Difference between revisions of "AbbA"

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* '''Description:''' inhibitor of AbrB activity<br/><br/>
+
* '''Description:''' inhibitor of [[AbrB]] activity<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'''
−
|''ykzF''
+
|''abbA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykzF''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-repressor
 
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of AbrB
+
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of [[AbrB]]
 +
|-
 +
|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=BSU14120 abbA]
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=AbbA AbbA]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.642   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.642   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 195 bp, 65 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 195 bp, 65 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuK]]'', ''[[ykuL]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykzF_nucleotide.txt    Gene sequence     (+200bp)  ]'''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14120 DNA_with_flanks]
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykzF_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykzF_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykzF_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=ykzF_1485118_1485315_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:abbA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14120]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
 +
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[transcription factors and their control]]}}
  
−
<br/><br/>
+
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[CcpA regulon]]}},
 +
{{SubtiWiki regulon|[[Spo0A regulon]]}}
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU14120
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14120&redirect=T BSU14120]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykzF.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13334]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13334]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''  
+
* '''[[Domains]]:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''[[Cofactors]]:'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' AbbA-[[AbrB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''[[SubtInteract|Interactions]]:'''
 +
** forms dimers {{PubMed|24534728}}
 +
** [[AbbA]]-[[AbrB]], [[AbbA]] binds the N-terminal DNA-binding domain of [[AbrB]] {{PubMed|24534728,18840696}}
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14120&redirect=T BSU14120]
  
−
* '''Structure:'''
+
* '''Structure:''' [http://pdb.org/pdb/explore/explore.do?structureId=2LZF 2LZF] {{PubMed|24534728}}
  
−
* '''Swiss prot entry:'''
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* '''UniProt:''' [http://www.uniprot.org/uniprot/O31697 O31697]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14120]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]-[[ccpC]]'' {{PubMed|16395550}}
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykzF_1485118_1485315_1 abbA] {{PubMed|22383849}}
  
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 +
** expressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|18840696,14651647}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
 +
** [[Spo0A]]: transcription activation by [[Spo0A]]~P {{PubMed|18840696,14651647}}
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP214 (deletion of ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]'', replaced by ''aphA3''), available in the [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
 
          
 
          
−
* '''lacZ fusion:'''
+
* '''lacZ fusion:''' pGP708 (in [[pAC5]]), available in [[Stülke]] lab, pGP712 (in [[pAC6]]), available in [[Stülke]] lab
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
Line 113: Line 137:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 144:
 
=References=
 
=References=
  
−
# Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in ''Bacillus subtilis''.''Proc. Natl. Acad. Sci. USA'' '''105:''' 15547-15552. [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
<pubmed> 24534728,18840696,14651647,12850135 18840696 12850135,16395550 </pubmed>
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
 
 +
[[Category:Protein-coding genes]]

Latest revision as of 13:35, 2 April 2014

  • Description: inhibitor of AbrB activity

Gene name abbA
Synonyms ykzF
Essential no
Product anti-repressor
Function inhibition of AbrB
Gene expression levels in SubtiExpress: abbA
Interactions involving this protein in SubtInteract: AbbA
MW, pI 7 kDa, 4.642
Gene length, protein length 195 bp, 65 aa
Immediate neighbours ykuK, ykuL
Sequences Protein DNA DNA_with_flanks
Genetic context
YkzF context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
AbbA expression.png















Categories containing this gene/protein

transcription factors and their control

This gene is a member of the following regulons

CcpA regulon, Spo0A regulon

The gene

Basic information

  • Locus tag: BSU14120

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: inhibition of AbrB activity PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Modification:
  • Effectors of protein activity:

Database entries

  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation:
    • repressed by glucose (4.3-fold) (CcpA) PubMed
    • expressed under conditions that trigger sporulation (Spo0A) PubMed
  • Additional information:

Biological materials

  • Expression vector:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Richard Losick, Harvard Univ., Cambridge, USA homepage

Your additional remarks

References

Ashley T Tucker, Benjamin G Bobay, Allison V Banse, Andrew L Olson, Erik J Soderblom, M Arthur Moseley, Richele J Thompson, Kristen M Varney, Richard Losick, John Cavanagh
A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA.
J Mol Biol: 2014, 426(9);1911-24
[PubMed:24534728] [WorldCat.org] [DOI] (I p)

Allison V Banse, Arnaud Chastanet, Lilah Rahn-Lee, Errett C Hobbs, Richard Losick
Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2008, 105(40);15547-52
[PubMed:18840696] [WorldCat.org] [DOI] (I p)

Hans-Matti Blencke, Irene Reif, Fabian M Commichau, Christian Detsch, Ingrid Wacker, Holger Ludwig, Jörg Stülke
Regulation of citB expression in Bacillus subtilis: integration of multiple metabolic signals in the citrate pool and by the general nitrogen regulatory system.
Arch Microbiol: 2006, 185(2);136-46
[PubMed:16395550] [WorldCat.org] [DOI] (P p)

Virginie Molle, Masaya Fujita, Shane T Jensen, Patrick Eichenberger, José E González-Pastor, Jun S Liu, Richard Losick
The Spo0A regulon of Bacillus subtilis.
Mol Microbiol: 2003, 50(5);1683-701
[PubMed:14651647] [WorldCat.org] [DOI] (P 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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