Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
(Undo revision 194476 by 134.76.70.252 (talk))
Line 1: Line 1:
−
* '''Achtung:''' [[transcription factors activating transcription at SigL-dependent promoters |transcriptional activator]] of the ''[[acoA]]-[[acoB]]-[[acoC]]-[[acoL]]'' operon <br/><br/>
+
* '''Description:''' AAA+ ATPase, replication initiation protein <br/><br/>
 +
 
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
−
|-Hallo
+
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''acoR''
+
|''dnaA''
−
|-
 
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfjG, yzcB ''
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
 
|-
 
|-
−
|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"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of acetoin utilization
+
|style="background:#ABCDEF;" align="center"| '''Product''' || replication initiation protein
 
|-
 
|-
−
|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=BSU33900 eno]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
 
|-
 
|-
−
|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/Eno Eno]
+
|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=BSU00010 dnaA]
 
|-
 
|-
−
|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]'''
+
|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=DnaA DnaA]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 66 kDa, 7.884  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1815 bp, 605 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acoL]]'', ''[[sspH]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[dnaN]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00100 Advanced_DNA]
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00010 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00010 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00010 DNA_with_flanks]
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:acoR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
 
  <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=acoR_883758_885575_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:acoR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33900]]
+
|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:dnaA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00010]]
 
|-
 
|-
 
|}
 
|}
Line 38: Line 37:
 
<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/><br/><br/><br/><br/>
 
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[utilization of specific carbon sources]]}},
+
{{SubtiWiki category|[[DNA replication]]}},
−
{{SubtiWiki category|[[transcription factors and their control]]}}
+
{{SubtiWiki category|[[essential genes]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[CcpA regulon]]}}
+
{{SubtiWiki regulon|[[Spo0A regulon]]}}
−
=The [[AcoR regulon]]: =
+
=The [[DnaA regulon]]=
−
* ''[[acoA]]-[[acoB]]-[[acoC]]-[[acoL]]''
 
−
 
 
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU08100
+
* '''Locus tag:''' BSU00010
  
 
===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/acoR-sspH.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11790]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
  
 
=== Additional information===
 
=== Additional information===
−
 
−
 
  
  
Line 77: Line 70:
  
 
* '''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:'''
+
* '''Protein family:''' dnaA family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 86: Line 80:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''  
+
* '''Domains:''' AAA+ domain
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 93: Line 87:
  
 
* '''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 either [[Soj]], [[YabA]] or [[DnaN]] with the AAA+ domain of DnaA {{PubMed|23909787,22286949}}
 +
** 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 {{PubMed|23909787}}
 +
** [[Soj]]-[[DnaA]] {{PubMed|22286949}}
 +
** [[DnaA]]-[[YabA]]  {{PubMed|23909787,12060778}}
 +
** [[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]]:'''
+
* '''[[Localization]]:'''  
 +
** throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 102: Line 109:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31551 O31551]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05648 P05648]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU08100]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00010]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 112: Line 119:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[acoR]]-[[sspH]]'' {{PubMed|11274109}}
+
* '''Operon:''' ''[[dnaA]]-[[dnaN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=acoR_883758_885575_1 acoR] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaA_410_1750_1 dnaA] {{PubMed|22383849}}
  
−
* '''Sigma factor:''' [[SigA]] {{PubMed|22900538}}
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
−
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
** negatively controlled by [[DnaA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed] and [[Spo0A]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 +
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 129: Line 137:
  
 
* '''Mutant:'''
 
* '''Mutant:'''
−
** 1S112 (no resistance), {{PubMed|3125155}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S112&Search=1S112 BGSC]
 
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 142: Line 149:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
+
* [[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]
−
[[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]
+
* [[Peter Graumann]], Freiburg University, Germany [http://www.biologie.uni-freiburg.de/data/bio2/graumann/index.htm homepage]
 +
* [[Alan Grossman]], MIT, Cambridge, MA, USA
 +
* [[Heath Murray]], Centre for Bacterial Cell Biology, Newcastle, UK [http://www.ncl.ac.uk/camb/staff/profile/heath.murray homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 20157337 21035377 21639790 22575476 22797751</pubmed>
  
−
<pubmed>11274109,10368162, 22900538,12850135 </pubmed>
+
==The [[DnaA regulon]]==
 +
<pubmed> 16120674, </pubmed>
 +
==Original publications==
 +
<pubmed>18854156,19011033, 11222620,14651647,17140409 10844689 ,11222620 12060778 16461910 2987848 2168872 11207367, 19737352 19081080 17932079 19968790 19682252 20511500 21097613 21239581 21895792 22286949 22821970 23909787 22396664,21911367</pubmed>
  
−
[[Category:Protein-coding genes]]hello
+
[[Category:Protein-coding genes]]

Revision as of 14:26, 11 November 2013

  • Description: AAA+ ATPase, replication initiation protein

Gene name dnaA
Synonyms dnaH, dnaJ, dnaK
Essential yes PubMed
Product replication initiation protein
Function DNA replication
Gene expression levels in SubtiExpress: dnaA
Interactions involving this protein in SubtInteract: DnaA
MW, pI 50 kDa, 6.035
Gene length, protein length 1338 bp, 446 aa
Immediate neighbours rpmH, dnaN
Sequences Protein DNA DNA_with_flanks
Genetic context
DnaA dnaN yaaA recF yaaB gyrB context.png
This image was kindly provided by SubtiList
Expression at a glance   PubMed
DnaA expression.png















Categories containing this gene/protein

DNA replication, essential genes

This gene is a member of the following regulons

Spo0A regulon

The DnaA regulon

The gene

Basic information

  • Locus tag: BSU00010

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • 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)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains: AAA+ domain
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
    • SirA displaces DnaA from the replication origin PubMed
    • YabA inhibits co-operative binding of DnaA to the oriC DNA PubMed
    • DnaA helix formation (and thus replication initiation) is inhibited by the interaction of either Soj, YabA or DnaN with the AAA+ domain of DnaA PubMed
    • interaction with DnaD inhibits the ability of DnaA to cooperatively bind to DNA PubMed

Database entries

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

Additional information

Expression and regulation

  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Reviews


The DnaA regulon

Original publications

Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=194478"