Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' AhrC represses the genes for arginine biosynthesis and activates the genes for arginine catabolism. <br/><br/>
+
* '''Description:''' two-component response regulator, initiation of sporulation <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'''
−
|''ahrC''
+
|''spo0A''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''argR''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0C, spo0G, spoIIL, sof-1 ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional regulator of arginine metabolic genes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16,7 kDa, 5.52
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.989 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 447 bp, 149 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 801 bp, 267 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqxC]]'', ''[[recN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqiG]]'', ''[[spoIVB]]''
 
|-
 
|-
 
|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:spo0A_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 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 2521558 - 2522004
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ahrC-recN.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spo0A.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10309]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10765]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 51: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcriptional activator/ repressor of genes involved in arginine metabolism
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' ArgR family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes controlled by Spo0A ===
 +
 +
* '''Activation by Spo0A:''' ''[[spoIIAA]]-[[spoIIAB]]-[[sigF]]'', ''[[spoIIE]]'',  ''[[spoIIGA]]-[[sigE]]-[[sigG]]''
 +
 +
* '''Repression by Spo0A:''' ''[[abrB]], [[kinA]], [[kinC]], [[spo0A]]'', ''[[metS]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 63: Line 70:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' receives phosphorylation from [[Spo0B]], dephosphorylation by [[Spo0E]]
  
−
* '''Cofactor(s):''' L-arginine is the co-factor required for transcription repression/ activation
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
Line 71: Line 78:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' Cytoplasm
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''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]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P17893]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU24250]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU24220]
 +
 
 +
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 85: Line 94:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''ahrC''-''[[recN]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' by small RNA [[sr1]]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' inhibtion of translation upon binding of [[sr1]] to the ''ahrC'' mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP729 (aphA3), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
Line 109: Line 120:
 
=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]
+
[[Tony Wilkinson]], York University, U.K. [http://www.york.ac.uk/depts/chem/staff/ajw.html 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]
+
[[Imrich Barak]], Slovak Academy of Science, Bratislava, Slovakia [http://imb.savba.sk/~barak/ homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 117: Line 128:
 
=References=
 
=References=
  
−
# 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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: two-component response regulator, initiation of sporulation

Gene name spo0A
Synonyms spo0C, spo0G, spoIIL, sof-1
Essential no
Product two-component response regulator
Function initiation of sporulation
MW, pI 29 kDa, 5.989
Gene length, protein length 801 bp, 267 aa
Immediate neighbours yqiG, spoIVB
Hier soll was neues rein
Genetic context
Spo0A context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Genes controlled by Spo0A

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: receives phosphorylation from Spo0B, dephosphorylation by Spo0E
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Tony Wilkinson, York University, U.K. homepage

Imrich Barak, Slovak Academy of Science, Bratislava, Slovakia homepage

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=55379"