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Product(s) |

Expression|

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Standard Name	plsY
Gene Synonym(s)	ECK3049, b3059, JW3031, ygiH^[1], JW3031, ygiH
Product Desc.	conserved inner membrane protein^[2]^[3] Probable acylphosphate:glycerol-3-phosphate acyltransferase^[4]
Product Synonyms(s)	conserved inner membrane protein^[1], B3059^[2]^[1], YgiH^[2]^[1] , ECK3049, JW3031, ygiH, b3059
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): plsY^[2]
Regulation/Activity
Quick Links
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Notes

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ygiH(plsY) and plsX are synthetic lethals and cannot be simultaneously deleted, implicating ygiH(plsY) involvement in phospholipid biosynthesis (Yoshimura, 2007). Homologous to the PlsY acylphosphate:glycerol-3-phosphate acyltransferase (UniProtKB:P0A4Q0) of S. pneumoniae, which identifies a function for the UPF0078 family (COG0344). S. pneumoniae PlsX and PlsY work together as a two-step glycerol-3-phosphate acylation, the first step in phosphatidic acid synthesis, an intermediate in phospholipid synthesis (Lu, 2006). PlsXY homologs are present in E. coli, but PlsXY apparently cannot substitute for the single step reaction catalyzed by PlsB, which is essental in E. coli.^[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	plsY
Mnemonic	Phospholipid synthesis
Synonyms	ECK3049, b3059, JW3031, ygiH^[1], JW3031, ygiH
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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	69.03 minutes	MG1655: 3202716..3203333 <gbrowseImage> name=NC_000913:3202716..3203333 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 3089864..3090481 <gbrowseImage> name=NC_012759:3089864..3090481 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3203350..3203967 <gbrowseImage> name=NC_007779:3203350..3203967 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3300461..3301078 <gbrowseImage> name=NC_010473:3300461..3301078 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)	Reference	Availability
ΔygiH (Keio:JW3031)	deletion	deletion	PMID:16738554	Shigen CGSC10315^[5]
ΔygiH751::kan			PMID:16738554	CGSC:105044
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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
JW3031	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTGCAATCGCGCCTGGAAT Primer 2:CCtTCGGGATCCTTTTCGCGCTT
19F2	Kohara Phage	Genobase	PMID:3038334
tolC210::Tn10	Linked marker	CAG12184 = CGSC7437^[5]	est. P1 cotransduction: 40% ^[6]
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[5]	est. P1 cotransduction: 65% ^[6] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
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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:EG11674	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1625	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3059
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C3809
EcoGene	EcoGene:EG11674	Escherichia coli str. K-12 substr. MG1655
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YGIH
ASAP	ASAP:ABE-0010042	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	ECOCYC:EG11674	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947561	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001617	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	PlsY
Synonyms	conserved inner membrane protein^[1], B3059^[2]^[1], YgiH^[2]^[1] , ECK3049, JW3031, ygiH, b3059
Product description	conserved inner membrane protein^[2]^[3] Probable acylphosphate:glycerol-3-phosphate acyltransferase^[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:0005886	plasma membrane	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01043	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003811	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020788	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008654	phospholipid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0594	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016747	transferase activity, transferring acyl groups other than amino-acyl groups	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.3.1	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	Notes	References	Evidence
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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
plasma membrane	C-terminus localized in the cytoplasm with 5 predicted transmembrane domains	Daley et al. (2005) ^[7]
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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 MSAIAPGMIL IAYLCGSISS AILVCRLCGL PDPRTSGSGN PGATNVLRIG GKGAAVAVLI FDVLKGMLPV WGAYELGVSP FWLGLIAIAA CLGHIWPVFF GFKGGKGVAT AFGAIAPIGW DLTGVMAGTW LLTVLLSGYS SLGAIVSALI APFYVWWFKP QFTFPVSMLS CLILLRHHDN IQRLWRRQET KIWTKFKRKR EKDPE
Length	205
Mol. Wt	22.193 kDa
pI	10.0 (calculated)
Extinction coefficient	55,460 - 56,085 (calc based on 4 Y, 9 W, and 5 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	Notes	References
Domain	10..185	PF02660 Domain of unknown function (DUF205)		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=ygiH 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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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:16130955	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947561	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010042	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P60782	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11674	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11674	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947561	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001617	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1625	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	200	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	93	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	134	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)
ygiH
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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_000913:3202696..3202736 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:b3059 (EcoliWiki Page)	NCBI GEO profiles for ygiH
microarray	GenExpDB:b3059 (EcoliWiki Page)	Summary of data for ygiH 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
	GFP Fusion	Intergenic region (3202156..3202393) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:E2^[8]
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Notes

Accessions Related to plsY Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11674	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1625	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3059
EcoGene	EcoGene:EG11674	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001617	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010042	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
Xenopus tropicalis	ENSXETP00000042756 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YGIH	From SHIGELLACYC
E. coli O157	YGIH	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)	PF02660 Domain of unknown function (DUF205)
EcoCyc	EcoCyc:EG11674	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11674	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001617	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1625	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010042	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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

plsY: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 plsY Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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