Difference between revisions of "CdaR"

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m (moved YbbR to CdaR)
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* '''Description:''' unknown <br/><br/>
+
* '''Description:''' effector protein controlling [[CdaA]] diadenylate cyclase activity <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'''
−
|''ybbR''
+
|''cdaR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ybbR''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || effector protein controlling [[CdaA]] diadenylate cyclase activity
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of c-di-AMP synthesis
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01760 ybbR]
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01760 cdaR]
 +
|-
 +
|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/CdaR CdaR]
 
|-
 
|-
 
|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/murein/index.html Murein recycling]'''
 
|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/murein/index.html Murein recycling]'''
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1449 bp, 483 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1449 bp, 483 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbP]]'', ''[[glmM]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cdaA]]'', ''[[glmM]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11952&#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:CAB11952&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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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|[[proteins of unknown function]]}}
+
{{SubtiWiki category|[[metabolism of signalling nucleotides]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
 +
** stimulates [[CdaA]] activity upon protein-protein interaction {{PubMed|23192352}}
  
 
* '''Protein family:'''
 
* '''Protein family:'''
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* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
 +
** [[CdaA]]-[[CdaR]], to stimulate [[CdaA]] activity {{PubMed|23192352}}
  
 
* '''[[Localization]]:'''
 
* '''[[Localization]]:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''
+
* '''Operon:''' ''[[cdaA]]-[[cdaR]]-[[glmM]]-[[glmS]]'' {{PubMed|23192352}}
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbR_197027_198478_1 ybbR] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbR_197027_198478_1 cdaR] {{PubMed|22383849}}
  
−
* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}  
+
* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|22211522}}  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  the ''[[ybbP]]-[[ybbR]]'' part of the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
+
* '''Additional information:'''  the ''[[cdaA]]-[[cdaR]]'' part of the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
  
 
=Biological materials =
 
=Biological materials =
  
 
* '''Mutant:'''
 
* '''Mutant:'''
−
** GP999 (''[[ybbR]]''::''cat''), available in [[Jörg Stülke]]'s lab  
+
** GP999 (''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab  
−
** GP985 (''[[ybbP]]''-''[[ybbR]]''::''cat''), available in [[Jörg Stülke]]'s lab  
+
** GP985 (''[[cdaA]]''-''[[cdaR]]''::''cat''), available in [[Jörg Stülke]]'s lab  
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
** IPTG inducible expression of Strep-''ybbR'' in ''E. coli'': pGP2565 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab
+
** IPTG inducible expression of Strep-''cdaR'' in ''E. coli'': pGP2565 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
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=References=
 
=References=
 
'''Additional publications:''' {{PubMed|22211522,21154411}}
 
'''Additional publications:''' {{PubMed|22211522,21154411}}
−
<pubmed>12884008, 16236721, </pubmed>
+
<pubmed>12884008, 16236721, 23192352 </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 11:45, 30 November 2012

  • Description: effector protein controlling CdaA diadenylate cyclase activity

Gene name cdaR
Synonyms ybbR
Essential no
Product effector protein controlling CdaA diadenylate cyclase activity
Function regulation of c-di-AMP synthesis
Gene expression levels in SubtiExpress: cdaR
Interactions involving this protein in SubtInteract: CdaR
Metabolic function and regulation of this protein in SubtiPathways:
Murein recycling
MW, pI 52 kDa, 4.719
Gene length, protein length 1449 bp, 483 aa
Immediate neighbours cdaA, glmM
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YbbR context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YbbR expression.png















Categories containing this gene/protein

metabolism of signalling nucleotides

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU01760

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
    • stimulates CdaA activity upon protein-protein interaction PubMed
  • 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: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information: the cdaA-cdaR part of the mRNA is very stable (half-life > 15 min) PubMed

Biological materials

  • Expression vector:
    • IPTG inducible expression of Strep-cdaR in E. coli: pGP2565 (in pGP172), available in Jörg Stülke's lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab. Respective plasmids: pGP1989 and pGP1992.
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Additional publications: PubMed

Felix M P Mehne, Katrin Gunka, Hinnerk Eilers, Christina Herzberg, Volkhard Kaever, Jörg Stülke
Cyclic di-AMP homeostasis in bacillus subtilis: both lack and high level accumulation of the nucleotide are detrimental for cell growth.
J Biol Chem: 2013, 288(3);2004-17
[PubMed:23192352] [WorldCat.org] [DOI] (I p)

Jun Yin, Paul D Straight, Shaun M McLoughlin, Zhe Zhou, Alison J Lin, David E Golan, Neil L Kelleher, Roberto Kolter, Christopher T Walsh
Genetically encoded short peptide tag for versatile protein labeling by Sfp phosphopantetheinyl transferase.
Proc Natl Acad Sci U S A: 2005, 102(44);15815-20
[PubMed:16236721] [WorldCat.org] [DOI] (P p)

G Hambraeus, C von Wachenfeldt, L Hederstedt
Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs.
Mol Genet Genomics: 2003, 269(5);706-14
[PubMed:12884008] [WorldCat.org] [DOI] (P p)

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