Difference between revisions of "Sandbox"

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−
* '''Description:''' protein serine phosphatase, energy PP2C, dephosphorylates RsbV <br/><br/>
+
* '''Description:''' Sigma subunit of the RNA polymerase, Sigma-54, Sigma L <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'''
−
|''rsbP''
+
|''sigL''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvfP ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || protein serine phosphatase, energy PP2C
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase sigma-54 factor (sigma-L)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of SigB activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of arginin, acetoin and fructose, <br/>required for cold adaptation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.827 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49,5 kDa, 7.79
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1209 bp, 403 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1308 bp, 436 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbQ]]'', ''[[yvfO]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvfG]]'', ''[[yvfH]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15416&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15425&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rsbP_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sigL_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>
 
|-
 
|-
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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 3511532 - 3512839
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
The mutant is cold-sensitive and unable to use arginine as a single carbon source. [http://www.ncbi.nlm.nih.gov/sites/entrez/16585774  PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigL.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12441]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10748]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 52: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Binding to promoters of the -12, -24 type
  
−
* '''Protein family:'''
+
* '''Protein family:''' sigma-54 factor family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes/ operons controlled by SigL ===
 +
''[[acoA]]-[[acoB]]-[[acoC]]-[[acoL]]'', ''[[rocA]]-[[rocB]]-[[rocC]]'', ''[[rocD]]-[[rocE]]-[[rocF]]'', ''[[rocG]]'', ''[[levD]]-[[levE]]-[[levF]]-[[levG]]-[[sacC]]'', ''[[ptb]]-[[bcd]]-[[buk]]-[[lpdV]]-[[bkdAA]]-[[bkdAB]]-[[bkdB]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 62: Line 66:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''  
+
* '''Domains:'''
 +
** DNA binding domain (H-T-H motif) (324–343)
 +
** pron box domain (413–421)
 +
** 3 x Compositional bias domain (6–21),(32–53),(112–136)
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 70: Line 77:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[RsbQ]]-[[RsbP]],  
+
* '''Interactions:''' [[SigL]]-[[YplP]], SigL-[[RpoB]]-[[RpoC]]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 78: Line 85:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P40399]
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P24219]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34110]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34200]
−
 
 
−
* '''E.C. number:'''
 
  
 
=== Additional information===
 
=== Additional information===
Line 92: Line 97:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  neg. regulated by [[CcpA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+16166551 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  transcriptional roadblock
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP146 (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=
 +
 +
[[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 118: Line 123:
 
=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
 
 +
# Ali, N. O., Bignon, J., Rapoport, G., and Débarbouillé, M. (2001) Regulation of the acetoin catabolic pathway is controlled by sigma L in Bacillus subtilis. J. Bacteriol. 183, 2497-2504. [http://www.ncbi.nlm.nih.gov/sites/entrez/11274109  PubMed]
 +
# Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305. [http://www.ncbi.nlm.nih.gov/sites/entrez/9829940  PubMed]
 +
# Choi SK, Saier MH Jr: (2005) Regulation of sigL expression by the catabolite control protein CcpA involves a roadblock mechanism in Bacillus subtilis: potential connection between carbon and nitrogen metabolism. J Bacteriol , 187:6856-6861. [http://www.ncbi.nlm.nih.gov/sites/entrez/16166551  PubMed]
 +
# Débarbouillé M, Martin-Verstraete I, Kunst F, Rapoport G: (1991) The Bacillus subtilis sigL gene encodes an equivalent of (Sigma)54 from Gram-negative bacteria. Proc Natl Acad Sci USA , 88:9092-9096. [http://www.ncbi.nlm.nih.gov/sites/entrez/1924373  PubMed]
 +
# Martin-Verstraete I, Débarbouillé M, Klier A, Rapoport G: (1992) Mutagenesis of the Bacillus subtilis ‘-12, -24’ promoter of the levanase operon and evidence for the existence of an upstream activating sequence. J Mol Biol , 226:85-99. [http://www.ncbi.nlm.nih.gov/sites/entrez/1619665  PubMed]
 +
# Wiegeshoff et al.  (2006) Sigma L is important for cold shock adaptation of ''Bacillus subtilis''. J Bacteriol , 188: 3130-3133. [http://www.ncbi.nlm.nih.gov/sites/entrez/16585774  PubMed]

Revision as of 23:21, 27 April 2009

  • Description: Sigma subunit of the RNA polymerase, Sigma-54, Sigma L

Gene name sigL
Synonyms
Essential no
Product RNA polymerase sigma-54 factor (sigma-L)
Function utilization of arginin, acetoin and fructose,
required for cold adaptation
MW, pI 49,5 kDa, 7.79
Gene length, protein length 1308 bp, 436 amino acids
Immediate neighbours yvfG, yvfH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SigL context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Coordinates: 3511532 - 3512839

Phenotypes of a mutant

The mutant is cold-sensitive and unable to use arginine as a single carbon source. PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Binding to promoters of the -12, -24 type
  • Protein family: sigma-54 factor family
  • Paralogous protein(s):

Genes/ operons controlled by SigL

acoA-acoB-acoC-acoL, rocA-rocB-rocC, rocD-rocE-rocF, rocG, levD-levE-levF-levG-sacC, ptb-bcd-buk-lpdV-bkdAA-bkdAB-bkdB

Extended information on the protein

  • Kinetic information:
  • Domains:
    • DNA binding domain (H-T-H motif) (324–343)
    • pron box domain (413–421)
    • 3 x Compositional bias domain (6–21),(32–53),(112–136)
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by glucose (CcpA) , neg. regulated by CcpA PubMed
  • Regulatory mechanism: CcpA: transcription repression, transcriptional roadblock
  • Additional information:

Biological materials

  • Mutant: GP146 (aphA3), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • Antibody:

Labs working on this gene/protein

Michel Debarbouille, Pasteur Institute, Paris, France Homepage

Your additional remarks

References

  1. Ali, N. O., Bignon, J., Rapoport, G., and Débarbouillé, M. (2001) Regulation of the acetoin catabolic pathway is controlled by sigma L in Bacillus subtilis. J. Bacteriol. 183, 2497-2504. PubMed
  2. Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305. PubMed
  3. Choi SK, Saier MH Jr: (2005) Regulation of sigL expression by the catabolite control protein CcpA involves a roadblock mechanism in Bacillus subtilis: potential connection between carbon and nitrogen metabolism. J Bacteriol , 187:6856-6861. PubMed
  4. Débarbouillé M, Martin-Verstraete I, Kunst F, Rapoport G: (1991) The Bacillus subtilis sigL gene encodes an equivalent of (Sigma)54 from Gram-negative bacteria. Proc Natl Acad Sci USA , 88:9092-9096. PubMed
  5. Martin-Verstraete I, Débarbouillé M, Klier A, Rapoport G: (1992) Mutagenesis of the Bacillus subtilis ‘-12, -24’ promoter of the levanase operon and evidence for the existence of an upstream activating sequence. J Mol Biol , 226:85-99. PubMed
  6. Wiegeshoff et al. (2006) Sigma L is important for cold shock adaptation of Bacillus subtilis. J Bacteriol , 188: 3130-3133. PubMed
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