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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

rne

Gene Synonym(s)

ECK1069, b1084, JW1071, ams, hmp1, rne_1, smbB[1]

Product Desc.

Rne[2][3];

Component of ribonuclease E[3]; degradosome[3]

RNase E; component of RNA degradosome; mRNA turnover; 5S and 16S RNA maturation[4]

Product Synonyms(s)

fused ribonucleaseE: endoribonuclease[1], RNA-binding protein[1], RNA degradosome binding protein[1], B1084[2][1], SmbB[2][1], Ams[2][1], Rne[2][1], RNase E[2][1]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rne[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(rne)    Textpresso(rne)

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See Help:Quickview for help with entering information in the Quickview table.

Notes

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The degradosome is organized with a helical cytoskeletal localization (Taghbalout, 2007).[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

rne

Mnemonic

RNase E

Synonyms

ECK1069, b1084, JW1071, ams, hmp1, rne_1, smbB[1]

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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.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

24.58 minutes 

MG1655: 1143590..1140405
gbrowse_img.php?coord=1140405..1143590&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 1158936..1155751
gbrowse_img.php?coord=1155751..1158936&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 1145944..1142759
gbrowse_img.php?coord=1142759..1145944&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 1199035..1195850
gbrowse_img.php?coord=1195850..1199035&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 1044330..1047515
gbrowse_img.php?coord=1044330..1047515&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

rne-3071(ts)

temperature sensitive

PMID:8320240 PMID:1846032

CGSC:7537


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW1071

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:gccAAAAGAATGTTAATCAACGCAACTCAG

Primer 2:cctTCAACAGGTTGCGGACGCGCAGGAGCG

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[5]

est. P1 cotransduction: % [6]

zce-726::Tn10

Linked marker

CAG12078 = CGSC7361[5]

est. P1 cotransduction: 59% [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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10859

EchoBASE (EcoliWiki Page)

EchoBASE:EB0852

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1084

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1353

EcoGene (EcoliWiki Page)

EcoGene:EG10859

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:RNE

CGSC (EcoliWiki Page)

CGSC:269

ASAP (EcoliWikiPage)

ASAP:ABE-0003668


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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

Rne

Synonyms

fused ribonucleaseE: endoribonuclease[1], RNA-binding protein[1], RNA degradosome binding protein[1], B1084[2][1], SmbB[2][1], Ams[2][1], Rne[2][1], RNase E[2][1]

Product description

Rne[2][3];

Component of ribonuclease E[3]; degradosome[3]

RNase E; component of RNA degradosome; mRNA turnover; 5S and 16S RNA maturation[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.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0005515

protein binding

PMID:15236960

IPI: Inferred from Physical Interaction

UniProtKB:P0A6P9

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0005515

protein binding

PMID:16139413

IPI: Inferred from Physical Interaction

UniProtKB:P0A6Y8

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0005515

protein binding

PMID:16139413

IPI: Inferred from Physical Interaction

UniProtKB:P0A8J8

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0042802

identical protein binding

PMID:15236960

IPI: Inferred from Physical Interaction

UniProtKB:P21513

F

Seeded from EcoCyc [8]

complete

GO:0016787

hydrolase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc [8]

complete

GO:0006396

RNA processing

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004659

P

Seeded from EcoCyc [8]

complete

GO:0005737

cytoplasm

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004659
SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0004540

ribonuclease activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004659

F

Seeded from EcoCyc [8]

complete

GO:0004519

endonuclease activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc [8]

complete

GO:0004518

nuclease activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc [8]

complete

GO:0003723

RNA binding

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR003029
SP_KW:KW-0694

F

Seeded from EcoCyc [8]

complete

GO:0006401

RNA catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

Protein

Subunits of ribonuclease E

could be indirect

Protein

deaD

PMID:15690043

Experiment(s):EBI-888473

Protein

dnaK

PMID:15690043

Experiment(s):EBI-888473, EBI-893488

Protein

eno

PMID:15690043

Experiment(s):EBI-888473, EBI-880413, EBI-885840, EBI-893488

Protein

fabZ

PMID:15690043

Experiment(s):EBI-888473

Protein

fruR

PMID:15690043

Experiment(s):EBI-888473

Protein

pnp

PMID:15690043

Experiment(s):EBI-888473, EBI-883913, EBI-891089, EBI-893488

Protein

rplA

PMID:15690043

Experiment(s):EBI-888473

Protein

rplB

PMID:15690043

Experiment(s):EBI-888473, EBI-893488

Protein

rplC

PMID:15690043

Experiment(s):EBI-888473, EBI-893488

Protein

rplD

PMID:15690043

Experiment(s):EBI-888473, EBI-893488

Protein

rplI

PMID:15690043

Experiment(s):EBI-888473

Protein

rplK

PMID:15690043

Experiment(s):EBI-888473, EBI-893488

Protein

rplV

PMID:15690043

Experiment(s):EBI-888473, EBI-893488

Protein

rpsB

PMID:15690043

Experiment(s):EBI-888473

Protein

rpsC

PMID:15690043

Experiment(s):EBI-888473

Protein

rpsD

PMID:15690043

Experiment(s):EBI-888473, EBI-893488

Protein

rpsG

PMID:15690043

Experiment(s):EBI-888473, EBI-893488

Protein

rpsU

PMID:15690043

Experiment(s):EBI-888473

Protein

srmB

PMID:15690043

Experiment(s):EBI-888473

Protein

tufA

PMID:15690043

Experiment(s):EBI-888473

Protein

rnr

PMID:15690043

Experiment(s):EBI-888473

Protein

ycbY

PMID:15690043

Experiment(s):EBI-888473

Protein

rluB

PMID:15690043

Experiment(s):EBI-888473

Protein

yfiQ

PMID:15690043

Experiment(s):EBI-888473

Protein

rplL

PMID:15690043

Experiment(s):EBI-893488

Protein

rplM

PMID:15690043

Experiment(s):EBI-893488

Protein

rplU

PMID:15690043

Experiment(s):EBI-893488

Protein

rplW

PMID:15690043

Experiment(s):EBI-893488

Protein

rplX

PMID:15690043

Experiment(s):EBI-893488

Protein

rpsE

PMID:15690043

Experiment(s):EBI-893488

Protein

rpsF

PMID:15690043

Experiment(s):EBI-893488

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-893488

Protein

rpsP

PMID:15690043

Experiment(s):EBI-893488

Protein

rpsT

PMID:15690043

Experiment(s):EBI-893488

Protein

yfiF

PMID:15690043

Experiment(s):EBI-893488

Protein

Subunits of degradosome

could be indirect


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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes

plasma membrane

Cytoplasm

PMID:2011493

EchoLocation:rne


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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.

Sequence

at EcoCyc 

MKRMLINATQ QEELRVALVD GQRLYDLDIE SPGHEQKKAN IYKGKITRIE PSLEAAFVDY
GAERHGFLPL KEIAREYFPA NYSAHGRPNI KDVLREGQEV IVQIDKEERG NKGAALTTFI
SLAGSYLVLM PNNPRAGGIS RRIEGDDRTE LKEALASLEL PEGMGLIVRT AGVGKSAEAL
QWDLSFRLKH WEAIKKAAES RPAPFLIHQE SNVIVRAFRD YLRQDIGEIL IDNPKVLELA
RQHIAALGRP DFSSKIKLYT GEIPLFSHYQ IESQIESAFQ REVRLPSGGS IVIDSTEALT
AIDINSARAT RGGDIEETAF NTNLEAADEI ARQLRLRDLG GLIVIDFIDM TPVRHQRAVE
NRLREAVRQD RARIQISHIS RFGLLEMSRQ RLSPSLGESS HHVCPRCSGT GTVRDNESLS
LSILRLIEEE ALKENTQEVH AIVPVPIASY LLNEKRSAVN AIETRQDGVR CVIVPNDQME
TPHYHVLRVR KGEETPTLSY MLPKLHEEAM ALPSEEEFAE RKRPEQPALA TFAMPDVPPA
PTPAEPAAPV VAPAPKAAPA TPAAPAQPGL LSRFFGALKA LFSGGEETKP TEQPAPKAEA
KPERQQDRRK PRQNNRRDRN ERRDTRSERT EGSDNREENR RNRRQAQQQT AETRESRQQA
EVTEKARTAD EQQAPRRERS RRRNDDKRQA QQEAKALNVE EQSVQETEQE ERVRPVQPRR
KQRQLNQKVR YEQSVAEEAV VAPVVEETVA AEPIVQEAPA PRTELVKVPL PVVAQTAPEQ
QEENNADNRD NGGMPRRSRR SPRHLRVSGQ RRRRYRDERY PTQSPMPLTV ACASPELASG
KVWIRYPIVR PQDVQVEEQR EQEEVHVQPM VTEVPVAAAI EPVVSAPVVE EVAGVVEAPV
QVAEPQPEVV ETTHPEVIAA AVTEQPQVIT ESDVAVAQEV AEQAEPVVEP QEETADIEEV
VETAEVVVAE PEVVAQPAAP VVAEVAAEVE TVAAVEPEVT VEHNHATAPM TRAPAPEYVP
EAPRHSDWQR PTFAFEGKGA AGGHTATHHA SAAPARPQPV E
Length

1,061

Mol. Wt

118.193 kDa

pI

5.5 (calculated)

Extinction coefficient

47,330 - 47,830 (calc based on 17 Y, 4 W, and 4 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.

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

Structures
  • Representative Escherichia coli structure:
    2VMK|A
    1-515 of 1061 residues (E-value: 4e-271) (Percent Identity: 100.00)
  • Representative homolog:
    3H1C|D (Shigella dysenteriae Sd197)
    1-41 of 1061 residues (E-value: 1e-18) (Percent Identity: 100.00)
  • View the PDB Table for rne
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10859-MONOMER

UniProt (EcoliWiki Page)

UniProt:P21513

PFAM (EcoliWiki Page)

PFAM:PF00575

RefSeq (EcoliWiki Page)

RefSeq:NP_415602


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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)

rne

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=1143570..1143610&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
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

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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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b1084 (EcoliWiki Page)

NCBI GEO profiles for rne

microarray

GenExpDB:b1084 (EcoliWiki Page)

Summary of data for rne 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 NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (1143514..1143708) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ04; Well:G4[9]

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Notes

Accessions Related to rne Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10859

EchoBASE (EcoliWiki Page)

EchoBASE:EB0852

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1084

EcoGene (EcoliWiki Page)

EcoGene:EG10859


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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.

OrganismHomologs (Statistics)Comments

Apis mellifera

  • ENSAPMP00000031901 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000020550 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000018040 (score: 0.051)

From Inparanoid:20070104

Danio rerio

  • ZDB-CDNA-050522-68 (score: 1.000; bootstrap: 100%)
  • ZDB-GENE-030131-5005 (score: 0.919)
  • ZDB-CDNA-040930-2 (score: 0.140)
  • ZDB-GENE-040930-2 (score: 0.140)
  • ZDB-CDNA-041114-95 (score: 0.119)
  • ZDB-GENE-041114-95 (score: 0.119)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0031264 (score: 1.000; bootstrap: 59%)
  • FBgn0000181 (score: 0.095)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA15126-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000286104 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000040217 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RNE

From SHIGELLACYC

E. coli O157

RNE

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00575


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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 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 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 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).
  7. ↑ 7.0 7.1 7.2 7.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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