Difference between revisions of "Sandbox"

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* '''Description:''' [[transcription factors activating transcription at SigL-dependent promoters |transcriptional activator]] of the ''[[acoA]]-[[acoB]]-[[acoC]]-[[acoL]]'' operon <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'''
−
|''dnaA''
+
|''acoR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfjG, yzcB ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || replication initiation protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || [[transcription factors activating transcription at SigL-dependent promoters |transcriptional activator]] (for [[SigL]]-dependent promoter)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of acetoin utilization
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU00010 BSU00010]
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU08100 acoR]
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/DnaA DnaA]
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/AcoR AcoR]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035 
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 66 kDa, 7.884 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[dnaN]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1815 bp, 605 aa
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11777&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acoL]]'', ''[[sspH]]''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12639&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:acoR_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=dnaA_410_1750_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sandbox_expression.png|500px]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=acoR_883758_885575_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:acoR_expression.png|500px]]
 
|-
 
|-
 
|}
 
|}
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<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
  
−
<br/><br/><br/><br/>
+
 
−
<br/><br/><br/><br/>
+
<br/><br/><br/><br/><br/><br/>
−
<br/><br/><br/><br/>
 
−
<br/><br/>
 
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[DNA replication]]}},
+
{{SubtiWiki category|[[utilization of specific carbon sources]]}},
−
{{SubtiWiki category|[[essential genes]]}}
+
{{SubtiWiki category|[[transcription factors and their control]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[Spo0A regulon]]}}
+
{{SubtiWiki regulon|[[CcpA regulon]]}}
−
=The [[DnaA regulon]]=
+
=The [[AcoR regulon]]: =
 +
* ''[[acoA]]-[[acoB]]-[[acoC]]-[[acoL]]''
 +
 
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00010
+
* '''Locus tag:''' BSU08100
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/acoR-sspH.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11790]
  
 
=== Additional information===
 
=== Additional information===
 +
 +
  
  
Line 74: Line 77:
  
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
−
** binds multiple regions in the oriC region, required for recruitment of proteins needed to load the replicative helicase [[DnaC]]
 
  
−
* '''Protein family:''' dnaA family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' AAA+ domain
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
−
** [[SirA]] displaces [[DnaA]] from the replication origin {{PubMed|19682252}}
 
−
** [[YabA]] inhibits co-operative binding of DnaA to the ''oriC'' DNA {{PubMed|21895792}}
 
−
** DnaA helix formation (and thus replication initiation) is inhibited by the interaction of [[Soj]] with the AAA+ domain of DnaA {{PubMed|22286949}}
 
−
** interaction with [[DnaD]] inhibits the ability of [[DnaA]] to cooperatively bind to DNA {{PubMed|22821970}}
 
  
 
* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
−
** [[DnaA]] assembles into a right-handed helical oligomer built upon interactions between neighbouring AAA+ domains
 
−
** [[Soj]]-[[DnaA]] {{PubMed|22286949}}
 
−
** [[DnaA]]-[[YabA]],  [[DnaA]]-[[YabA]]-[[DnaN]] {{PubMed|12060778}}
 
−
** [[DnaA]]-[[DnaD]] {{PubMed|22821970,11222620}}
 
−
** [[SirA]]-[[DnaA]] {{PubMed|19682252,21239581}}
 
−
** [[YqaH]]-[[DnaA]] {{PubMed|12060778}}
 
−
** part of the [[primosome]]: [[DnaA]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[DnaB]] {{PubMed|22797751}}
 
  
−
* '''[[Localization]]:''' throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
+
* '''[[Localization]]:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 111: Line 102:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05648 P05648]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31551 O31551]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00010]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU08100]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 119: Line 110:
 
=== Additional information===
 
=== Additional information===
  
−
=Biological materials =
+
=Expression and regulation=
 +
 
 +
* '''Operon:''' ''[[acoR]]-[[sspH]]'' {{PubMed|11274109}}
  
−
* '''Mutant:'''
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=acoR_883758_885575_1 acoR] {{PubMed|22383849}}
−
** 1A912 ( ''acoR''::''kan''), {{PubMed|16585774}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A912&Search=1A912 BGSC]
 
  
−
* '''Expression vector:'''
+
* '''Sigma factor:''' [[SigA]] {{PubMed|22900538}}
−
       
 
−
* '''lacZ fusion:'''
 
  
−
* '''GFP fusion:'''
+
* '''Regulation:'''  
 +
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
  
−
* '''two-hybrid system:'''  
+
* '''Regulatory mechanism:'''  
 +
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
  
−
* '''Antibody:'''
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
 
* '''Mutant:'''
 
* '''Mutant:'''
−
** 1A912 ( ''acoR''::''kan''), {{PubMed|16585774}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A912&Search=1A912 BGSC]
 
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 148: Line 139:
  
 
* '''Antibody:'''
 
* '''Antibody:'''
 +
 +
=Labs working on this gene/protein=
 +
 +
[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
==Reviews==
 
−
<pubmed> 20157337 21035377 21639790 22575476 22797751</pubmed>
 
  
−
==The [[DnaA regulon]]==
+
<pubmed>11274109,10368162, 22900538,12850135 </pubmed>
−
<pubmed> 16120674, </pubmed>
 
−
==Original publications==
 
−
'''Additional publications:''' {{PubMed|22396664,21911367}}
 
−
<pubmed>18854156,19011033, 11222620,14651647,17140409 10844689 ,11222620 12060778 16461910 2987848 2168872 11207367, 19737352 19081080 17932079 19968790 19682252 20511500 21097613 21239581 21895792 22286949 22821970</pubmed>
 
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 06:55, 19 September 2012

Gene name acoR
Synonyms yfjG, yzcB
Essential no
Product transcriptional activator (for SigL-dependent promoter)
Function regulation of acetoin utilization
Gene expression levels in SubtiExpress: acoR
Interactions involving this protein in SubtInteract: AcoR
Metabolic function and regulation of this protein in SubtiPathways:
Central C-metabolism
MW, pI 66 kDa, 7.884
Gene length, protein length 1815 bp, 605 aa
Immediate neighbours acoL, sspH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AcoR context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
AcoR expression.png




























Categories containing this gene/protein

utilization of specific carbon sources, transcription factors and their control

This gene is a member of the following regulons

CcpA regulon

The AcoR regulon:

The gene

Basic information

  • Locus tag: BSU08100

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Michel Debarbouille, Pasteur Institute, Paris, France Homepage

Your additional remarks

References

Bogumiła C Marciniak, Monika Pabijaniak, Anne de Jong, Robert Dűhring, Gerald Seidel, Wolfgang Hillen, Oscar P Kuipers
High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis.
BMC Genomics: 2012, 13;401
[PubMed:22900538] [WorldCat.org] [DOI] (I e)

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)

N O Ali, J Bignon, G Rapoport, M Debarbouille
Regulation of the acetoin catabolic pathway is controlled by sigma L in Bacillus subtilis.
J Bacteriol: 2001, 183(8);2497-504
[PubMed:11274109] [WorldCat.org] [DOI] (P p)

M Huang, F B Oppermann-Sanio, A Steinbüchel
Biochemical and molecular characterization of the Bacillus subtilis acetoin catabolic pathway.
J Bacteriol: 1999, 181(12);3837-41
[PubMed:10368162] [WorldCat.org] [DOI] (P p)

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