Difference between revisions of "Sandbox"

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−
* '''Description:''' DNA integrity scanning protein, delays sporulation in the case of chromosome damage, has diadenylate cyclase activity <br/><br/>
+
* '''Description:''' replication initiation protein <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'''
−
|''disA''
+
|''dnaA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacK''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA integrity scanning protein, has diadenylate cyclase activity
+
|style="background:#ABCDEF;" align="center"| '''Product''' || replication initiation protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.569  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1080 bp, 360 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[radA]]'', ''[[yacL]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[dnaN]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11864&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|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)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yacK_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>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00880
+
* '''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/ctsR-mcsAB-clpC-radA-yacK.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10150]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 56:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' disA family (according to Swiss-Prot)
+
* '''Protein family:''' dnaA family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 70: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[DnaA]]-[[YabA]],  [[DnaA]]-[[YabA]]-[[DnaN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed], [[DnaA]]-[[DnaD]] [http://www.ncbi.nlm.nih.gov/sites/entrez/11222620 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot),  throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3C23 3C23]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37573 P37573]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05648 P05648]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00880]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00010]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
+
* '''Operon:''' ''[[dnaA]]-[[dnaN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
−
 
 
−
''disA''
 
−
 
 
−
* '''[[Sigma factor]]:''' ''[[ctsR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]
 
  
−
''disA'': [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]
+
* '''Regulation:''' 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]
  
−
* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 117: Line 115:
  
 
=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]
 +
 +
[[Peter Graumann]], Freiburg University, Germany [http://www.biologie.uni-freiburg.de/data/bio2/graumann/index.htm homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 123:
 
=References=
 
=References=
  
−
<pubmed>11544224 17434969, </pubmed>
+
<pubmed>10844689 11222620 12060778 16461910 2987848 2168872 14651647, </pubmed>
−
# Petersohn et al. (2001) Global Analysis of the General Stress Response of ''Bacillus subtilis''. ''J Bacteriol.'' '''183:''' 5617-5631 [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
# Imai et al. (2000) Subcellular localization of Dna-initiation proteins of ''Bacillus subtilis'': evidence that chromosome replication begins at either edge of the nucleoids. ''Mol. Microbiol.'' '''36:''' 1037-1048. [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
−
# Jervis et al. 2007. SigM-responsive genes of ''Bacillus subtilis'' and their promoters. J. Bacteriol. 189: 4534-4538. [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]
+
# Ishigo-Oka et al. (2001) DnaD protein of ''Bacillus subtilis'' interacts with DnaA, the initiator protein of replication. ''J. Bacteriol.'' '''183:''' 2148-2150. [http://www.ncbi.nlm.nih.gov/sites/entrez/11222620 PubMed]
 +
# Noirot-Gros et al. (2002) An expanded view of bacterial DNA replication. ''Proc. Natl. Acad. Sci. USA'' '''99:''' 8342-8347. [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed]
 +
# Noirot-Gros et al. (2002) Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus Title ''Proc. Natl. Acad. Sci. USA'' '''103:''' 2368-2373. [http://www.ncbi.nlm.nih.gov/sites/entrez/16461910 PubMed]
 +
# Ogasawara et al. (1985) Structure and function of the region of the replication origin of the ''Bacillus subtilis'' chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.''Nucl. Acids Res.'' '''11:''' 2267-2279. [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
 +
# Fukuoka et al.  (1990) Purification and characterization of an initiation protein for chromosomal replication, DnaA, in ''Bacillus subtilis''. ''J. Biochem.'' '''107:''' 732-739. [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed]
 +
# Molle et al. (2003) The Spo0A regulon of ''Bacillus subtilis''.''Mol. Microbiol.'' '''50:''' 1683-1701. [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 14:01, 8 June 2009

  • Description: replication initiation protein

Gene name dnaA
Synonyms dnaH, dnaJ, dnaK
Essential yes PubMed
Product replication initiation protein
Function DNA replication
MW, pI 50 kDa, 6.035
Gene length, protein length 1338 bp, 446 aa
Immediate neighbours rpmH, dnaN
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DnaA dnaN yaaA recF yaaB gyrB context.png
This image was kindly provided by SubtiList



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:
  • Protein family: dnaA family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cytoplasm (according to Swiss-Prot), throughout the cytoplasm 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

Philippe Noirot, Jouy-en-Josas, France homepage

Peter Graumann, Freiburg University, Germany homepage

Your additional remarks

References

  1. Imai et al. (2000) Subcellular localization of Dna-initiation proteins of Bacillus subtilis: evidence that chromosome replication begins at either edge of the nucleoids. Mol. Microbiol. 36: 1037-1048. PubMed
  2. Ishigo-Oka et al. (2001) DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication. J. Bacteriol. 183: 2148-2150. PubMed
  3. Noirot-Gros et al. (2002) An expanded view of bacterial DNA replication. Proc. Natl. Acad. Sci. USA 99: 8342-8347. PubMed
  4. Noirot-Gros et al. (2002) Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus Title Proc. Natl. Acad. Sci. USA 103: 2368-2373. PubMed
  5. Ogasawara et al. (1985) Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.Nucl. Acids Res. 11: 2267-2279. PubMed
  6. Fukuoka et al. (1990) Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis. J. Biochem. 107: 732-739. PubMed
  7. Molle et al. (2003) The Spo0A regulon of Bacillus subtilis.Mol. Microbiol. 50: 1683-1701. PubMed
  8. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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