAGGATTTTTTCAG Primer 2:CCAATTAAGCCAGTAGCGGCCGC
16B12	Kohara Phage	Genobase	PMID:3038334
uvrC279::Tn10	Linked marker	CAG12156 = CGSC7394^[5]	est. P1 cotransduction: 88% ^[6]
zed-3069::Tn10	Linked marker	CAG18451 = CGSC7395^[5]	est. P1 cotransduction: 16% ^[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:EG10935	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10935	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000924	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946421	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0928	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006381	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	SdiA
Synonyms	DNA-binding transcriptional activator^[1], B1916^[2]^[1], SdiA^[2]^[1] , ECK1915, JW1901, uvrX, b1916
Product description	SdiA transcriptional activator^[2]; SdiA transcriptional dual regulator^[3] Quorum-sensing ftsQAZ-P2, acrABCDE transcriptional activator; fluoroquinolone resistance; overproduction confers drug resistance by stimulating the acr genes; SdiA senses exogenous N-acyl homoserine lactones^[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:0000156	two-component response regulator activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016032	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016032	P	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016032	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:IPR000792	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000792	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016032	C	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:IPR000792	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:IPR016032	P	Seeded from EcoCyc (v14.0)	complete
	GO:0007049	cell cycle	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0131	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043565	sequence-specific DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000792	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051301	cell division	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0132	P	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	glvG	PMID:16606699	Experiment(s):EBI-1141330
Protein	groL	PMID:16606699	Experiment(s):EBI-1141330
Protein	rplD	PMID:16606699	Experiment(s):EBI-1141330
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1141330
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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 MQDKDFFSWR RTMLLRFQRM ETAEEVYHEI ELQAQQLEYD YYSLCVRHPV PFTRPKVAFY TNYPEAWVSY YQAKNFLAID PVLNPENFSQ GHLMWNDDLF SEAQPLWEAA RAHGLRRGVT QYLMLPNRAL GFLSFSRCSA REIPILSDEL QLKMQLLVRE SLMALMRLND EIVMTPEMNF SKREKEILRW TAEGKTSAEI AMILSISENT VNFHQKNMQK KINAPNKTQV ACYAAATGLI
Length	240
Mol. Wt	28.117 kDa
pI	7.0 (calculated)
Extinction coefficient	42,400 - 42,775 (calc based on 10 Y, 5 W, and 3 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	22..165	PF03472 Autoinducer binding domain	PMID:19920124
Domain	177..234	PF00196 Bacterial regulatory proteins, luxR family	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=sdiA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

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:16129863	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946421	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006381	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P07026	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10935	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10935	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946421	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000924	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0928	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	Notes	Reference(s)
Protein	Ecoli K-12	11.684+/-0.134	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.023545706	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	434	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	87	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	563	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)
sdiA
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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_000913:1994836..1994876 source=MG1655 flip=1 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:b1916 (EcoliWiki Page)	NCBI GEO profiles for sdiA
microarray	GenExpDB:b1916 (EcoliWiki Page)	Summary of data for sdiA 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 sdiA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10935	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0928	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1916
EcoGene	EcoGene:EG10935	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000924	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006381	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	SDIA	From SHIGELLACYC
E. coli O157	SDIA	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)	PF03472 Autoinducer binding domain
Pfam (EcoliWiki Page)	PF00196 Bacterial regulatory proteins, luxR family
Superfamily (EcoliWiki Page)	SUPERFAMILY:46894
Superfamily (EcoliWiki Page)	SUPERFAMILY:75516
EcoCyc	EcoCyc:EG10935	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10935	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000924	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0928	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006381	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 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 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).

sdiA: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 sdiA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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