hfq:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

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[5]

IEP: Inferred from Expression Pattern

P

complete

GO:0003681

bent DNA binding

PMID:10551881[6]

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[7]

Experiment(s):EBI-880595

Protein

rng

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

deaD

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

dnaJ

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

dnaK

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

eno

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

skp

PMID:15690043[7]

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

Protein

hrpA

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

hupA

PMID:15690043[7]

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

Protein

lon

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

lpxD

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

pnp

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rho

PMID:15690043[7]

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

Protein

rne

PMID:15690043[7]

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

Protein

rplA

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rplB

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rplC

PMID:15690043[7]

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

Protein

rplD

PMID:15690043[7]

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

Protein

rpoA

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rpoB

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rpoC

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rpsA

PMID:15690043[7]

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

Protein

rpsB

PMID:15690043[7]

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

Protein

rpsC

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rpsD

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rpsM

PMID:15690043[7]

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

Protein

secA

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

selB

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

spoT

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

tgt

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

tig

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

tufA

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rnr

PMID:15690043[7]

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

Protein

ycbY

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

rluB

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

yfiF

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

ygiF

PMID:15690043[7]

Experiment(s):EBI-880595

Protein

cspC

PMID:15690043[7]

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

Protein

csrA

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

hupB

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

nfi

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplI

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplL

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplM

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplO

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplS

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplT

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplU

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplV

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplX

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rpmB

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rpsE

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rpsF

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rpsG

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rpsP

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rpsR

PMID:15690043[7]

Experiment(s):EBI-886556

Protein

rplN

PMID:16606699[8]

Experiment(s):EBI-1147620

Protein

ygbA

PMID:16606699[8]

Experiment(s):EBI-1147620

Protein

uspG

PMID:16606699[8]

Experiment(s):EBI-1147620

Protein

rpsD

PMID:16606699[8]

Experiment(s):EBI-1147620

Protein

rplB

PMID:16606699[8]

Experiment(s):EBI-1147620

Protein

rob

PMID:16606699[8]

Experiment(s):EBI-1147620

Protein

yciH

PMID:16606699[8]

Experiment(s):EBI-1147620

Protein

tig

PMID:19402753[9]

MALDI(Z-score):31.467557

Protein

secA

PMID:19402753[9]

MALDI(Z-score):18.689223

Protein

eno

PMID:19402753[9]

MALDI(Z-score):25.940163

Protein

tufB

PMID:19402753[9]

MALDI(Z-score):19.802224

Protein

rpsP

PMID:19402753[9]

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

Protein

rplT

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753[9]

MALDI(Z-score):34.289130

Protein

hupB

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplO

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753[9]

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

Protein

rpsA

PMID:19402753[9]

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

Protein

rpsF

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsR

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753[9]

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

Protein

lon

PMID:19402753[9]

MALDI(Z-score):19.371612

Protein

rpsM

PMID:19402753[9]

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

Protein

rplU

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rho

PMID:19402753[9]

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

Protein

rplX

PMID:19402753[9]

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

Protein

rplM

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753[9]

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

Protein

rpsD

PMID:19402753[9]

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

Protein

rng

PMID:19402753[9]

MALDI(Z-score):21.170257

Protein

rplA

PMID:19402753[9]

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

Protein

nfi

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753[9]

MALDI(Z-score):33.016691

Protein

skp

PMID:19402753[9]

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

Protein

rpoA

PMID:19402753[9]

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

Protein

ygiF

PMID:19402753[9]

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

Protein

rlmL

PMID:19402753[9]

MALDI(Z-score):28.362205

Protein

lpxD

PMID:19402753[9]

MALDI(Z-score):21.449871

Protein

rnr

PMID:19402753[9]

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

Protein

yfiF

PMID:19402753[9]

MALDI(Z-score):32.328504

Protein

rplD

PMID:19402753[9]

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

Protein

pnp

PMID:19402753[9]

MALDI(Z-score):28.049574

Protein

hrpA

PMID:19402753[9]

MALDI(Z-score):18.932128

Protein

csrA

PMID:19402753[9]

LCMS(ID Probability):99.3

Protein

tgt

PMID:19402753[9]

MALDI(Z-score):27.516532

Protein

deaD

PMID:19402753[9]

MALDI(Z-score):27.100042

Protein

selB

PMID:19402753[9]

MALDI(Z-score):23.285153

Protein

rplL

PMID:19402753[9]

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[10]

RNA

rpoS

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

PMID:8654929[11]

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[12]

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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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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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Pulvermacher, SC et al. (2009) Role of the sRNA GcvB in regulation of cycA in Escherichia coli. Microbiology (Reading, Engl.) 155 106-14 PubMed
  6. ↑ Azam, TA & Ishihama, A (1999) Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 274 33105-13 PubMed
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 7.15 7.16 7.17 7.18 7.19 7.20 7.21 7.22 7.23 7.24 7.25 7.26 7.27 7.28 7.29 7.30 7.31 7.32 7.33 7.34 7.35 7.36 7.37 7.38 7.39 7.40 7.41 7.42 7.43 7.44 7.45 7.46 7.47 7.48 7.49 7.50 7.51 7.52 7.53 7.54 7.55 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  9. ↑ 9.00 9.01 9.02 9.03 9.04 9.05 9.06 9.07 9.08 9.09 9.10 9.11 9.12 9.13 9.14 9.15 9.16 9.17 9.18 9.19 9.20 9.21 9.22 9.23 9.24 9.25 9.26 9.27 9.28 9.29 9.30 9.31 9.32 9.33 9.34 9.35 9.36 9.37 9.38 9.39 9.40 9.41 9.42 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  10. ↑ Vytvytska, O et al. (1998) Host factor I, Hfq, binds to Escherichia coli ompA mRNA in a growth rate-dependent fashion and regulates its stability. Proc. Natl. Acad. Sci. U.S.A. 95 14118-23 PubMed
  11. ↑ Muffler, A et al. (1996) The RNA-binding protein HF-I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS translation in Escherichia coli. Genes Dev. 10 1143-51 PubMed
  12. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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