Difference between revisions of "CymR"

From SubtiWiki
Jump to: navigation, search
(→‎Extended information on the protein)
 
(65 intermediate revisions by 8 users not shown)
Line 1: Line 1:
−
* '''Description:''' write here <br/><br/>
+
* '''Description:''' pleiotropic regulator of [[sulfur metabolism]] <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
Line 8: Line 8:
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yrzC''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yrzC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of [[sulfur metabolism]]
 +
|-
 +
|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"| '''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 18: Line 24:
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 333 bp, 111 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 333 bp, 111 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrvO]]'', ''[[yrvN]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yrzC_nucleotide.txt    Gene sequence     (+200bp)  ]'''
+
|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]
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yrzC_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|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>
 +
|-
 +
|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/>
+
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[sulfur metabolism]]}},
 +
{{SubtiWiki category|[[transcription factors and their control]]}},
 +
{{SubtiWiki category|[[regulators of core metabolism]]}}
  
 +
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[stringent response]]}}
 +
=The [[CymR regulon]]=
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU27520
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
* impaired growth in the presence of cystine and increased sensitivity to hydrogen peroxide-, disulfide-, paraquat- and tellurite-induced stresses {{PubMed|20608979}}
 +
* increased intracellular cysteine pool and hydrogen sulfide formation {{PubMed|20608979}}
 +
* depletion of branched-chain amino acids {{PubMed|20608979}}
  
 
=== 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/yrzC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cymR-yrvO-trmU.html]
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13813]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13813]
Line 57: Line 83:
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes repressed by CymR ===
 +
* ''[[ytmI]]-[[tcyJ]]-[[tcyK]]-[[tcyL]]-[[tcyM]]-[[tcyN]]-[[ytmO]]-[[ytnI]]-[[ytnJ]]-[[ribR]]-[[ytnL]]-[[ytnM]]'' {{PubMed|16109943}}
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 66: Line 95:
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' [[CysK]] acts as corepressor [http://www.ncbi.nlm.nih.gov/sites/entrez/18974048 PubMed]
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:'''  
  
−
* '''Interactions:''' [[CymR]]-[[CysK]]
+
* '''[[SubtInteract|Interactions]]:'''
 +
** [[CymR]]-[[CysK]], the complex is formed in the presence of cysteine, and results in DNA binding and repression of genes of cysteine biosynthesis [http://www.ncbi.nlm.nih.gov/sites/entrez/18974048 PubMed]
  
−
* '''Localization:'''
+
* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU27520&redirect=T BSU27520]
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=2Y75 2Y75] {{PubMed|21624051}}
  
−
* '''Swiss prot entry:'''
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34527 O34527]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27520]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 87: Line 118:
  
 
=Expression and regulation=
 
=Expression and regulation=
 +
* '''Operon:''' ''[[cymR]]-[[yrvO]]-[[trmU]]'' {{PubMed|16885442}}
  
−
* '''Operon:'''  
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cymR_2811717_2812133_-1 cymR] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]] {{PubMed|16885442}}
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed|11948165}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''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 113: Line 148:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Isabelle Martin-Verstraete]], Institute Pasteur, Paris, France
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
==The [[CymR regulon]]==
 +
<pubmed>16513748, </pubmed>
 +
==Other original publications==
 +
<pubmed>18974048,17056751,16109943,16885442 11948165 , 15668000 20608979 21624051</pubmed>
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
[[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

Sergine Even, Pierre Burguière, Sandrine Auger, Olga Soutourina, Antoine Danchin, Isabelle Martin-Verstraete
Global control of cysteine metabolism by CymR in Bacillus subtilis.
J Bacteriol: 2006, 188(6);2184-97
[PubMed:16513748] [WorldCat.org] [DOI] (P p)

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