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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	rpoN
Gene Synonym(s)	ECK3191, b3202, JW3169, glnF, ntrA^[1], ntrA
Product Desc.	sigma54 factor^[2]; RNA polymerase, sigma 54 (sigma N) factor^[3]; Component of RNA polymerase sigma54^[2]; RNA polymerase sigma 54^[3] RNA polymerase subunit, sigma 54; needed for expression of various regulons, promoter specificity set by various activator proteins required for sigma 54 recruitment^[4]
Product Synonyms(s)	RNA polymerase, sigma 54 (sigma N) factor^[1], B3202^[2]^[1], NtrA^[2]^[1], GlnF^[2]^[1], RpoN^[2]^[1], sigma N factor^[2]^[1], sigma 54 factor^[3]^[1], sigma N^[3]^[1] , ECK3191, glnF, JW3169, ntrA, b3202
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): lptB-rpoN-yhbH-ptsN-yhbJ^[2], yhbG-rpoN-yhbH-ptsN-yhbJ, rpoN-yhbH-ptsN-yhbJ-npr^[2], rpoN-ORFII-ORF-III-ORF-IV-ORFV, rpoN-yhbH-ptsN-yhbJ-ptsO, rpoN^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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RpoN, aslo called sigma N, was originally identified as the sigma factor for nitrogen-controlled genes. The rpoN operon contains rpoN-hpf-ptsN-yhbJ-npr.^[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	rpoN
Mnemonic	RNA polymerase
Synonyms	ECK3191, b3202, JW3169, glnF, ntrA^[1], ntrA
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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	72.05 minutes	MG1655: 3342739..3344172 <gbrowseImage> name=NC_000913:3342739..3344172 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3279952..3281385 <gbrowseImage> name=NC_012967:3279952..3281385 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3229887..3231320 <gbrowseImage> name=NC_012759:3229887..3231320 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3344572..3346005 <gbrowseImage> name=NC_007779:3344572..3346005 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3440484..3441917 <gbrowseImage> name=NC_010473:3440484..3441917 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
ΔrpoN (Keio:JW3169)	deletion	deletion			PMID:16738554	Shigen CGSC10404^[5]
rpoN::Tn5KAN-I-SceI (FB21065)	Insertion at nt 324 in Minus orientation				PMID:15262929	E. coli Genome Project:FB21065	contains pKD46
ΔrpoN::kan	deletion		Biolog:respiration	unable to respire a-Hydroxybutyrate	PMID:16095938
ΔrpoN::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
rpoN208::Tn10					PMID:6131062	CGSC:88039
ΔrpoN730::kan					PMID:16738554	CGSC:102792
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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
JW3169	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGCAAGGTTTGCAACTCAG Primer 2:CCAACGAGTTGTTTACGCTGGTT
7E3	Kohara Phage	Genobase	PMID:3038334
3G10	Kohara Phage	Genobase	PMID:3038334
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[5]	est. P1 cotransduction: 67% ^[6] Synonyms:zgj-203::Tn10, zha-203::Tn10
zhc-6::Tn10	Linked marker	CAG12153 = CGSC7442^[5]	est. P1 cotransduction: 46% ^[6] Synonyms:zha-6::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:EG10898	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10898	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000889	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947714	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0891	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010514	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	RpoN
Synonyms	RNA polymerase, sigma 54 (sigma N) factor^[1], B3202^[2]^[1], NtrA^[2]^[1], GlnF^[2]^[1], RpoN^[2]^[1], sigma N factor^[2]^[1], sigma 54 factor^[3]^[1], sigma N^[3]^[1] , ECK3191, glnF, JW3169, ntrA, b3202
Product description	sigma54 factor^[2]; RNA polymerase, sigma 54 (sigma N) factor^[3]; Component of RNA polymerase sigma54^[2]; RNA polymerase sigma 54^[3] RNA polymerase subunit, sigma 54; needed for expression of various regulons, promoter specificity set by various activator proteins required for sigma 54 recruitment^[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:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000394	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007046	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:IPR000394	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003899	DNA-directed RNA polymerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000394	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003899	DNA-directed RNA polymerase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0240	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:0006352	transcription initiation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000394	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006352	transcription initiation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007046	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:IPR000394	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0731	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006525	arginine metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0056	P	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:0016779	nucleotidyltransferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0548	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016987	sigma factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000394	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016987	sigma factor activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0731	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
Protein	Subunits of RNA polymerase sigma54	could be indirect
Protein	dnaK		PMID:15690043	Experiment(s):EBI-879445, EBI-883645
Protein	manX		PMID:15690043	Experiment(s):EBI-879445
Protein	rplD		PMID:15690043	Experiment(s):EBI-879445
Protein	rplM		PMID:15690043	Experiment(s):EBI-879445
Protein	rpoA		PMID:15690043	Experiment(s):EBI-879445, EBI-883645
Protein	rpoC		PMID:15690043	Experiment(s):EBI-879445
Protein	yraM		PMID:15690043	Experiment(s):EBI-879445
Protein	rpoC		PMID:16606699	Experiment(s):EBI-1145142
Protein	rpsC		PMID:16606699	Experiment(s):EBI-1145142
Protein	rpoA		PMID:16606699	Experiment(s):EBI-1145142
Protein	rpsG		PMID:16606699	Experiment(s):EBI-1145142
Protein	nagZ		PMID:16606699	Experiment(s):EBI-1145142
Protein	rpoB		PMID:16606699	Experiment(s):EBI-1145142
Protein	rplB		PMID:16606699	Experiment(s):EBI-1145142
Protein	phnN		PMID:16606699	Experiment(s):EBI-1145142
Protein	yagS		PMID:16606699	Experiment(s):EBI-1145142
Protein	manX		PMID:19402753	MALDI(Z-score):24.617987
Protein	yraM		PMID:19402753	MALDI(Z-score):17.053160
Protein	rplM		PMID:19402753	MALDI(Z-score):20.474034
Protein	rpoB		PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):20.106361
Protein	rpoA		PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):39.202085
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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 MKQGLQLRLS QQLAMTPQLQ QAIRLLQLST LELQQELQQA LESNPLLEQI DTHEEIDTRE TQDSETLDTA DALEQKEMPE ELPLDASWDT IYTAGTPSGT SGDYIDDELP VYQGETTQTL QDYLMWQVEL TPFSDTDRAI ATSIVDAVDE TGYLTVPLED ILESIGDEEI DIDEVEAVLK RIQRFDPVGV AAKDLRDCLL IQLSQFDKTT PWLEEARLII SDHLDLLANH DFRTLMRVTR LKEDVLKEAV NLIQSLDPRP GQSIQTGEPE YVIPDVLVRK HNGHWTVELN SDSIPRLQIN QHYASMCNNA RNDGDSQFIR SNLQDAKWLI KSLESRNDTL LRVSRCIVEQ QQAFFEQGEE YMKPMVLADI AQAVEMHEST ISRVTTQKYL HSPRGIFELK YFFSSHVNTE GGGEASSTAI RALVKKLIAA ENPAKPLSDS KLTSLLSEQG IMVARRTVAK YRESLSIPPS NQRKQLV
Length	477
Mol. Wt	53.99 kDa
pI	4.5 (calculated)
Extinction coefficient	43,890 - 44,265 (calc based on 11 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	3..51	PF00309 Sigma-54 factor, Activator interacting domain (AID)	PMID:19920124
Domain	106..304	PF04963 Sigma-54 factor, core binding domain	PMID:19920124
Domain	316..475	PF04552 Sigma-54, DNA binding domain	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=rpoN taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16131092	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947714	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010514	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P24255	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10898	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10898	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947714	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000889	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0891	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	42.382+/-0.303	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.199930216	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	459	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	316	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	413	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)
lptB-rpoN-yhbH-ptsN-yhbJ
rpoN-yhbH-ptsN-yhbJ-npr
rpoN
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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_000913:3342719..3342759 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b3202 (EcoliWiki Page)	NCBI GEO profiles for rpoN
microarray	GenExpDB:b3202 (EcoliWiki Page)	Summary of data for rpoN 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 rpoN Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10898	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0891	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3202
EcoGene	EcoGene:EG10898	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000889	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010514	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	RPON	From SHIGELLACYC
E. coli O157	RPON	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)	PF00309 Sigma-54 factor, Activator interacting domain (AID)
Pfam (EcoliWiki Page)	PF04963 Sigma-54 factor, core binding domain
Pfam (EcoliWiki Page)	PF04552 Sigma-54, DNA binding domain
EcoCyc	EcoCyc:EG10898	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10898	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000889	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0891	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010514	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 ^1.14 ^1.15 ^1.16 ^1.17 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 ^2.12 ^2.13 ^2.14 ^2.15 ^2.16 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 ^3.7 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).

rpoN: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 rpoN Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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