Difference between revisions of "Sandbox"

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−
* '''Description:''' 1-deoxyxylulose-5-phosphate synthase <br/><br/>
+
* '''Description:''' AhrC represses the genes for arginine biosynthesis and activates the genes for arginine catabolism. <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'''
−
|''dxs''
+
|''ahrC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqiE ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''argR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || 1-deoxyxylulose-5-phosphate synthase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of thiamine
+
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional regulator of arginine metabolic genes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 69 kDa, 6.002 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16,7 kDa, 5.52
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1899 bp, 633 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 447 bp, 149 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqxC]]'', ''[[yqiD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqxC]]'', ''[[recN]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ahrC_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dxs_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>
 
|-
 
|-
Line 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 2521558 - 2522004
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ahrC-recN.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11715]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10309]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 56: Line 51:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' transcriptional activator/ repressor of genes involved in arginine metabolism
  
−
* '''Protein family:'''
+
* '''Protein family:''' ArgR family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 70: Line 65:
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' L-arginine is the co-factor required for transcription repression/ activation
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
Line 76: Line 71:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' Cytoplasm
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=18637 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/18455186 PubMed],N-Terminus [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=60156 NCBI], C-Terminus [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=60157 NCBI], complex with an 18bp DNA operator [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=62912 NCBI]
−
 
 
−
* '''Swiss prot entry:'''
 
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU24270]
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P17893]
  
−
* '''E.C. number:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU24250]
  
 
=== Additional information===
 
=== Additional information===
Line 92: Line 85:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''ahrC''-''[[recN]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' by small RNA [[sr1]]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' inhibtion of translation upon binding of [[sr1]] to the ''ahrC'' mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP729 (aphA3), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
       
+
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
−
 
−
* '''two-hybrid system:'''
 
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Simon Phillips|Simon Phillips]], Leeds University, UK [http://www.astbury.leeds.ac.uk/People/staffpage.php?StaffID=SEVP Homepage]
 +
 +
[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 117:
 
=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Van Hoy BE et al. (1990) Characterization of the ''spoIVB'' and ''recN'' loci of ''Bacillus subtilis'' ''J Bacteriol.'' '''172:''' 1306-1311. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+2106508 PubMed]
 +
# Heidrich et al. (2006) The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol. Microbiol. 62: 520-536. [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
 +
# Heidrich et al. (2007) In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucl. Acids Res. 35: 4331-4346. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576690 PubMed]
 +
# Garnett et al. (2008) Structure and function of the arginine repressor-operator complex from Bacillus subtilis. J. Mol. Biol. 379: 284-298. [http://www.ncbi.nlm.nih.gov/sites/entrez/18455186 PubMed]
 +
# Garnett et al. (2007) Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor L-arginine. Acta Cryst. Sect. F. 63: 918-921. [http://www.ncbi.nlm.nih.gov/sites/entrez/18007040 PubMed]
 +
# Garnett et al. (2007) A high-resolution structure of the DNA-binding domain of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Cryst. Sect. F. 63: 914-917. [http://www.ncbi.nlm.nih.gov/sites/entrez/18007039 PubMed]
 +
# Dennis et al. (2002) The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Cryst. Sect. D. 58:421-430. [http://www.ncbi.nlm.nih.gov/sites/entrez/11856827 PubMed]
 +
# Makarova et al. (2001) Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2: RESEARCH0013. [http://www.ncbi.nlm.nih.gov/sites/entrez/11305941 PubMed]
 +
# Miller et al. (1997) Operator interactions by the Bacillus subtilis arginine repressor/ activator, AhrC: novel positioning and DNA-mediated assembly of a transcriptional activator at catabolic sites. Mol. Microbiol. 26: 37-48. [http://www.ncbi.nlm.nih.gov/sites/entrez/9383188 PubMed]
 +
# Klingel et al. (1995) A binding site for activation by the Bacillus subtilis AhrC protein, a repressor/ activator of arginine metabolism. Mol. Gen. Genet. 248:329-340. [http://www.ncbi.nlm.nih.gov/sites/entrez/7565595 PubMed]
 +
# Czaplewski et al. (1992) Purification and initial characterization of AhrC: the regulator of arginine metabolism genes in Bacillus subtilis. Mol. Microbiol. 6:267-275. [http://www.ncbi.nlm.nih.gov/sites/entrez/1312212 PubMed]
 +
# North et al. (1989) Nucleotide sequence of a Bacillus subtilis arginine regulatory gene and homology of its product to the Escherichia coli arginine repressor. Gene 80:29-38. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID: 2507400 PubMed]

Revision as of 18:50, 15 April 2009

  • Description: AhrC represses the genes for arginine biosynthesis and activates the genes for arginine catabolism.

Gene name ahrC
Synonyms argR
Essential no
Product transcriptional regulator
Function transcriptional regulator of arginine metabolic genes
MW, pI 16,7 kDa, 5.52
Gene length, protein length 447 bp, 149 amino acids
Immediate neighbours yqxC, recN
Hier soll was neues rein
Genetic context
AhrC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates: 2521558 - 2522004

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcriptional activator/ repressor of genes involved in arginine metabolism
  • Protein family: ArgR family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s): L-arginine is the co-factor required for transcription repression/ activation
  • Effectors of protein activity:
  • Interactions:
  • Localization: Cytoplasm

Database entries

  • Swiss prot entry: [3]
  • KEGG entry: [4]

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation: by small RNA sr1
  • Regulatory mechanism: inhibtion of translation upon binding of sr1 to the ahrC mRNA PubMed
  • Additional information:

Biological materials

  • Mutant: GP729 (aphA3), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • Antibody:

Labs working on this gene/protein

Simon Phillips, Leeds University, UK Homepage

Michel Debarbouille, Pasteur Institute, Paris, France Homepage

Your additional remarks

References

  1. Van Hoy BE et al. (1990) Characterization of the spoIVB and recN loci of Bacillus subtilis J Bacteriol. 172: 1306-1311. PubMed
  2. Heidrich et al. (2006) The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol. Microbiol. 62: 520-536. PubMed
  3. Heidrich et al. (2007) In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucl. Acids Res. 35: 4331-4346. PubMed
  4. Garnett et al. (2008) Structure and function of the arginine repressor-operator complex from Bacillus subtilis. J. Mol. Biol. 379: 284-298. PubMed
  5. Garnett et al. (2007) Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor L-arginine. Acta Cryst. Sect. F. 63: 918-921. PubMed
  6. Garnett et al. (2007) A high-resolution structure of the DNA-binding domain of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Cryst. Sect. F. 63: 914-917. PubMed
  7. Dennis et al. (2002) The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Cryst. Sect. D. 58:421-430. PubMed
  8. Makarova et al. (2001) Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2: RESEARCH0013. PubMed
  9. Miller et al. (1997) Operator interactions by the Bacillus subtilis arginine repressor/ activator, AhrC: novel positioning and DNA-mediated assembly of a transcriptional activator at catabolic sites. Mol. Microbiol. 26: 37-48. PubMed
  10. Klingel et al. (1995) A binding site for activation by the Bacillus subtilis AhrC protein, a repressor/ activator of arginine metabolism. Mol. Gen. Genet. 248:329-340. PubMed
  11. Czaplewski et al. (1992) Purification and initial characterization of AhrC: the regulator of arginine metabolism genes in Bacillus subtilis. Mol. Microbiol. 6:267-275. PubMed
  12. North et al. (1989) Nucleotide sequence of a Bacillus subtilis arginine regulatory gene and homology of its product to the Escherichia coli arginine repressor. Gene 80:29-38. 2507400 PubMed
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