Difference between revisions of "Sandbox"

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−
* '''Description:''' Sigma subunit of the RNA polymerase, Sigma-54, Sigma L <br/><br/>
+
* '''Description:''' lactate permease <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'''
−
|''sigL''
+
|''lutP''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvfH ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase sigma-54 factor (sigma-L)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || lactate permease
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of arginin, acetoin and fructose, <br/>required for cold adaptation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || lactate uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49,5 kDa, 7.79
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 59 kDa, 9.476 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1308 bp, 436 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1689 bp, 563 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvfG]]'', ''[[yvfH]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lutR]]'', ''[[sigL]]''
 
|-
 
|-
 
|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:sigL_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yvfH_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:''' 3511532 - 3512839
+
* '''Coordinates:'''
  
 
===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]
+
poor growth with lactate as single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
−
 
+
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigL.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10748]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11875]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Binding to promoters of the -12, -24 type
+
* '''Catalyzed reaction/ biological activity:''' lactate uptake [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]
  
−
* '''Protein family:''' sigma-54 factor family
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[LctP]]
−
 
 
−
=== 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 ===
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* '''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:'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' SigL-[[RpoB]]-[[RpoC]]
+
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P24219]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34200]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34190]
 +
 
 +
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 95: Line 91:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
−
* '''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]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  transcriptional roadblock
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP146 (aphA3), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
Line 117: Line 115:
 
=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]
+
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 123: Line 121:
 
=References=
 
=References=
  
−
 
+
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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 17:42, 15 April 2009

  • Description: lactate permease

Gene name lutP
Synonyms yvfH
Essential no
Product lactate permease
Function lactate uptake
MW, pI 59 kDa, 9.476
Gene length, protein length 1689 bp, 563 aa
Immediate neighbours lutR, sigL
Hier soll was neues rein
Genetic context
YvfH context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

poor growth with lactate as single carbon source PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: lactate uptake PubMed
  • Protein family:
  • Paralogous protein(s): LctP

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane associated PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

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

Biological materials

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

Labs working on this gene/protein

Richard Losick, Harvard Univ., Cambridge, USA homepage

Your additional remarks

References

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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