Difference between revisions of "YcnK"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
* '''Description:''' transcription repressor of  the ''[[ycnK]]-[[ycnJ]]-[[ycnI]]'' operon <br/><br/>
+
* '''Description:''' copper-responsive transcription repressor of  the ''[[ycnK]]-[[ycnJ]]-[[ycnI]]'' operon <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor, [[DeoR family]]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of copper uptake
 
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of copper uptake
Line 42: Line 42:
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[AbrB regulon]]}}
+
{{SubtiWiki regulon|[[AbrB regulon]]}},
 +
{{SubtiWiki regulon|[[YcnK regulon]]}}
 +
 
 
=The [[YcnK regulon]]:=
 
=The [[YcnK regulon]]:=
 
* ''[[ycnK]]-[[ycnJ]]-[[ycnI]]''
 
* ''[[ycnK]]-[[ycnJ]]-[[ycnI]]''
 +
 
=The gene=
 
=The gene=
  
Line 52: Line 55:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 
+
* elevated expression of ''[[ycnJ]]'' under conditions of copper excess [http://www.ncbi.nlm.nih.gov/sites/entrez/19168619 PubMed]
elevated expression of ''[[ycnJ]]'' under conditions of copper excess [http://www.ncbi.nlm.nih.gov/sites/entrez/19168619 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 68: Line 70:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' repression of ''[[ycnJ]]'' expression [http://www.ncbi.nlm.nih.gov/sites/entrez/19168619 PubMed]
+
* '''Catalyzed reaction/ biological activity:''' repression of ''[[ycnK]]-[[ycnJ]]-[[ycnI]]'' expression in the presence of excess copper {{PubMed|22904286,19168619}}
  
 
* '''Protein family:''' DeoR family of transcription factors
 
* '''Protein family:''' DeoR family of transcription factors
Line 87: Line 89:
  
 
* '''[[SubtInteract|Interactions]]:'''  
 
* '''[[SubtInteract|Interactions]]:'''  
 +
** forms dimers {{PubMed|22904286}}
  
 
* '''[[Localization]]:'''
 
* '''[[Localization]]:'''
Line 108: Line 111:
 
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycnK_448461_449033_-1 ycnK] {{PubMed|22383849}}
 
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycnK_448461_449033_-1 ycnK] {{PubMed|22383849}}
  
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]] {{PubMed|22904286}}
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15101989 PubMed]
 
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15101989 PubMed]
 +
** induced by copper limitation ([[YcnK]]) {{PubMed|22904286}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15101989 PubMed]
 
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15101989 PubMed]
 +
** [[YcnK]]: transcription repression {{PubMed|22904286}}
  
 
* '''Additional information:'''
 
* '''Additional information:'''

Revision as of 08:14, 23 August 2012

  • Description: copper-responsive transcription repressor of the ycnK-ycnJ-ycnI operon

Gene name ycnK
Synonyms
Essential no
Product transcription repressor, DeoR family
Function regulation of copper uptake
Gene expression levels in SubtiExpress: ycnK
MW, pI 21 kDa, 7.371
Gene length, protein length 570 bp, 190 aa
Immediate neighbours ycnJ, ycnL
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YcnK context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YcnK expression.png















Categories containing this gene/protein

trace metal homeostasis (Cu, Zn, Ni, Mn, Mo), transcription factors and their control

This gene is a member of the following regulons

AbrB regulon, YcnK regulon

The YcnK regulon:

The gene

Basic information

  • Locus tag: BSU03960

Phenotypes of a mutant

  • elevated expression of ycnJ under conditions of copper excess PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: repression of ycnK-ycnJ-ycnI expression in the presence of excess copper PubMed
  • Protein family: DeoR family of transcription factors
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s): copper acts as corepressor PubMed
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Mohamed Marahiel, Marburg University, Germany homepage

Your additional remarks

References

Kazutake Hirooka, Takayosh Edahiro, Kosuke Kimura, Yasutaro Fujita
Direct and indirect regulation of the ycnKJI operon involved in copper uptake through two transcriptional repressors, YcnK and CsoR, in Bacillus subtilis.
J Bacteriol: 2012, 194(20);5675-87
[PubMed:22904286] [WorldCat.org] [DOI] (I p)

Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A T Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, Jan Maarten van Dijl, Michael Hecker, Uwe Völker, Philippe Bessières, Philippe Noirot
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science: 2012, 335(6072);1103-6
[PubMed:22383849] [WorldCat.org] [DOI] (I p)

Shashi Chillappagari, Marcus Miethke, Hein Trip, Oscar P Kuipers, Mohamed A Marahiel
Copper acquisition is mediated by YcnJ and regulated by YcnK and CsoR in Bacillus subtilis.
J Bacteriol: 2009, 191(7);2362-70
[PubMed:19168619] [WorldCat.org] [DOI] (I p)

Mélanie A Hamon, Nicola R Stanley, Robert A Britton, Alan D Grossman, Beth A Lazazzera
Identification of AbrB-regulated genes involved in biofilm formation by Bacillus subtilis.
Mol Microbiol: 2004, 52(3);847-60
[PubMed:15101989] [WorldCat.org] [DOI] (P p)