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Product(s) |

Expression|

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Standard Name	raiA
Gene Synonym(s)	yfiA, ECK2594, b2597, JW2578, urf1, pY^[1]^[2]^[3]
Product Desc.	stationary phase translation inhibitor and ribosome stability factor^[3]^[2] Protein Y, associated with 30S ribosomal subunit; inhibits 70S dimer formation; stabilizes the ribosomal 70S complex against dissociation at low magnesium ion concentrations; counteracts miscoding under stress conditions ^[4]
Product Synonyms(s)	cold shock protein associated with 30S ribosomal subunit^[1], B2597^[3]^[1], YfiA^[3]^[1], Urf1^[3]^[1], RaiA^[3]^[1], pY^[3]^[1] , ECK2594, JW2578, yfiA, b2597
Function from GO	<GO_nr />
Knock-Out Phenotype	Non-essential ^[5]
Regulation/Expression	transcription unit(s): yfiA^[3]
Regulation/Activity
Quick Links
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Notes

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RaiA is a ribosome-associated factor that is induced in stationary phase. hpf paralog has opposite effect on 70S dimers.^[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	raiA
Mnemonic	ribosome-associated inhibitor A
Synonyms	yfiA, ECK2594, b2597, JW2578, urf1, pY^[1]^[2]^[3]
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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	58.95 minutes	MG1655: 2735176..2735517 <gbrowseImage> name=NC_000913:2735176..2735517 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2620988..2621329 <gbrowseImage> name=NC_012759:2620988..2621329 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2735810..2736151 <gbrowseImage> name=NC_007779:2735810..2736151 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
Coding Start (SO:0000323)	MG1655	2735179	Edman degradation	PMID:8740179 PMID:9298646 PMID:10535924 PMID:11168583
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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
ΔyfiA760::kan					PMID:16738554	CGSC:104792
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
21D7	Kohara Phage	Genobase	PMID:3038334
E8F2	Kohara Phage	Genobase	PMID:3038334
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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:EG11151	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11151	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001134	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947129	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1140	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008540	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	RaiA
Synonyms	cold shock protein associated with 30S ribosomal subunit^[1], B2597^[3]^[1], YfiA^[3]^[1], Urf1^[3]^[1], RaiA^[3]^[1], pY^[3]^[1] , ECK2594, JW2578, yfiA, b2597
Product description	stationary phase translation inhibitor and ribosome stability factor^[3]^[2] Protein Y, associated with 30S ribosomal subunit; inhibits 70S dimer formation; stabilizes the ribosomal 70S complex against dissociation at low magnesium ion concentrations; counteracts miscoding under stress conditions ^[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:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003489	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006417	regulation of translation	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0810	P	Seeded from EcoCyc (v14.0)	complete
	GO:0022627	cytosolic small ribosomal subunit	PMID:10535924	IDA: Inferred from Direct Assay		C	Purified protein Y was incubated with purified 70S ribosomes or purified 30S or 50S subunits. The binding mixture was filtered through Amicon filters that would retain ribosomal particles, but not protein Y (Fig. 3).	complete
	GO:0006950	response to stress	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0346	P	Seeded from EcoCyc (v14.0)	complete
	GO:0022627	cytosolic small ribosomal subunit	PMID:15502846	IDA: Inferred from Direct Assay		C	X-ray crystal structures of 70S ribosomes with and without YfiA protein. The purified YfiA protein was soaked into the crystals.	complete
	GO:0044238	primary metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003489	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	Notes	References	Evidence
	30S ribosomal subunit	Binding to 30S subunit shown by biochemical studies.^[6] Binding to 30S subunit shown by X-ray crystal structures of 70S ribosomes with and without YfiA protein. <ref name=PMID:15502846>
Protein	matC		PMID:16606699	Experiment(s):EBI-1143442
Protein	rpmB		PMID:16606699	Experiment(s):EBI-1143442
Protein	yciN		PMID:16606699	Experiment(s):EBI-1143442
Protein	cybC		PMID:16606699	Experiment(s):EBI-1143442
Protein	greB		PMID:16606699	Experiment(s):EBI-1143442
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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
cytoplasm			From EcoCyc^[2]
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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 MTMNITSKQM EITPAIRQHV ADRLAKLEKW QTHLINPHII LSKEPQGFVA DATINTPNGV LVASGKHEDM YTAINELINK LERQLNKLQH KGEARRAATS VKDANFVEEV EEE
Length	113
Mol. Wt	12.784 kDa
pI	6.7 (calculated)
Extinction coefficient	6,990 (calc based on 1 Y, 1 W, and 0 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
Initiator Methionine	1	Removed	UniProt:P0AD49
Domain	2..95	PF02482 Sigma 54 modulation protein / S30EA ribosomal protein		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=raiA taxon=562,83333 </beststructure>

Models

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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:16130518	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947129	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008540	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AD49	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11151	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11151	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947129	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001134	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1140	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	555.169+/-2.236	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.93535+/-0.05292	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.357771261	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	3606	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	5010	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	3438	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)
yfiA
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File:.jpg

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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_000913:2735156..2735196 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:b2597 (EcoliWiki Page)	NCBI GEO profiles for raiA
microarray	GenExpDB:b2597 (EcoliWiki Page)	Summary of data for raiA 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 raiA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11151	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1140	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2597
EcoGene	EcoGene:EG11151	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001134	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008540	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	YFIA	From SHIGELLACYC
E. coli O157	YFIA	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)	PF02482 Sigma 54 modulation protein / S30EA ribosomal protein
Superfamily (EcoliWiki Page)	SUPERFAMILY:69754
PFAM (EcoliWiki Page)	PFAM:PF02482
EcoCyc	EcoCyc:EG11151	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11151	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001134	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1140	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008540	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 ^3.11 ^3.12 ^3.13 ^3.14 EcoCyc (release 10.6; 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.
↑ Bubunenko, M et al. (2007) Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J. Bacteriol. 189 2844-53 PubMed
↑ Agafonov, DE et al. (1999) A protein residing at the subunit interface of the bacterial ribosome. Proc. Natl. Acad. Sci. U.S.A. 96 12345-9 PubMed

raiA: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 raiA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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