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Standard Name	rssB
Gene Synonym(s)	ECK1230, b1235, JW1223, hnr, mviA, sprE, ychI, ychL^[1], verA, ychL
Product Desc.	regulator of RpoS^[2]^[3] Two-component response regulator, affecting RpoS regulon; anti-RpoS activity, phosphorylated form binds to RpoS and initiates proteolysis by ClpXP^[4]
Product Synonyms(s)	B1235^[2], SprE^[2], YchL^[2], Hnr^[2] , ECK1230, hnr, JW1223, mviA, sprE, verA, ychL, b1235
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rssAB^[2], rssB^[2]
Regulation/Activity
Quick Links
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Notes

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A yliE rssB9(hnr) double null mutant has significantly increased lycopene production in 1X M9; the effect may be salt-suppressible as it is not seen in 2X M9 (Alper, 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	rssB
Mnemonic	Regulation of Sigma S
Synonyms	ECK1230, b1235, JW1223, hnr, mviA, sprE, ychI, ychL^[1], verA, ychL
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Notes

Location(s) and DNA Sequence

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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	27.79 minutes	MG1655: 1289465..1290478 <gbrowseImage> name=NC_000913:1289465..1290478 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1290036..1291049 <gbrowseImage> name=NC_012967:1290036..1291049 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1179050..1179976 <gbrowseImage> name=NC_012759:1179050..1179976 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1291819..1292832 <gbrowseImage> name=NC_007779:1291819..1292832 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1329706..1330719 <gbrowseImage> name=NC_010473:1329706..1330719 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
ΔrssB (Keio:JW1223)	deletion	deletion			PMID:16738554	Shigen CGSC9109^[5]
ΔsprE::kan	deletion		Biolog:respiration	unable to respire D-Galactoniate	PMID:16095938
ΔsprE::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔsprE::kan	deletion		Biolog:respiration	unable to respire a-Hydroxybutyrate	PMID:16095938
ΔsprE::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
ΔsprE::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
ΔsprE::kan	deletion		Biolog:respiration	unable to respire Succinate	PMID:16095938
ΔsprE::kan	deletion		Biolog:respiration	unable to respire Bromosuccinate	PMID:16095938
ΔsprE::kan	deletion		Biolog:respiration	unable to respire L-Alanine	PMID:16095938
ΔsprE::kan	deletion		Biolog:respiration	unable to respire L-Asparagine	PMID:16095938
ΔrssB1273						CGSC:77156
ΔrssB744::kan					PMID:16738554	CGSC:102826
overproduction			Growth Phenotype	toxic			Suppressed by pcnA and hfq mutants PMID:19767441
CAG45114 rssB::Tet	insertion		Sigma^E activity	Increase in sigma^E activity	PMID:23224554	Paternal Strain: CAG45114 Experimental Strain: SMR15271	See table S11 for full experimental data.
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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
JW1223	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACGCAGCCATTGGTCGGAAA Primer 2:CCTTCTGCAGACAACATCAAGCG
12H9	Kohara Phage	Genobase	PMID:3038334
4D8	Kohara Phage	Genobase	PMID:3038334
3D5	Kohara Phage	Genobase	PMID:3038334
fadR13::Tn10	Linked marker	CAG18497 = CGSC7365^[5]	est. P1 cotransduction: 7% ^[6]
oppC506::Tn10	Linked marker	CAG12169 = CGSC7369^[5]	est. P1 cotransduction: 61% ^[6] Synonyms:zch-506::Tn10, zci-506::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:EG12121	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12121	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002024	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945855	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2042	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004147	Escherichia coli str. K-12 substr. MG1655
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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	RssB
Synonyms	B1235^[2], SprE^[2], YchL^[2], Hnr^[2] , ECK1230, hnr, JW1223, mviA, sprE, verA, ychL, b1235
Product description	regulator of RpoS^[2]^[3] Two-component response regulator, affecting RpoS regulon; anti-RpoS activity, phosphorylated form binds to RpoS and initiates proteolysis by ClpXP^[4]
EC number (for enzymes)
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Notes

Function

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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:IPR001789	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:IPR001789	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0902	P	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: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:IPR001789	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	ynfE	PMID:16606699^[7]	Experiment(s):EBI-1139265
	IraD	PMID:18383615^[8]
	IraP	PMID:16600914^[9]
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Notes

Localization

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Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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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 MTQPLVGKQI LIVEDEQVFR SLLDSWFSSL GATTVLAADG VDALELLGGF TPDLMICDIA MPRMNGLKLL EHIRNRGDQT PVLVISATEN MADIAKALRL GVEDVLLKPV KDLNRLREMV FACLYPSMFN SRVEEEERLF RDWDAMVDNP AAAAKLLQEL QPPVQQVISH CRVNYRQLVA ADKPGLVLDI AALSENDLAF YCLDVTRAGH NGVLAALLLR ALFNGLLQEQ LAHQNQRLPE LGALLKQVNH LLRQANLPGQ FPLLVGYYHR ELKNLILVSA GLNATLNTGE HQVQISNGVP LGTLGNAYLN QLSQRCDAWQ CQIWGTGGRL RLMLSAE
Length	337
Mol. Wt	37.302 kDa
pI	5.7 (calculated)
Extinction coefficient	30,940 - 31,690 (calc based on 6 Y, 4 W, and 6 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..121	PF00072 Response regulator receiver domain		PMID:19920124^[10]
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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=rssB taxon=562,83333 </beststructure>

Models

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Structure figures

Notes

Gene Product Resources

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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:16129196	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945855	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004147	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AEV1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12121	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12121	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945855	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002024	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2042	Escherichia coli str. K-12 substr. MG1655
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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	170	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	116	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	121	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)
rssAB
rssB
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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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<gbrowseImage> name=NC_000913:1289445..1289485 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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

</protect>

Notes

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Experimental

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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:b1235 (EcoliWiki Page)	NCBI GEO profiles for rssB
microarray	GenExpDB:b1235 (EcoliWiki Page)	Summary of data for rssB 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 (1289273..1289543) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:E5^[11]
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Notes

Accessions Related to rssB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12121	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2042	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1235
EcoGene	EcoGene:EG12121	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002024	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004147	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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Organism	Homologs (Statistics)	Comments
Shigella flexneri	HNR	From SHIGELLACYC
E. coli O157	HNR	From ECOO157CYC
Arabidopsis thaliana	AT1G10470 (score: 1.000; bootstrap: 100%) AT1G59940 (score: 0.588)	From Inparanoid:20070104
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Notes

Families

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:52172
Pfam (EcoliWiki Page)	PF00072 Response regulator receiver domain
EcoCyc	EcoCyc:EG12121	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12121	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002024	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2042	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004147	Escherichia coli str. K-12 substr. MG1655
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Notes

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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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 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).
↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ Bougdour, A et al. (2008) Multiple pathways for regulation of sigmaS (RpoS) stability in Escherichia coli via the action of multiple anti-adaptors. Mol. Microbiol. 68 298-313 PubMed
↑ Bougdour, A et al. (2006) Modulating RssB activity: IraP, a novel regulator of sigma(S) stability in Escherichia coli. Genes Dev. 20 884-97 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

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Alleles and Phenotypes

Notes

Genetic Interactions

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Genetic Resources

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Accessions in Other Databases

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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 rssB Expression

Notes

Links

Evolution

Homologs in Other Organisms

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Notes

Families

Notes

Links

References

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