Difference between revisions of "Hfq"

From SubtiWiki
Jump to: navigation, search
(→‎Original publications)
 
(10 intermediate revisions by 3 users not shown)
Line 14: Line 14:
 
|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://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU17340 hfq]
+
|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   
Line 22: Line 22:
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[miaA]]'', ''[[ymzC]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[miaA]]'', ''[[ymzC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13618&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|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]
 
|-
 
|-
 
|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>
 
  <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]]
+
|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]]
 
|-
 
|-
 
|}
 
|}
Line 41: Line 41:
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
 
  
 
=The gene=
 
=The gene=
Line 52: Line 51:
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU17340&redirect=T BSU17340]
  
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
Line 89: Line 89:
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU17340&redirect=T BSU17340]
  
 
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3HSB 3HSB] (complex with an RNA aptamer) {{PubMed|22053080}}
 
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3HSB 3HSB] (complex with an RNA aptamer) {{PubMed|22053080}}
Line 102: Line 103:
 
=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}}
 
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymaH_1867373_1867594_1 hfq] {{PubMed|22383849}}
Line 108: Line 109:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose (7.7-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
+
* '''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:''' GP22 (cat), available in the [[Stülke]] lab
+
* '''Mutant:''' GP22 (cat), available in the [[Jörg Stülke]]'s lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
 
          
 
          
−
* '''lacZ fusion:''' pGP460 (in [[pAC7]]), available in [[Stülke]] lab
+
* '''lacZ fusion:''' pGP460 (in [[pAC7]]), available in [[Jörg Stülke]]'s lab
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
  
 
* '''FLAG-tag construct:'''  
 
* '''FLAG-tag construct:'''  
Line 140: Line 145:
  
 
==Original publications==
 
==Original publications==
−
'''Additional publications:''' {{PubMed|22965117,22053080}}
+
<pubmed>12850135, 20445260 23457461 22965117,22053080 24932523 25150227 25915524</pubmed>
−
<pubmed>12850135, 20445260 23457461 </pubmed>
 
 
[[Category:Protein-coding genes]]
 
[[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


Original publications

Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Hfq&oldid=207802"