Difference between revisions of "RibR"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' cryptic riboflavin kinase, binds leader (RFN) rib operon mRNA, may have a regulatory role <br/><br/>
+
* '''Description:''' cryptic riboflavin kinase, binds leader (RFN) rib operon mRNA, may have a regulatory role, required for the conversion of S-methyl-cysteine to cysteine<br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
Line 12: Line 12:
 
|style="background:#ABCDEF;" align="center"| '''Product''' || cryptic riboflavin kinase
 
|style="background:#ABCDEF;" align="center"| '''Product''' || cryptic riboflavin kinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of rib operon expression  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of S-methyl-cysteine, regulation of rib operon expression  
 
|-
 
|-
 
|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=BSU29300 ribR]
 
|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=BSU29300 ribR]
Line 22: Line 22:
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 690 bp, 230 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 690 bp, 230 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytnL]]'', ''[[ytnJ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sndA]]'', ''[[cmoJ]]''
 
|-
 
|-
 
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29300 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29300 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29300 DNA_with_flanks]
 
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29300 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29300 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29300 DNA_with_flanks]
Line 37: Line 37:
 
<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/><br/><br/>
 
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}}
+
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
 +
{{SubtiWiki category|[[sulfur metabolism]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
 
{{SubtiWiki regulon|[[CymR regulon]]}},
 
{{SubtiWiki regulon|[[CymR regulon]]}},
−
{{SubtiWiki regulon|[[YtlI regulon]]}}
+
{{SubtiWiki regulon|[[AscR regulon]]}}
  
 
=The gene=
 
=The gene=
Line 57: Line 54:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
* no growth with S-methyl cysteine {{PubMed|23944997}}
  
 
=== Database entries ===
 
=== Database entries ===
Line 108: Line 106:
  
 
=Expression and regulation=
 
=Expression and regulation=
−
* '''Operon:''' ''[[ytmI]]-[[tcyJ]]-[[tcyK]]-[[tcyL]]-[[tcyM]]-[[tcyN]]-[[ytmO]]-[[ytnI]]-[[ytnJ]]-[[ribR]]-[[ytnL]]-[[ytnM]]'' {{PubMed|15668000}}
+
* '''Operon:''' ''[[snaA]]-[[tcyJ]]-[[tcyK]]-[[tcyL]]-[[tcyM]]-[[tcyN]]-[[cmoO]]-[[cmoI]]-[[cmoJ]]-[[ribR]]-[[sndA]]-[[ytnM]]'' {{PubMed|15668000}}
  
 
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rbfK_3000985_3001677_-1 ribR] {{PubMed|22383849}}
 
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rbfK_3000985_3001677_-1 ribR] {{PubMed|22383849}}
  
−
* '''Sigma factor:''' [[SigA]] {{PubMed|15272571}}
+
* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15272571}}
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 
** repressed in the presence of cysteine ([[CymR]]) {{PubMed|16109943}}
 
** repressed in the presence of cysteine ([[CymR]]) {{PubMed|16109943}}
 +
** induced in the presence of S-methyl-cysteine ([[AscR]]) {{PubMed|23944997}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 
** [[CymR]]: transcription repression {{PubMed|16109943}}
 
** [[CymR]]: transcription repression {{PubMed|16109943}}
−
** [[YtlI]]: transcription activation {{PubMed|16109943}}  
+
** [[AscR]]: transcription activation {{PubMed|16109943}}  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 142: Line 141:
  
 
=References=
 
=References=
−
'''Additional publications:''' {{PubMed|15272571}}
+
<pubmed>17590224, 15668000 16109943 15272571 23944997</pubmed>
−
<pubmed>17590224, 15668000 16109943</pubmed>
 
−
 
 
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 11:28, 18 August 2013

  • Description: cryptic riboflavin kinase, binds leader (RFN) rib operon mRNA, may have a regulatory role, required for the conversion of S-methyl-cysteine to cysteine

Gene name ribR
Synonyms ytnK
Essential no
Product cryptic riboflavin kinase
Function utilization of S-methyl-cysteine, regulation of rib operon expression
Gene expression levels in SubtiExpress: ribR
Metabolic function and regulation of this protein in SubtiPathways:
Riboflavin / FAD
MW, pI 26 kDa, 9.278
Gene length, protein length 690 bp, 230 aa
Immediate neighbours sndA, cmoJ
Sequences Protein DNA DNA_with_flanks
Genetic context
RibR context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
RibR expression.png















Categories containing this gene/protein

poorly characterized/ putative enzymes, sulfur metabolism

This gene is a member of the following regulons

CymR regulon, AscR regulon

The gene

Basic information

  • Locus tag: BSU29300

Phenotypes of a mutant

  • no growth with S-methyl cysteine PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • 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: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
    • repressed in the presence of cysteine (CymR) PubMed
    • induced in the presence of S-methyl-cysteine (AscR) PubMed
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Che-Man Chan, Antoine Danchin, Philippe Marlière, Agnieszka Sekowska
Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis.
Environ Microbiol: 2014, 16(1);101-17
[PubMed:23944997] [WorldCat.org] [DOI] (I p)

Yuhei Higashitsuji, Annemarie Angerer, Sabine Berghaus, Birgit Hobl, Matthias Mack
RibR, a possible regulator of the Bacillus subtilis riboflavin biosynthetic operon, in vivo interacts with the 5'-untranslated leader of rib mRNA.
FEMS Microbiol Lett: 2007, 274(1);48-54
[PubMed:17590224] [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)

I M Solov'eva, R A Kreneva, L L Erraĭs, A S Mironov, D A Perumov
[Study of the mechanism for regulating ribR gene activity in Bacillus subtilis]. [Issledovanie mekhanizma reguliatsii aktivnosti gena ribR u Bacillus subtilis.]
Genetika: 2004, 40(5);716-20
[PubMed:15272571] [WorldCat.org] (P p)

Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=RibR&oldid=193760"