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* '''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"  
|-
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yrzC''
|''cymR ''
|-
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cymR ''
|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   
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|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__
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<br/><br/><br/><br/>
<br/><br/><br/><br/>
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<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 54: Line 80:
* '''Catalyzed reaction/ biological activity:'''  
* '''Catalyzed reaction/ biological activity:'''  


* '''Protein family:'''
* '''Protein family:''' Rrf2 family of transcription regulators


* '''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 ===
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* '''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:'''
* '''[[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
This image was kindly provided by SubtiList
Expression at a glance   PubMed



























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

<pubmed>16513748, </pubmed>

Other original publications

<pubmed>18974048,17056751,16109943,16885442 11948165 , 15668000 20608979 21624051</pubmed>

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