rpoZ:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

rpoZ

Gene Synonym(s)

ECK3639, b3649, JW3624, spoS[1], spoS

Product Desc.

RNA polymerase, ω subunit[2][3]

RNA polymerase subunit, omega subunit; assembly factor; chaperone-like function stabilizes RNAP[4]

Product Synonyms(s)

RNA polymerase, omega subunit[1], B3649[2][1], SpoS[2][1], RpoZ[2][1] , ECK3639, JW3624, spoS, b3649

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rpoZ-spoT-trmH-recG[2], rpoZ-spoTU-recG

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Stimulates ppGpp responsiveness of RNAP in vitro. Binds TrxA (Kumar, 2004).[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

rpoZ

Mnemonic

RNA polymerase

Synonyms

ECK3639, b3649, JW3624, spoS[1], spoS

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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

82.34 minutes 

MG1655: 3820129..3820404
<gbrowseImage> name=NC_000913:3820129..3820404 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3760463..3760738
<gbrowseImage> name=NC_012967:3760463..3760738 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3708456..3708731
<gbrowseImage> name=NC_012759:3708456..3708731 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3818309..3818034
<gbrowseImage> name=NC_007779:3818034..3818309 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3917707..3917982
<gbrowseImage> name=NC_010473:3917707..3917982 source=DH10B preset=GeneLocation </gbrowseImage>

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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

3820132

Edman degradation

PMID:9868784


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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

ΔrpoZ (Keio:JW3624)

deletion

deletion

PMID:16738554

Shigen
CGSC10664[5]

ΔrpoZ::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938

ΔrpoZ::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938

ΔrpoZ::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938

ΔrpoZ754::kan

PMID:16738554

CGSC:102796


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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

JW3624

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCACGCGTAACTGTTCAGGA

Primer 2:CCACGACGACCTTCAGCAATAGC

7F3

Kohara Phage

Genobase

PMID:3038334

2A6

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: % [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: 77% [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:EG10899

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10899

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000890

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948160

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0892

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011933

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

RpoZ

Synonyms

RNA polymerase, omega subunit[1], B3649[2][1], SpoS[2][1], RpoZ[2][1] , ECK3639, JW3624, spoS, b3649

Product description

RNA polymerase, ω subunit[2][3]

RNA polymerase subunit, omega subunit; assembly factor; chaperone-like function stabilizes RNAP[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:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00366

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006110

F

Seeded from EcoCyc (v14.0)

complete

GO:0003899

DNA-directed RNA polymerase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00366

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:IPR003716

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:IPR006110

F

Seeded from EcoCyc (v14.0)

complete

GO:0003899

DNA-directed RNA polymerase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.7.6

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:0006351

transcription, DNA-dependent

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00366

P

Seeded from EcoCyc (v14.0)

complete

GO:0006351

transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003716

P

Seeded from EcoCyc (v14.0)

complete

GO:0006351

transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006110

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:0030880

RNA polymerase complex

PMID:2152188

IMP: Inferred from Mutant Phenotype

C

Fig 5.

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

dnaK

PMID:16606699

Experiment(s):EBI-1146407

Protein

rpoB

PMID:16606699

Experiment(s):EBI-1146407

Protein

rhsA

PMID:16606699

Experiment(s):EBI-1146407

Protein

nusA

PMID:15690043

Experiment(s):EBI-879161, EBI-893117

Protein

nusG

PMID:15690043

Experiment(s):EBI-879161, EBI-882858

Protein

rplB

PMID:15690043

Experiment(s):EBI-879161

Protein

dnaK

PMID:15690043

Experiment(s):EBI-879161

Protein

rpoA

PMID:15690043

Experiment(s):EBI-879161, EBI-879354, EBI-883271

Protein

rpoB

PMID:15690043

Experiment(s):EBI-879161, EBI-879304, EBI-882858, EBI-883170

Protein

rpoC

PMID:15690043

Experiment(s):EBI-879161, EBI-879261, EBI-882858, EBI-883046

Protein

rpsB

PMID:15690043

Experiment(s):EBI-879161

Protein

rpsG

PMID:15690043

Experiment(s):EBI-879161

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-879161

Protein

rpsM

PMID:15690043

Experiment(s):EBI-879161

Protein

spoT

PMID:15690043

Experiment(s):EBI-879161

Protein

tig

PMID:15690043

Experiment(s):EBI-879161

Protein

rapA

PMID:15690043

Experiment(s):EBI-879161

Protein

rplL

PMID:15690043

Experiment(s):EBI-882858

Protein

rplW

PMID:15690043

Experiment(s):EBI-882858

Protein

rpsT

PMID:15690043

Experiment(s):EBI-882858

Protein

thiG

PMID:15690043

Experiment(s):EBI-882858

Protein

ygjI

PMID:15690043

Experiment(s):EBI-882858

Protein

ykgC

PMID:15690043

Experiment(s):EBI-882858

Protein

tig

PMID:19402753

MALDI(Z-score):31.397743

Protein

thiG

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

ygjI

PMID:19402753

LCMS(ID Probability):99.6

Protein

ykgC

PMID:19402753

LCMS(ID Probability):99.6

Protein

nusG

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.362047

Protein

rpoB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):25.777742

Protein

rpoC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):23.637460

Protein

rapA

PMID:19402753

MALDI(Z-score):18.094045

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

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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 

MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN
NQILDVRERQ EQQEQEAAEL QAVTAIAEGR R
Length

91

Mol. Wt

10.235 kDa

pI

4.7 (calculated)

Extinction coefficient

0 (calc based on 0 Y, 0 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

Domain

7..63

PF01192 RNA polymerase Rpb6

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=rpoZ 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:16131520

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948160

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011933

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A800

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10899

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10899

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948160

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000890

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0892

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

E. coli K-12 MC4100

2.09E+04

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

658.288+/-3.223

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

1.0321+/-0.01957

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.36

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

29488

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

7159

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

15071

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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<protect>

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

Transcription unit(s)

rpoZ-spoT-trmH-recG

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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_000913:3820109..3820149 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:b3649 (EcoliWiki Page)

NCBI GEO profiles for rpoZ

microarray

GenExpDB:b3649 (EcoliWiki Page)

Summary of data for rpoZ 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 rpoZ Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10899

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0892

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3649

EcoGene

EcoGene:EG10899

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000890

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011933

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

RPOZ

From SHIGELLACYC

E. coli O157

RPOZ

From ECOO157CYC

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Do-It-Yourself Web Tools

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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:63562

Pfam (EcoliWiki Page)

PF01192 RNA polymerase Rpb6

EcoCyc

EcoCyc:EG10899

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10899

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000890

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0892

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011933

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).

Categories

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