rlmE:On One Page

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

Quickview

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Standard Name

rlmE

Gene Synonym(s)

ECK3168, b3179, JW3146, ftsJ, mrsF, rrmJ[1], mrsF, rrmJ

Product Desc.

23S rRNA m2U2552 methyltransferase[2][3]

23S rRNA U2552 ribose 2'-O-methyltransferase, SAM-dependent; involved in cell division and growth; heat inducible; suppresssed by cloned ObgE and Der[4]

Product Synonyms(s)

23S rRNA methyltransferase[1], B3179[2][1], RrmJ[2][1], MrsF[2][1], FtsJ[2][1] , ECK3168, ftsJ, JW3146, mrsF, rrmJ, b3179

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rlmE-hflB[2]

Regulation/Activity
Quick Links

porteco.png

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

rlmE

Mnemonic

rRNA large-subunit methylation

Synonyms

ECK3168, b3179, JW3146, ftsJ, mrsF, rrmJ[1], mrsF, rrmJ

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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

71.67 minutes 

MG1655: 3325686..3325057
<gbrowseImage> name=NC_000913:3325057..3325686 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3212205..3212834
<gbrowseImage> name=NC_012759:3212205..3212834 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3327519..3326890
<gbrowseImage> name=NC_007779:3326890..3327519 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3423431..3422802
<gbrowseImage> name=NC_010473:3422802..3423431 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

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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

ΔrrmJ (Keio:JW3146)

deletion

deletion

PMID:16738554

Shigen
CGSC10390[5]

rlmED83A

D83A

5-fold decrease in activity. Increase in Km for 50S subunit and for S- adenosyl-L-methionine. Loss of S- adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmES197A

S197A

No change in activity. Increase in Km for 50S subunit

seeded from UniProt:P0C0R7

rlmEE199A

E199A

16-fold decrease in activity. No change in S-adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmED20A

D20A

2-fold decrease in activity. Increase in Km for 50S subunit

seeded from UniProt:P0C0R7

rlmEY22A

Y22A

No change in activity

seeded from UniProt:P0C0R7

rlmER32A

R32A

4-fold decrease in activity and increase in Km for 50S subunit; when associated with A-34

seeded from UniProt:P0C0R7

rlmER34A

R34A

4-fold decrease in activity and increase in Km for 50S subunit; when associated with A-32

seeded from UniProt:P0C0R7

rlmEK38A

K38A

Loss of activity. Almost no change in S-adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmED124A

D124A

Loss of activity. Loss of S- adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmED136N

D136N

2-fold decrease in activity

seeded from UniProt:P0C0R7

rlmEK164A

K164A

Loss of activity. No change in S- adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmEK189A

K189A

9-fold decrease in activity

seeded from UniProt:P0C0R7

rlmER194A

R194A

No change in activity. Increase in Km for 50S subunit

seeded from UniProt:P0C0R7

rlmEY201A

Y201A

5-fold decrease in activity. Almost no change in S-adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

ΔrrmJ786::kan

PMID:16738554

CGSC:102804

rlmE

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484

fig 2

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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

JW3146

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACAGGTAAGAAGCGTTCTGC

Primer 2:CCGGGTTTACGCCCGGTCGCTAC

18H7

Kohara Phage

Genobase

PMID:3038334

14F11

Kohara Phage

Genobase

PMID:3038334

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: % [6]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: 81% [6]
Synonyms:zgj-203::Tn10, zha-203::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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3179

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3936

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:FTSJ

CGSC (EcoliWiki Page)

CGSC:33511

EcoCyc (EcoliWiki Page)

ECOCYC:EG11507

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947689

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

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

RlmE

Synonyms

23S rRNA methyltransferase[1], B3179[2][1], RrmJ[2][1], MrsF[2][1], FtsJ[2][1] , ECK3168, ftsJ, JW3146, mrsF, rrmJ, b3179

Product description

23S rRNA m2U2552 methyltransferase[2][3]

23S rRNA U2552 ribose 2'-O-methyltransferase, SAM-dependent; involved in cell division and growth; heat inducible; suppresssed by cloned ObgE and Der[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:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002877

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01547

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006950

response to stress

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0346

P

Seeded from EcoCyc (v14.0)

complete

GO:0008650

rRNA (uridine-2'-O-)-methyltransferase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01547

F

Seeded from EcoCyc (v14.0)

complete

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

aceF

PMID:15690043

Experiment(s):EBI-881132

Protein

clpA

PMID:15690043

Experiment(s):EBI-881132

Protein

ffh

PMID:15690043

Experiment(s):EBI-881132

Protein

lon

PMID:15690043

Experiment(s):EBI-881132

Protein

rplA

PMID:15690043

Experiment(s):EBI-881132

Protein

rplC

PMID:15690043

Experiment(s):EBI-881132

Protein

rplD

PMID:15690043

Experiment(s):EBI-881132

Protein

rplV

PMID:15690043

Experiment(s):EBI-881132

Protein

rpsB

PMID:15690043

Experiment(s):EBI-881132

Protein

rpsD

PMID:15690043

Experiment(s):EBI-881132

Protein

rpsE

PMID:15690043

Experiment(s):EBI-881132

Protein

rpsG

PMID:15690043

Experiment(s):EBI-881132

Protein

tufA

PMID:15690043

Experiment(s):EBI-881132

Protein

rplJ

PMID:15690043

Experiment(s):EBI-881132

Protein

groL

PMID:16606699

Experiment(s):EBI-1145040

Protein

yfdQ

PMID:16606699

Experiment(s):EBI-1145040

Protein

rplJ

PMID:16606699

Experiment(s):EBI-1145040

Protein

speD

PMID:16606699

Experiment(s):EBI-1145040

Protein

ygbA

PMID:16606699

Experiment(s):EBI-1145040

Protein

rplA

PMID:19402753

MALDI(Z-score):23.770470

Protein

tufB

PMID:19402753

MALDI(Z-score):23.014924

Protein

lon

PMID:19402753

MALDI(Z-score):28.131900

Protein

clpA

PMID:19402753

MALDI(Z-score):24.748640

Protein

ffh

PMID:19402753

MALDI(Z-score):34.290099

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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

MTGKKRSASS SRWLQEHFSD KYVQQAQKKG LRSRAWFKLD EIQQSDKLFK PGMTVVDLGA
APGGWSQYVV TQIGGKGRII ACDLLPMDPI VGVDFLQGDF RDELVMKALL ERVGDSKVQV
VMSDMAPNMS GTPAVDIPRA MYLVELALEM CRDVLAPGGS FVVKVFQGEG FDEYLREIRS
LFTKVKVRKP DSSRARSREV YIVATGRKP
Length

209

Mol. Wt

23.334 kDa

pI

9.8 (calculated)

Extinction coefficient

23,950 - 24,200 (calc based on 5 Y, 3 W, and 2 C residues)


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

31..207

PF01728 FtsJ-like methyltransferase

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=rrmJ 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:16131069

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947689

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0C0R7

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947689

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

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

Ecoli K-12

10.389+/-0.147

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

Protein

E. coli K-12 MG1655

1629

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

325

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

1851

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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)

rrmJ-hflB

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_000913:3325666..3325706 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


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

Type Reference Notes

microarray

GEO Profiles:b3179 (EcoliWiki Page)

NCBI GEO profiles for rrmJ

microarray

GenExpDB:b3179 (EcoliWiki Page)

Summary of data for rrmJ from multiple microarray studies


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 (3325205..3325479) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ11; Well:E1[7]

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Notes

Accessions Related to rlmE Expression

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

Database Accession Notes

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3179

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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

Anopheles gambiae

  • ENSANGP00000014205 (score: 1.000; bootstrap: 53%)
  • ENSANGP00000026202 (score: 0.067)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000017171 (score: 1.000; bootstrap: 98%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G25730 (score: 1.000; bootstrap: 76%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000003214 (score: 1.000; bootstrap: 65%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00040049 (score: 1.000; bootstrap: 55%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00009735 (score: 1.000; bootstrap: 64%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000024186 (score: 1.000; bootstrap: 68%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000009727 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-041114-83 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-041114-83 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0168604 (score: 1.000; bootstrap: 56%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0038737 (score: 1.000; bootstrap: 60%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA11008-PA (score: 1.000; bootstrap: 61%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000006732 (score: 1.000; bootstrap: 64%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000327660 (score: 1.000; bootstrap: 69%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000022396 (score: 1.000; bootstrap: 69%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000012180 (score: 1.000; bootstrap: 54%)

From Inparanoid:20070104

Mus musculus

  • MGI:1915267 (score: 1.000; bootstrap: 66%)

From Inparanoid:20070104

Oryza gramene

  • Q688W3 (score: 1.000; bootstrap: 85%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000032192 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000001702 (score: 1.000; bootstrap: 67%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YGL136C (score: 1.000; bootstrap: 66%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC4F103c (score: 1.000; bootstrap: 66%)
  • SPAC16871 (score: 0.104)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000138138 (score: 1.000; bootstrap: 57%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00010080001 (score: 1.000; bootstrap: 65%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000012452 (score: 1.000; bootstrap: 89%)

From Inparanoid:20070104

Shigella flexneri

FTSJ

From SHIGELLACYC

E. coli O157

FTSJ

From ECOO157CYC


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)

PF01728 FtsJ-like methyltransferase

Superfamily (EcoliWiki Page)

SUPERFAMILY:53335

Panther (EcoliWiki Page)

PTHR10920:SF11

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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 1.11 1.12 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 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

Categories

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