Difference between revisions of "Sandbox"

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−
* '''Description:''' trigger enzyme: catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression  <br/><br/>
+
* '''Description:''' Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon <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'''
−
|''rocG''
+
|''ccpA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''graR, alsA, amyR''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate dehydrogenase (major)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine utilization, controls the activity of [[GltC]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates carbon catabolite repression (CCR)
 
|-
 
|-
−
|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/glutamate.html Ammonium/ glutamate]'''
+
|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/nucleosides_catabolism.html Nucleoside catabolism], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val],<br/>[http://subtiwiki.uni-goettingen.de/pathways/histidine.html His], [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46.2 kDa, 6.28
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36,8 kDa, 5.06
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1272 bp, 424 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1002 bp, 334 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yweA]]'', ''[[rocA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[aroA]]'', ''[[motP]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15806&#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:CAB14952&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rocG_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ccpA_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>
 
|-
 
|-
Line 38: Line 38:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU37790
+
* '''Locus tag:''' BSU29740
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
Poor growth on complex media such as SP (sporulation medium). No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants ([[gudB |''gudB1'']])
+
Loss of carbon catabolite repression.
 +
Loss of PTS-dependent sugar transport due to excessive phosphorylation of [[PtsH |HPr]] by [[HprK]].
 +
The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocG.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpA-motPS.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10621]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10376]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 58:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' L-glutamate + H<sub>2</sub>O + NAD<sup>+</sup> = 2-oxoglutarate + NH<sub>3</sub> + NADH (according to Swiss-Prot) L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the [[GltC]] transcription activator [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
+
* '''Catalyzed reaction/ biological activity:''' transcriptional regulator of carbon catabolite repression (CCR)
  
−
* '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family (according to Swiss-Prot) Glu/Leu/Phe/Val dehydrogenases family
+
* '''Protein family:''' LacI family
  
−
* '''Paralogous protein(s):''' [[GudB]]
+
* '''Paralogous protein(s):'''
 +
 
 +
=== Genes controlled by CcpA ===
 +
 
 +
* '''Activation by CcpA:''' ''[[pta]]'', ''[[ackA]]'', ''[[ilvB]]-[[ilvH]]-[[ilvC]]-[[leuA]]-[[leuB]]-[[leuC]]-[[leuD]]''
 +
 
 +
* '''Repression by CcpA:''' ''[[abbA]], [[amyE]]'', ''[[bglP]]-[[bglH]]'', ''[[bglS]]'', ''[[cccA]]'', ''[[citZ]]-[[icd]]-[[mdh]]'', ''[[levD]]-[[levE]]-[[levF]]-[[levG]]-[[sacC]]'', ''[[licB]]-[[licC]]-[[licA]]-[[licH]]'', ''[[phoP]]-[[phoR]]'', ''[[xylA]]-[[xylB]]'', ''[[xynP]]-[[xynB]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 67: Line 75:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
 +
** HTH lacI-type Domain (1 – 58)
 +
** DNA binding Domain  (6 – 25)
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' [[PtsH |HPr]]-Ser46-P, Crh-Ser-46-P
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:'''glucose-6-phosphate, fructose-1,6-bisphosphate [http://www.ncbi.nlm.nih.gov/pubmed/17376479?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Pubmed]
  
−
* '''Interactions:''' RocG-[[GltC]], this interaction prevents transcription activation of the ''[[gltA]]-[[gltB]]'' operon by GltC [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]  
+
* '''Interactions:''' CcpA-[[PtsH |HPr]] [http://www.ncbi.nlm.nih.gov/pubmed/15369672?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed], CcpA-[[Crh]] [http://www.ncbi.nlm.nih.gov/pubmed/16316990?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 80: Line 90:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' CcpA-Crh-DNA-complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], complex with P-Ser-[[PtsH |HPr]] and sulphate ions [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39857 NCBI]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39633 P39633]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P25144 P25144]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37790]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29740]
−
 
 
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2 1.4.1.2]  1.4.1.2]
 
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''rocG''
+
* '''Operon:''' ''[[ccpA]] [[motP]] [[motS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]
  
−
* '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]), ornithine or proline, subject to carbon catabolite repression ([[CcpA]])
+
* '''Regulation:''' constitutively  expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]
  
−
* '''Regulatory mechanism:''' [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]; [[AhrC]]: transcription activation ; [[CcpA]]: transcription repression
+
* '''Additional information:''' there are about 3.000 molecules of CcpA per cell [http://www.ncbi.nlm.nih.gov/sites/entrez/8000527 PubMed]
−
 
 
−
* '''Additional information:'''
 
−
Activation by [[RocR]] requires binding of RocG to a downstream element [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]
 
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP747 (spc), GP726 (aphA3), GP810 (tet) available in [[Stülke]] lab
+
* '''Mutant:''' QB5407 (spc), GP302 (erm), GP300 (an in frame deletion of ''[[ccpA]]''), available in [[Stülke]] lab
  
−
* '''Expression vector:'''  
+
* '''Expression vector:''' pGP643 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
−
** expression of native ''rocG'' in ''B. subtilis'': pGP529 (in [[pBQ200]]), available in [[Stülke]] lab
 
−
** for purification of RocG carrying an N-terminal Strep-tag: pGP902 (in [[pGP172]]), a series of ''rocG'' variants is also available in [[pGP172]], available in [[Stülke]] lab
 
 
 
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
Line 116: Line 118:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''Antibody:''' available in [[Hillen]] and [[Stülke]] labs
  
−
* '''Antibody:''' available in [[Stülke]] lab
+
=Labs working on this gene/protein=
  
−
=Labs working on this gene/protein=
+
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
 +
 
 +
[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]
 +
 
 +
[[Milton H. Saier]], University of California at San Diego, USA [http://biology.ucsd.edu/faculty/saier.html Homepage]
 +
 
 +
[[Yasutaro Fujita]], University of Fukuyama, Japan
  
−
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
+
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
  
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
+
[[Oscar Kuipers]], University of Groningen, The Netherlands
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
+
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 131: Line 139:
 
=References=
 
=References=
  
−
'''Enzymatic activity of RocG'''
+
'''Reviews'''
−
<pubmed>18603778,,16244435 16195607 ,18326565, 9829940 </pubmed>
+
 
−
   
+
<pubmed> 8598282 , 19202299,14665673,18628769 ,18359269, 18628769    </pubmed>
−
'''Function in the control of [[GltC]] activity'''
+
 
−
<pubmed>15150225,17994626 ,17608797 17183217  </pubmed>
+
'''General and physiological studies'''
 +
 
 +
<pubmed>1904524 ,10941796 ,12123463,8000527, 18757537,16547058,14523131 </pubmed>
 +
 
 +
'''Global analyses (proteome, transcriptome)'''
 +
 
 +
<pubmed>12850135 ,11251851,10559165, 11160890,17183215 </pubmed>
 +
 
 +
'''Repression of target genes by CcpA'''
 +
 
 +
<pubmed>15150224 ,16166551 ,11929549 , 7913927 ,17827291 ,11985717 ,12100558,7592486 </pubmed>
 +
 
 +
'''Positive regulation of gene expression by CcpA'''
 +
 
 +
<pubmed>8226682 ,12193635 ,10559153 ,15916605, 9811655 ,10986270 </pubmed>
 +
 
 +
'''Control of CcpA activity'''
 +
 
 +
<pubmed>7623661 ,9973552 ,9334231 ,12051938, 9689125 </pubmed>
 +
 
 +
'''CcpA-DNA interaction'''
 +
 
 +
<pubmed>8596444 ,10666464 ,15885105,7665492 ,9254709 </pubmed>
 +
 
 +
'''Functional analysis of CcpA'''
 +
 
 +
<pubmed>10383986 ,10601226 ,11557150,9252590 ,9988473  </pubmed>
  
−
'''Expression of ''rocG'''''
+
'''Structural analyses'''
−
<pubmed>12634342,15150224 10468601 9829940  </pubmed>
 
  
−
'''Structural analysis of glutamate dehydrogenase'''
+
<pubmed>15369672 ,16316990 ,17376479 </pubmed>
−
<pubmed>8263917 </pubmed>
 

Revision as of 15:27, 16 July 2009

  • Description: Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon

Gene name ccpA
Synonyms graR, alsA, amyR
Essential no
Product transcriptional regulator
Function mediates carbon catabolite repression (CCR)
Metabolic function and regulation of this protein in SubtiPathways:
Nucleoside catabolism, Nucleotides (regulation), Ile, Leu, Val,
His, Coenzyme A, Central C-metabolism
MW, pI 36,8 kDa, 5.06
Gene length, protein length 1002 bp, 334 amino acids
Immediate neighbours aroA, motP
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CcpA context.gif
This image was kindly provided by SubtiList








The gene

Basic information

  • Locus tag: BSU29740

Phenotypes of a mutant

Loss of carbon catabolite repression. Loss of PTS-dependent sugar transport due to excessive phosphorylation of HPr by HprK. The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcriptional regulator of carbon catabolite repression (CCR)
  • Protein family: LacI family
  • Paralogous protein(s):

Genes controlled by CcpA

Extended information on the protein

  • Kinetic information:
  • Domains:
    • HTH lacI-type Domain (1 – 58)
    • DNA binding Domain (6 – 25)
  • Modification:
  • Cofactor(s): HPr-Ser46-P, Crh-Ser-46-P
  • Effectors of protein activity:glucose-6-phosphate, fructose-1,6-bisphosphate Pubmed
  • Localization:

Database entries

  • Structure: CcpA-Crh-DNA-complex NCBI, complex with P-Ser-HPr and sulphate ions NCBI
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation: constitutively expressed PubMed
  • Additional information: there are about 3.000 molecules of CcpA per cell PubMed

Biological materials

  • Mutant: QB5407 (spc), GP302 (erm), GP300 (an in frame deletion of ccpA), available in Stülke lab
  • Expression vector: pGP643 (N-terminal Strep-tag, purification from B. subtilis, for SPINE, in pGP380), available in Stülke lab
  • lacZ fusion:
  • GFP fusion:

Labs working on this gene/protein

Wolfgang Hillen, Erlangen University, Germany Homepage

Richard Brennan, Houston, Texas, USA Homepage

Milton H. Saier, University of California at San Diego, USA Homepage

Yasutaro Fujita, University of Fukuyama, Japan

Jörg Stülke, University of Göttingen, Germany Homepage

Oscar Kuipers, University of Groningen, The Netherlands Homepage

Your additional remarks

References

Reviews


General and physiological studies


Global analyses (proteome, transcriptome)


Repression of target genes by CcpA


Positive regulation of gene expression by CcpA


Control of CcpA activity


CcpA-DNA interaction


Functional analysis of CcpA


Structural analyses

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