rhlB: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

rhlB

Gene Synonym(s)

ECK3772, b3780, JW3753, mmrA, G704[1][2], mmrA?

Product Desc.

EG10844[2][3];

Component of RhlB, ATP-dependent RNA helicase of the RNA degradosome[3]; degradosome[3]

ATP-dependent RNA helicase; unwinds dsRNA; component of RNA degradosome; also binds PNPase directly; DEAD box family[4]

Product Synonyms(s)

ATP-dependent RNA helicase[1], B3780[2][1], MmrA[2][1], RhlB[2][1] , ECK3772, JW3753, mmrA?, b3780

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rhlB[2]

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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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

rhlB

Mnemonic

RNA helicase like

Synonyms

ECK3772, b3780, JW3753, mmrA, G704[1][2], mmrA?

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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

85.4 minutes 

MG1655: 3963653..3962388
<gbrowseImage> name=NC_000913:3962388..3963653 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3927430..3926165
<gbrowseImage> name=NC_012967:3926165..3927430 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3852057..3853322
<gbrowseImage> name=NC_012759:3852057..3853322 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3671051..3672316
<gbrowseImage> name=NC_007779:3671051..3672316 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4062573..4061308
<gbrowseImage> name=NC_010473:4061308..4062573 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

3962391

Edman degradation

PMID:8610017


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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

ΔrhlB (Keio:JW3753)

deletion

deletion

PMID:16738554

Shigen
CGSC10739[5]

ΔrhlB731::kan

PMID:16738554

CGSC:102690


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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

JW3753

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCAAAACACATTTAACAGA

Primer 2:CCACCTGAACGACGACGATTACG

7B1

Kohara Phage

Genobase

PMID:3038334

2A8

Kohara Phage

Genobase

PMID:3038334

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[5]

est. P1 cotransduction: 73% [6]
Synonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[5]

est. P1 cotransduction: 13% [6]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

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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:EG10844

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10844

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000835

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948290

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0837

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012351

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

RhlB

Synonyms

ATP-dependent RNA helicase[1], B3780[2][1], MmrA[2][1], RhlB[2][1] , ECK3772, JW3753, mmrA?, b3780

Product description

EG10844[2][3];

Component of RhlB, ATP-dependent RNA helicase of the RNA degradosome[3]; degradosome[3]

ATP-dependent RNA helicase; unwinds dsRNA; component of RNA degradosome; also binds PNPase directly; DEAD box family[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:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000629

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0003724

RNA helicase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00661

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0347

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00661

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000629

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0006401

RNA catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00661

P

Seeded from EcoCyc (v14.0)

complete

GO:0008026

ATP-dependent helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000629

F

Seeded from EcoCyc (v14.0)

complete

GO:0008026

ATP-dependent helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

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 RhlB, ATP-dependent RNA helicase of the RNA degradosome

could be indirect

Protein

aceE

PMID:15690043

Experiment(s):EBI-886554

Protein

dnaK

PMID:15690043

Experiment(s):EBI-886554

Protein

eno

PMID:15690043

Experiment(s):EBI-886554, EBI-892949

Protein

pnp

PMID:15690043

Experiment(s):EBI-886554, EBI-883913, EBI-891089, EBI-892949

Protein

rne

PMID:15690043

Experiment(s):EBI-886554, EBI-888473, EBI-892949, EBI-893488

Protein

rplC

PMID:15690043

Experiment(s):EBI-886554, EBI-892949

Protein

rplI

PMID:15690043

Experiment(s):EBI-886554

Protein

rplK

PMID:15690043

Experiment(s):EBI-886554

Protein

rplV

PMID:15690043

Experiment(s):EBI-886554, EBI-892949

Protein

rpsC

PMID:15690043

Experiment(s):EBI-886554

Protein

rpsD

PMID:15690043

Experiment(s):EBI-886554

Protein

rpsG

PMID:15690043

Experiment(s):EBI-886554, EBI-892949

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-886554

Protein

tufA

PMID:15690043

Experiment(s):EBI-886554

Protein

rplA

PMID:15690043

Experiment(s):EBI-892949

Protein

rplM

PMID:15690043

Experiment(s):EBI-892949

Protein

rplS

PMID:15690043

Experiment(s):EBI-892949

Protein

rplU

PMID:15690043

Experiment(s):EBI-892949

Protein

rpmB

PMID:15690043

Experiment(s):EBI-892949

Protein

rpsE

PMID:15690043

Experiment(s):EBI-892949

Protein

rpsF

PMID:15690043

Experiment(s):EBI-892949

Protein

rpsP

PMID:15690043

Experiment(s):EBI-892949

Protein

rpsS

PMID:15690043

Experiment(s):EBI-892949

Protein

rpsT

PMID:15690043

Experiment(s):EBI-892949

Protein

dacA

PMID:16606699

Experiment(s):EBI-1146674

Protein

nfrA

PMID:16606699

Experiment(s):EBI-1146674

Protein

rplK

PMID:19402753

MALDI(Z-score):17.053160

Protein

rpsM

PMID:19402753

LCMS(ID Probability):98.5 MALDI(Z-score):29.418568

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.527596

Protein

rplI

PMID:19402753

MALDI(Z-score):17.053160

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

eno

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):37.169715

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsD

PMID:19402753

LCMS(ID Probability):97.9 MALDI(Z-score):33.652594

Protein

rne

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.418106

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.

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 

MSKTHLTEQK FSDFALHPKV VEALEKKGFH NCTPIQALAL PLTLAGRDVA GQAQTGTGKT
MAFLTSTFHY LLSHPAIADR KVNQPRALIM APTRELAVQI HADAEPLAEA TGLKLGLAYG
GDGYDKQLKV LESGVDILIG TTGRLIDYAK QNHINLGAIQ VVVLDEADRM YDLGFIKDIR
WLFRRMPPAN QRLNMLFSAT LSYRVRELAF EQMNNAEYIE VEPEQKTGHR IKEELFYPSN
EEKMRLLQTL IEEEWPDRAI IFANTKHRCE EIWGHLAADG HRVGLLTGDV AQKKRLRILD
EFTRGDLDIL VATDVAARGL HIPAVTHVFN YDLPDDCEDY VHRIGRTGRA GASGHSISLA
CEEYALNLPA IETYIGHSIP VSKYNPDALM TDLPKPLRLT RPRTGNGPRR TGAPRNRRRS G
Length

421

Mol. Wt

47.127 kDa

pI

7.7 (calculated)

Extinction coefficient

35,870 - 36,370 (calc based on 13 Y, 3 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.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P0A8J8

Domain

33..209

PF00270 DEAD/DEAH box helicase

PMID:19920124

Domain

274..351

PF00271 Helicase conserved C-terminal 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=rhlB 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:16131636

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948290

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012351

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A8J8

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10844

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10844

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948290

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000835

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0837

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

2.41E+02

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

41.154+/-0.507

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.135968379

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

3459

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

1055

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

1986

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)

rhlB

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Figure courtesy of RegulonDB

</protect>

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_000913:3963633..3963673 source=MG1655 flip=1 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:b3780 (EcoliWiki Page)

NCBI GEO profiles for rhlB

microarray

GenExpDB:b3780 (EcoliWiki Page)

Summary of data for rhlB 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 (3963176..3963341) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ18; Well:C8[7]

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Notes

Accessions Related to rhlB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10844

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0837

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3780

EcoGene

EcoGene:EG10844

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000835

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012351

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

RHLB

From SHIGELLACYC

E. coli O157

RHLB

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

Pfam (EcoliWiki Page)

PF00271 Helicase conserved C-terminal domain

Pfam (EcoliWiki Page)

PF00270 DEAD/DEAH box helicase

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

EcoCyc

EcoCyc:EG10844

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10844

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000835

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0837

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012351

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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 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 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 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).
  7. ↑ 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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