hfq: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

hfq

Gene Synonym(s)

ECK4168, b4172, JW4130, HF-I, HF-1[1][2]

Product Desc.

RNA-binding protein that affects many cellular processes; homolog of mammalian Sm/Sm-like proteins[2][3];

Component of HF-I, host factor for RNA phage Q β replication[3]

Global regulator of sRNA function; host factor for RNA phage Q beta replication; HF-I; DNA- and RNA-binding protein; RNA chaperone; multiple regulatory roles: destabilzes ompA mRNA, improves rpoS translation, sRNA DsrA co-factor; binds RNAP; ATPase[4]

Product Synonyms(s)

HF-I, host factor for RNA phage Q beta replication[1], B4172[2][1], Hfq[2][1], HF-I[2][1], host factor I[2][1] , ECK4168, JW4130, b4172

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yjeFE-amiB-mutL-miaA-hfq-hflXKC[2], ORF55-ORF17-amiB-mutL-miaA-hfq-hflXKC

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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The C-terminal of Hfq is not necessary for hexamerization. RNA binding is located primarily at the N-terminal. Hfq has intrinsic ATPase activity (Sukhodolets, 2003; Arluison, 2007).[4]

Hfq enhances RNA-RNA pairing. [5]


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

hfq

Mnemonic

Host factor for Q beta

Synonyms

ECK4168, b4172, JW4130, HF-I, HF-1[1][2]

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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

94.8 minutes 

MG1655: 4398311..4398619
<gbrowseImage> name=NC_000913:4398311..4398619 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4378443..4378751
<gbrowseImage> name=NC_012967:4378443..4378751 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4337046..4337354
<gbrowseImage> name=NC_012759:4337046..4337354 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4404968..4405276
<gbrowseImage> name=NC_007779:4404968..4405276 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4498673..4498981
<gbrowseImage> name=NC_010473:4498673..4498981 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

4398314

Edman degradation

PMID:805130
PMID:2020545
PMID:8809757
PMID:9245691


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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

hfq(del) (Keio:JW4130)

deletion

deletion

PMID:16738554

Shigen
CGSC10973[6]

hfq-722(del)::kan

PMID:16738554

CGSC:101354

hfq2::omega

Insertion of omega cassette near the end of hfq sequence

Growth Phenotype

hfq maintained limited if not full activity

PMID:7984093

the resulting phenotypes showed no substantial difference from hfq+ parent

hfq1::omega

Insertion of omega cassette near the start of hfq sequence

Cell Shape

Elongated Cells(Fig 3).

PMID:7984093

hfq1::omega

Insertion of omega cassette near the start of hfq sequence

Growth Phenotype

Decreased growth and yield (table 2).

PMID:7984093

hfq1::omega

Insertion of omega cassette near the start of hfq sequence

Cell Shape

Relaxed coiling (Fig. 4)

PMID:7984093

hfq1::omega

Insertion of omega cassette near the start of hfq sequence

Sensitivity to

Increased sensitivity to Ultraviolet (u.v.) light

PMID:7984093

hfq1::omega

Insertion of omega cassette near the start of hfq sequence

Growth Phenotype

spontaneous mutagenesis

PMID:7984093

hfq1

Growth Phenotype

stabilizes ompA mRNA

PMID:9826663

disruption of hfq1 results in an increase of ompA mRNA half-life but does not affect the level of degradosomal components

hfq1::omega

Insertion of omega cassette near the start of hfq sequence

oxidation

Increased oxidation of various carbon sources (Fig. 5).

PMID:7984093

Hfq-Q8A

Glutamine to Alanine at postion 8

suppression

Hfq binding protein regulates mRNA translation by binding to OxyS to repress rpoS mRNA translation. Proximal surface mutation exhibit a 2.3 to 3.2-fold decrease in affinity to rpoS compared to wildtype Hfq, table 1.

PMID:21889623

Hfq-R16A

Argenine to Alanine at position 16.

suppression

Proximal surface mutation exhibit a 2.3 to 3.2-fold decrease in affinity to DsrA compared to wildtype Hfq. Thus translation cannot continue, table 1.

PMID:21889623

Hfq-F39A

Phenylalanine to alanine at position 39

suppression

Proximal surface mutation exhibit a 2.3 to 3.2-fold decrease in affinity to DsrA compared to wildtype Hfq. Thus translation cannot continue, table 1.

PMID:21889623

hfq1::omega

A disruption in the middle of the hfq gene

Change in gene expression

strongly reduced sigma levels during entry into stationary phase

PMID:8654929

Error in labeling see Figure 2

hfq1::omega

A disruption in the middle of the hfq gene

A change in gene expression

the translation of rpoS::lacZ is disrupted in the mutant strain.

PMID:8654929

See Figure 3

hfq1::omega

A disruption in the middle of the hfq gene

A change in gene expression

Despite any increase in osmotic upshift there is no increase in cellular sigma content.

PMID:8654929

Error in labeling see Figure 1

hfq::omega

A disruption in the middle of the hfq gene

A change in gene expression

osmotic induction of the translational rpoS742::lacZ fusion is impaired.

PMID:8654929

See figure 4

F42A

Phenylalanine to alanine at position 42

suppression

Mutation causes a decrease in biding affinity to rpsO, table 1.

PMID:21889623

hfq::omega

A disruption in the middle of hfq gene

A change in gene expression

Residual amounts of sigma in exhibit normal regulation

PMID:8654929

See Figure 6

hfq(del)

Null mutation

Change in the expression of a gene

Overexpression of rybB in both the exponential and stationary growth phase.

PMID:17416652

See Figure 5 C.

hfq772(del)::FRT

Deletion

Mutagenesis Rate

Decrease in stress induced mutagenesis (SIM).

PMID:23224554

The mutation conferred a strong decrease in SIM, the mutant frequency was reduced by over 90 % of the wild type levels. See table S3 for full experimental data.

hfq772(del)::FRT

Deletion

Sensitivity to

Increase UV sensitivity

PMID:23224554

The mutation conferred an increase in sensitivity toward UV. See tables S7 and S1 for summarized results.

hfq772(del)::FRT

Deletion

Sensitivity to

Increase sensitivity toward SDS-EDTA

PMID:23224554

The mutation conferred an increase in SDS-EDTA sensitivity. See table S7 and S1 for summarized results.

SMR4562 yiaG-yfp FRTcatFRT hfq722(del)::FRTKanFRT

Deletion

SigmaS activity

Decrease in Sigma S activity

PMID:23224554

Parental Strain: SMR10582 Experimental Strain: SMR14295

See table S8 for full experimental results.

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Notes

Genetic Interactions

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<protect>

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

JW4130

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCTAAGGGGCAATCTTTACA

Primer 2:CCTTCGGTTTCTTCGCTGTCCTG

3A1

Kohara Phage

Genobase

PMID:3038334

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[6]

est. P1 cotransduction: 17% [7]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[6]

est. P1 cotransduction: 34% [7]

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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:EG10438

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10438

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000431

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948689

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0433

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013659

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

Hfq

Synonyms

HF-I, host factor for RNA phage Q beta replication[1], B4172[2][1], Hfq[2][1], HF-I[2][1], host factor I[2][1] , ECK4168, JW4130, b4172

Product description

RNA-binding protein that affects many cellular processes; homolog of mammalian Sm/Sm-like proteins[2][3];

Component of HF-I, host factor for RNA phage Q β replication[3]

Global regulator of sRNA function; host factor for RNA phage Q beta replication; HF-I; DNA- and RNA-binding protein; RNA chaperone; multiple regulatory roles: destabilzes ompA mRNA, improves rpoS translation, sRNA DsrA co-factor; binds RNAP; ATPase[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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00436

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005001

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:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005001

P

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:0040033

negative regulation of translation, ncRNA-mediated

PMID:19118351

IEP: Inferred from Expression Pattern

P

complete

GO:0003681

bent DNA binding

PMID:10551881

IDA: Inferred from Direct Assay

F

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 HF-I, host factor for RNA phage Q β replication

could be indirect

Protein

aidB

PMID:15690043

Experiment(s):EBI-880595

Protein

rng

PMID:15690043

Experiment(s):EBI-880595

Protein

deaD

PMID:15690043

Experiment(s):EBI-880595

Protein

dnaJ

PMID:15690043

Experiment(s):EBI-880595

Protein

dnaK

PMID:15690043

Experiment(s):EBI-880595

Protein

eno

PMID:15690043

Experiment(s):EBI-880595

Protein

skp

PMID:15690043

Experiment(s):EBI-880595, EBI-886556

Protein

hrpA

PMID:15690043

Experiment(s):EBI-880595

Protein

hupA

PMID:15690043

Experiment(s):EBI-880595, EBI-886556

Protein

lon

PMID:15690043

Experiment(s):EBI-880595

Protein

lpxD

PMID:15690043

Experiment(s):EBI-880595

Protein

pnp

PMID:15690043

Experiment(s):EBI-880595

Protein

rho

PMID:15690043

Experiment(s):EBI-880595, EBI-886556

Protein

rne

PMID:15690043

Experiment(s):EBI-880595, EBI-893488

Protein

rplA

PMID:15690043

Experiment(s):EBI-880595

Protein

rplB

PMID:15690043

Experiment(s):EBI-880595

Protein

rplC

PMID:15690043

Experiment(s):EBI-880595, EBI-886556

Protein

rplD

PMID:15690043

Experiment(s):EBI-880595, EBI-886556

Protein

rpoA

PMID:15690043

Experiment(s):EBI-880595

Protein

rpoB

PMID:15690043

Experiment(s):EBI-880595

Protein

rpoC

PMID:15690043

Experiment(s):EBI-880595

Protein

rpsA

PMID:15690043

Experiment(s):EBI-880595, EBI-886556

Protein

rpsB

PMID:15690043

Experiment(s):EBI-880595, EBI-886556

Protein

rpsC

PMID:15690043

Experiment(s):EBI-880595

Protein

rpsD

PMID:15690043

Experiment(s):EBI-880595

Protein

rpsM

PMID:15690043

Experiment(s):EBI-880595, EBI-886556

Protein

secA

PMID:15690043

Experiment(s):EBI-880595

Protein

selB

PMID:15690043

Experiment(s):EBI-880595

Protein

spoT

PMID:15690043

Experiment(s):EBI-880595

Protein

tgt

PMID:15690043

Experiment(s):EBI-880595

Protein

tig

PMID:15690043

Experiment(s):EBI-880595

Protein

tufA

PMID:15690043

Experiment(s):EBI-880595

Protein

rnr

PMID:15690043

Experiment(s):EBI-880595, EBI-886556

Protein

ycbY

PMID:15690043

Experiment(s):EBI-880595

Protein

rluB

PMID:15690043

Experiment(s):EBI-880595

Protein

yfiF

PMID:15690043

Experiment(s):EBI-880595

Protein

ygiF

PMID:15690043

Experiment(s):EBI-880595

Protein

cspC

PMID:15690043

Experiment(s):EBI-886556, EBI-883980

Protein

csrA

PMID:15690043

Experiment(s):EBI-886556

Protein

hupB

PMID:15690043

Experiment(s):EBI-886556

Protein

nfi

PMID:15690043

Experiment(s):EBI-886556

Protein

rplI

PMID:15690043

Experiment(s):EBI-886556

Protein

rplL

PMID:15690043

Experiment(s):EBI-886556

Protein

rplM

PMID:15690043

Experiment(s):EBI-886556

Protein

rplO

PMID:15690043

Experiment(s):EBI-886556

Protein

rplS

PMID:15690043

Experiment(s):EBI-886556

Protein

rplT

PMID:15690043

Experiment(s):EBI-886556

Protein

rplU

PMID:15690043

Experiment(s):EBI-886556

Protein

rplV

PMID:15690043

Experiment(s):EBI-886556

Protein

rplX

PMID:15690043

Experiment(s):EBI-886556

Protein

rpmB

PMID:15690043

Experiment(s):EBI-886556

Protein

rpsE

PMID:15690043

Experiment(s):EBI-886556

Protein

rpsF

PMID:15690043

Experiment(s):EBI-886556

Protein

rpsG

PMID:15690043

Experiment(s):EBI-886556

Protein

rpsP

PMID:15690043

Experiment(s):EBI-886556

Protein

rpsR

PMID:15690043

Experiment(s):EBI-886556

Protein

rplN

PMID:16606699

Experiment(s):EBI-1147620

Protein

ygbA

PMID:16606699

Experiment(s):EBI-1147620

Protein

uspG

PMID:16606699

Experiment(s):EBI-1147620

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1147620

Protein

rplB

PMID:16606699

Experiment(s):EBI-1147620

Protein

rob

PMID:16606699

Experiment(s):EBI-1147620

Protein

yciH

PMID:16606699

Experiment(s):EBI-1147620

Protein

tig

PMID:19402753

MALDI(Z-score):31.467557

Protein

secA

PMID:19402753

MALDI(Z-score):18.689223

Protein

eno

PMID:19402753

MALDI(Z-score):25.940163

Protein

tufB

PMID:19402753

MALDI(Z-score):19.802224

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):6.030298

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753

MALDI(Z-score):34.289130

Protein

hupB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):10.835608

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):26.483554

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):7.741650

Protein

lon

PMID:19402753

MALDI(Z-score):19.371612

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):13.880177

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rho

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):39.920671

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):5.243101

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753

LCMS(ID Probability):97.0 MALDI(Z-score):19.110485

Protein

rpsD

PMID:19402753

LCMS(ID Probability):88.3 MALDI(Z-score):38.038080

Protein

rng

PMID:19402753

MALDI(Z-score):21.170257

Protein

rplA

PMID:19402753

LCMS(ID Probability):86.0 MALDI(Z-score):31.573966

Protein

nfi

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753

MALDI(Z-score):33.016691

Protein

skp

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):30.407482

Protein

rpoA

PMID:19402753

LCMS(ID Probability):86.4 MALDI(Z-score):32.797009

Protein

ygiF

PMID:19402753

LCMS(ID Probability):85.9 MALDI(Z-score):34.947118

Protein

rlmL

PMID:19402753

MALDI(Z-score):28.362205

Protein

lpxD

PMID:19402753

MALDI(Z-score):21.449871

Protein

rnr

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.407921

Protein

yfiF

PMID:19402753

MALDI(Z-score):32.328504

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):18.730532

Protein

pnp

PMID:19402753

MALDI(Z-score):28.049574

Protein

hrpA

PMID:19402753

MALDI(Z-score):18.932128

Protein

csrA

PMID:19402753

LCMS(ID Probability):99.3

Protein

tgt

PMID:19402753

MALDI(Z-score):27.516532

Protein

deaD

PMID:19402753

MALDI(Z-score):27.100042

Protein

selB

PMID:19402753

MALDI(Z-score):23.285153

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

RNA

ompA mRNA

cells lacking Hfq lose growth rate-dependent regulation; knockout of the hfq gene results in a longer half-life of the ompA mRNA

PMID:9826663

RNA

rpoS

HF-1 is necessary for establishing normal rates of translation of rpoS

PMID:8654929

used pulse-chase experiments and analyzed rpoS::lacZ fusions

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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

cytoplasm

From EcoCyc[3]


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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 

MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV SQMVYKHAIS
TVVPSRPVSH HSNNAGGGTS SNYHHGSSAQ NTSAQQDSEE TE
Length

102

Mol. Wt

11.165 kDa

pI

7.8 (calculated)

Extinction coefficient

4,470 (calc based on 3 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

Initiator Methionine

1

Removed

UniProt:P0A6X3

Domain

10..64

PF01423 LSM 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=hfq 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:16131994

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948689

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013659

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A6X3

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10438

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10438

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948689

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000431

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0433

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

5.85E+03

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

1513.053+/-6.963

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.72468+/-0.01652

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

1.813311688

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

27919

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

8277

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

18677

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)

yjeFE-amiB-mutL-miaA-hfq-hflXKC

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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_000913:4398291..4398331 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:b4172 (EcoliWiki Page)

NCBI GEO profiles for hfq

microarray

GenExpDB:b4172 (EcoliWiki Page)

Summary of data for hfq 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 (4397696..4397888) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ02; Well:E12[8]

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Notes

Accessions Related to hfq Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10438

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0433

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4172

EcoGene

EcoGene:EG10438

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000431

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013659

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

HFQ

From SHIGELLACYC

E. coli O157

HFQ

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)

PF01423 LSM domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:50182

EcoCyc

EcoCyc:EG10438

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10438

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000431

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0433

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013659

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 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 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. ↑ Zhang, A et al. (2002) The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol. Cell 9 11-22 PubMed
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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).
  8. ↑ 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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