Difference between revisions of "Sandbox"

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* '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme <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'''
−
|''gapA''
+
|''dnaA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of chromosome replication
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35.7 kDa, 5.03
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cggR]]'', ''[[pgk]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gapA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gapA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gapA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaA_context.gif]]
 
|-
 
|-
 
|}
 
|}
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<br/><br/>
 
<br/><br/>
  
−
 
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3480732 - 3481736
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
+
essential
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
  
−
* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 54: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' glyceraldehyde-3-phosphate dehydrogenase, (NADH-dependent). Catalyzes the reaction from glyceraldehyde-3-phosphate to 1.3-bi-phosphoglycerate. This reaction is part of the glycolysis.
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[GapB]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:''' K(M) for NAD: 5.7 mM, K(cat) for NAD: 70/sec (determined for GapA from ''Geobacillus stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]
+
* '''Kinetic information:'''
  
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' Phosphorylation (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 72: Line 71:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''  
+
* '''Interactions:''' [[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]
−
** GapA-[[PtsH]]: [[PtsH|HPr(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
 
−
** GapA-[[Crh]]: [[Crh|Crh(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
 
  
−
* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed], loosely membrane associated[http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:''' throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''  
+
* '''Structure:'''
−
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3CMC 3CMC] (from ''Geobacillus stearothermophilus'')
 
−
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NQO 1NQO] (from ''Geobacillus stearothermophilus'', mutant with cys 149 replaced by ser, complex with NAD+ und D-Glyceraldehyde-3-Phosphate)
 
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P09124 P09124]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33940 KEGG]
+
* '''KEGG entry:'''
  
−
* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?1.2.1.12 1.2.1.12]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]). Moreover, mutations in ''gapA'' from ''B. subtilis'' can suppress mutations in genes involved in DNA replication ([http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]).
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[dnaA]]-[[dnaN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
−
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]''
 
−
** ''[[cggR]]-[[gapA]]''
 
  
−
The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. The processing event requires the [[Rny]] protein.
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Sigma factor:''' [[SigA]]  
+
* '''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]
  
−
* '''Regulation:''' [[CggR]] represses the operon in the absence of glycolytic sugars [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12622823 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Regulatory mechanism:''' repression
+
* '''Additional information:'''
−
 
 
−
* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]
 
−
 
 
−
* '''Additional information:''' GapA is one of the most abundant proteins in the cell. In the presence of glucose, there are about 25,000 GapA molecules per cell ([http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]).
 
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' essential
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP90 (N-terminal Strep-tag, purification from ''B. subtilis'', in [[pGP380]]), pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)
+
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in [[Stülke]] lab
+
* '''Antibody:'''
  
 
=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]
−
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 
−
 
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 137: Line 120:
 
=References=
 
=References=
  
−
# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 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]
−
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. subm.
+
# 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]
−
# Doan, T., and S. Aymerich. 2003. Regulation of the central glycolytic pathways in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate. Mol. Microbiol. 47: 1709-1721. [http://www.ncbi.nlm.nih.gov/sites/entrez/12622823 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]
−
# Evguenieva-Hackenberg, E., Schiltz, E., and Klug, G. (2002) Dehydrogenases from all three domains of life cleave RNA. J Biol Chem 277, 46145-46150. [http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 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]
−
# Fillinger, S., Boschi-Muller, S., Azza, S., Dervyn, E., Branlant, G., and Aymerich, S. (2000) Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J Biol Chem 275, 14031-14037. [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 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]
−
# Jannière, L., Canceill, D., Suski, C., Kanga, S., Dalmais, B., Lestini, R., Monnier, A. F., Chapuis, J., Bolotin, A., Titok, M., Le Chatelier, E., and Ehrlich, S. D. (2007) Genetic evidence for a link between glycolysis and DNA replication. PLoS ONE 2, e447. [http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 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]
−
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422.[http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 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]
−
# Ludwig, H., Rebhan, N., Blencke, H.-M., Merzbacher, M. & Stülke, J. (2002). Control of the glycolytic ''gapA'' operon by the catabolite control protein A in ''Bacillus subtilis'': a novel mechanism of CcpA-mediated regulation. Mol Microbiol 45, 543-553.[http://www.ncbi.nlm.nih.gov/sites/entrez/12123463 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
 
−
# Meinken, C., Blencke, H. M., Ludwig, H., and Stülke, J. (2003) Expression of the glycolytic ''gapA'' operon in ''Bacillus subtilis'': differential synthesis of proteins encoded by the operon. Microbiology 149, 751-761. [http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]
 
−
# Pompeo ''et al.'' (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in ''Bacillus subtilis''? J Bacteriol 189, 1154-1157.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
 
−
# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
 
−
# Tobisch, S., Zühlke, D., Bernhardt, J., Stülke, J., and Hecker, M. (1999) Role of CcpA in regulation of the central pathways of carbon catabolism in ''Bacillus subtilis''. J Bacteriol 181, 6996-7004.[http://www.ncbi.nlm.nih.gov/sites/entrez/10559165 PubMed]
 

Revision as of 13:16, 11 February 2009

  • Description: replication initiation protein

Gene name dnaA
Synonyms dnaH, dnaJ, dnaK
Essential yes
Product
Function initiation of chromosome replication
MW, pI 50 kDa, 6.035
Gene length, protein length 1338 bp, 446 aa
Immediate neighbours
Gene sequence (+200bp) Protein sequence
Genetic context
DnaA context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential

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:
  • Localization: throughout the cytoplasm PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • 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

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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