Difference between revisions of "CymR"

From SubtiWiki
Jump to: navigation, search
(→‎Extended information on the protein)
 
(12 intermediate revisions by 3 users not shown)
Line 14: Line 14:
 
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of [[sulfur metabolism]]
 
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of [[sulfur metabolism]]
 
|-
 
|-
−
|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/CymR CymR]
+
|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=BSU27520 cymR]
 
|-
 
|-
−
|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/riboflavin.html Riboflavin / FAD], [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation]'''
+
|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=CymR CymR]
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=cymR cymR]'''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 9.879   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 9.879   
Line 24: Line 26:
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrvO]]'', ''[[yrvN]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrvO]]'', ''[[yrvN]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14694&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU27520 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU27520 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU27520 DNA_with_flanks]
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yrzC_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yrzC_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>
 +
|-
 +
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cymR_2811717_2812133_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cymR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU27520]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<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/>
Line 55: Line 65:
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU27520&redirect=T BSU27520]
  
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cymR-yrvO-trmU.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cymR-yrvO-trmU.html]
Line 94: Line 105:
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU27520&redirect=T BSU27520]
  
 
* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=2Y75 2Y75] {{PubMed|21624051}}
 
* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=2Y75 2Y75] {{PubMed|21624051}}
Line 108: Line 120:
 
* '''Operon:''' ''[[cymR]]-[[yrvO]]-[[trmU]]'' {{PubMed|16885442}}
 
* '''Operon:''' ''[[cymR]]-[[yrvO]]-[[trmU]]'' {{PubMed|16885442}}
  
−
* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|16885442}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cymR_2811717_2812133_-1 cymR] {{PubMed|22383849}}
 +
 
 +
* '''Sigma factor:''' [[SigA]] {{PubMed|16885442}}
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 116: Line 130:
  
 
* '''Additional information:'''
 
* '''Additional information:'''
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 508 {{PubMed|24696501}}
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 1039 {{PubMed|24696501}}
  
 
=Biological materials =
 
=Biological materials =
Line 141: Line 157:
 
<pubmed>16513748, </pubmed>
 
<pubmed>16513748, </pubmed>
 
==Other original publications==
 
==Other original publications==
−
'''Additional publications:''' {{PubMed|21624051}}
+
<pubmed>18974048,17056751,16109943,16885442 11948165 , 15668000 20608979 21624051</pubmed>
−
<pubmed>18974048,17056751,16109943,16885442 11948165 , 15668000 20608979</pubmed>
 
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Latest revision as of 09:35, 17 April 2014

Gene name cymR
Synonyms yrzC
Essential no
Product transcription repressor
Function regulation of sulfur metabolism
Gene expression levels in SubtiExpress: cymR
Interactions involving this protein in SubtInteract: CymR
Metabolic function and regulation of this protein in SubtiPathways:
cymR
MW, pI 11 kDa, 9.879
Gene length, protein length 333 bp, 111 aa
Immediate neighbours yrvO, yrvN
Sequences Protein DNA DNA_with_flanks
Genetic context
YrzC context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
CymR expression.png



























Categories containing this gene/protein

sulfur metabolism, transcription factors and their control, regulators of core metabolism

This gene is a member of the following regulons

stringent response

The CymR regulon

The gene

Basic information

  • Locus tag: BSU27520

Phenotypes of a mutant

  • impaired growth in the presence of cystine and increased sensitivity to hydrogen peroxide-, disulfide-, paraquat- and tellurite-induced stresses PubMed
  • increased intracellular cysteine pool and hydrogen sulfide formation PubMed
  • depletion of branched-chain amino acids PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: Rrf2 family of transcription regulators
  • Paralogous protein(s):

Genes repressed by CymR

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Effectors of protein activity:
  • Interactions:
    • CymR-CysK, the complex is formed in the presence of cysteine, and results in DNA binding and repression of genes of cysteine biosynthesis PubMed

Database entries

  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
    • RelA dependent downregulation (Class I) during stringent response PubMed
  • Regulatory mechanism:
  • Additional information:
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 508 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 1039 PubMed

Biological materials

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

Labs working on this gene/protein

Isabelle Martin-Verstraete, Institute Pasteur, Paris, France

Your additional remarks

References

The CymR regulon

Other original publications

William Shepard, Olga Soutourina, Emmanuelle Courtois, Patrick England, Ahmed Haouz, Isabelle Martin-Verstraete
Insights into the Rrf2 repressor family--the structure of CymR, the global cysteine regulator of Bacillus subtilis.
FEBS J: 2011, 278(15);2689-701
[PubMed:21624051] [WorldCat.org] [DOI] (I p)

Marie-Françoise Hullo, Isabelle Martin-Verstraete, Olga Soutourina
Complex phenotypes of a mutant inactivated for CymR, the global regulator of cysteine metabolism in Bacillus subtilis.
FEMS Microbiol Lett: 2010, 309(2);201-7
[PubMed:20608979] [WorldCat.org] [DOI] (I p)

Catherine Tanous, Olga Soutourina, Bertrand Raynal, Marie-Françoise Hullo, Peggy Mervelet, Anne-Marie Gilles, Philippe Noirot, Antoine Danchin, Patrick England, Isabelle Martin-Verstraete
The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis.
J Biol Chem: 2008, 283(51);35551-60
[PubMed:18974048] [WorldCat.org] [DOI] (P p)

Marie-Françoise Hullo, Sandrine Auger, Olga Soutourina, Octavian Barzu, Mireille Yvon, Antoine Danchin, Isabelle Martin-Verstraete
Conversion of methionine to cysteine in Bacillus subtilis and its regulation.
J Bacteriol: 2007, 189(1);187-97
[PubMed:17056751] [WorldCat.org] [DOI] (P p)

Soon-Yong Choi, Dindo Reyes, Montira Leelakriangsak, Peter Zuber
The global regulator Spx functions in the control of organosulfur metabolism in Bacillus subtilis.
J Bacteriol: 2006, 188(16);5741-51
[PubMed:16885442] [WorldCat.org] [DOI] (P p)

Pierre Burguière, Juliette Fert, Isabelle Guillouard, Sandrine Auger, Antoine Danchin, Isabelle Martin-Verstraete
Regulation of the Bacillus subtilis ytmI operon, involved in sulfur metabolism.
J Bacteriol: 2005, 187(17);6019-30
[PubMed:16109943] [WorldCat.org] [DOI] (P p)

Irina M Solovieva, Rimma A Kreneva, Lubov Errais Lopes, Daniel A Perumov
The riboflavin kinase encoding gene ribR of Bacillus subtilis is a part of a 10 kb operon, which is negatively regulated by the yrzC gene product.
FEMS Microbiol Lett: 2005, 243(1);51-8
[PubMed:15668000] [WorldCat.org] [DOI] (P p)

Christine Eymann, Georg Homuth, Christian Scharf, Michael Hecker
Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis.
J Bacteriol: 2002, 184(9);2500-20
[PubMed:11948165] [WorldCat.org] [DOI] (P p)

Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=CymR&oldid=203313"