Difference between revisions of "Hfq"

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(New page: * '''Description:''' write here <br/><br/> {| align="right" border="1" cellpadding="2" |- |style="background:#ABCDEF;" align="center"|'''Gene name''' |''ymaH'' |- |style="background:#ABC...)
 
(→‎Original publications)
 
(55 intermediate revisions by 7 users not shown)
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* '''Description:''' write here <br/><br/>
+
* '''Description:''' RNA chaperone <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''ymaH''
+
|''hfq ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymaH''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA chaperone
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU17340 hfq]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 8.698   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 8.698   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 219 bp, 73 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 219 bp, 73 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[miaA]]'', ''[[ymzC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ymaH_nucleotide.txt    Gene sequence     (+200bp)  ]'''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU17340 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU17340 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU17340 DNA_with_flanks]
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ymaH_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ymaH_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ymaH_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 +
|-
 +
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymaH_1867373_1867594_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:hfq_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU17340]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
  
−
<br/><br/>
+
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[RNA chaperones]]}}
 +
 
 +
= This gene is a member of the following [[regulons]] =
  
 
=The gene=
 
=The gene=
Line 35: Line 46:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU17340
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU17340&redirect=T BSU17340]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ymaH.html]
+
* '''DBTBS entry:''' no entry
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13416]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13416]
  
 
=== Additional information===
 
=== Additional information===
 +
 +
  
  
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' hfq family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU17340&redirect=T BSU17340]
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3HSB 3HSB] (complex with an RNA aptamer) {{PubMed|22053080}}
  
−
* '''Swiss prot entry:'''
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31796 O31796]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17340]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[hfq]]'' {{PubMed|23457461}}   
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymaH_1867373_1867594_1 hfq] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed by glucose (7.7-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
 +
** expression (mRNA levels) is quite constant during growth in minimal medium {{PubMed|23457461}} 
 +
** the Hfq protein amount increases upon transition to stationary phase {{PubMed|23457461}} 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 46 {{PubMed|24696501}}
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP22 (cat), available in the [[Jörg Stülke]]'s lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
 
          
 
          
−
* '''lacZ fusion:'''
+
* '''lacZ fusion:''' pGP460 (in [[pAC7]]), available in [[Jörg Stülke]]'s lab
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
 +
 
 +
* '''FLAG-tag construct:'''
 +
** GP1067 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
  
 
* '''Antibody:'''
 
* '''Antibody:'''
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=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 17395525 15009882 21760622 </pubmed>
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
==Original publications==
 +
<pubmed>12850135, 20445260 23457461 22965117,22053080 24932523 25150227 25915524</pubmed>
 +
[[Category:Protein-coding genes]]

Latest revision as of 15:41, 29 April 2015

  • Description: RNA chaperone

Gene name hfq
Synonyms ymaH
Essential no
Product RNA chaperone
Function unknown
Gene expression levels in SubtiExpress: hfq
MW, pI 8 kDa, 8.698
Gene length, protein length 219 bp, 73 aa
Immediate neighbours miaA, ymzC
Sequences Protein DNA DNA_with_flanks
Genetic context
YmaH context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
Hfq expression.png















Categories containing this gene/protein

RNA chaperones

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU17340

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: hfq family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure: 3HSB (complex with an RNA aptamer) PubMed
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
    • repressed by glucose (7.7-fold) PubMed
    • expression (mRNA levels) is quite constant during growth in minimal medium PubMed
    • the Hfq protein amount increases upon transition to stationary phase PubMed
  • Regulatory mechanism:
  • Additional information:
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 46 PubMed

Biological materials

  • Expression vector:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Reviews

Jörg Vogel, Ben F Luisi
Hfq and its constellation of RNA.
Nat Rev Microbiol: 2011, 9(8);578-89
[PubMed:21760622] [WorldCat.org] [DOI] (I e)

Richard G Brennan, Todd M Link
Hfq structure, function and ligand binding.
Curr Opin Microbiol: 2007, 10(2);125-33
[PubMed:17395525] [WorldCat.org] [DOI] (P p)

Poul Valentin-Hansen, Maiken Eriksen, Christina Udesen
The bacterial Sm-like protein Hfq: a key player in RNA transactions.
Mol Microbiol: 2004, 51(6);1525-33
[PubMed:15009882] [WorldCat.org] [DOI] (P p)


Original publications

Tatiana Rochat, Olivier Delumeau, Nara Figueroa-Bossi, Philippe Noirot, Lionello Bossi, Etienne Dervyn, Philippe Bouloc
Tracking the Elusive Function of Bacillus subtilis Hfq.
PLoS One: 2015, 10(4);e0124977
[PubMed:25915524] [WorldCat.org] [DOI] (I e)

Alexander R Kovach, Kirsten E Hoff, John T Canty, Jillian Orans, Richard G Brennan
Recognition of U-rich RNA by Hfq from the Gram-positive pathogen Listeria monocytogenes.
RNA: 2014, 20(10);1548-59
[PubMed:25150227] [WorldCat.org] [DOI] (I p)

Hermann Hämmerle, Fabian Amman, Branislav Večerek, Jörg Stülke, Ivo Hofacker, Udo Bläsi
Impact of Hfq on the Bacillus subtilis transcriptome.
PLoS One: 2014, 9(6);e98661
[PubMed:24932523] [WorldCat.org] [DOI] (I e)

Michael Dambach, Irnov Irnov, Wade C Winkler
Association of RNAs with Bacillus subtilis Hfq.
PLoS One: 2013, 8(2);e55156
[PubMed:23457461] [WorldCat.org] [DOI] (I p)

Nicola Horstmann, Jillian Orans, Poul Valentin-Hansen, Samuel A Shelburne, Richard G Brennan
Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract.
Nucleic Acids Res: 2012, 40(21);11023-35
[PubMed:22965117] [WorldCat.org] [DOI] (I p)

Tatsuhiko Someya, Seiki Baba, Mai Fujimoto, Gota Kawai, Takashi Kumasaka, Kouji Nakamura
Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq.
Nucleic Acids Res: 2012, 40(4);1856-67
[PubMed:22053080] [WorldCat.org] [DOI] (I p)

Seiki Baba, Tatsuhiko Someya, Gota Kawai, Kouji Nakamura, Takashi Kumasaka
Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.
Acta Crystallogr Sect F Struct Biol Cryst Commun: 2010, 66(Pt 5);563-6
[PubMed:20445260] [WorldCat.org] [DOI] (I p)

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

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