Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional repressor of gluconeogenetic genes and of [[sr1]]. repression in the presence of glucose <br/><br/>
+
* '''Description:''' trigger enzyme: major glucose permease of the PTS, EIICBA(Glc) <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'''
|''ccpN''
+
|''ptsG''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqzB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ptsX, crr''
 
|-
 
|-
 
|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''' || glucose-specific enzyme IICBA component
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || repressor of genes involved in gluconeogenesis (''[[gapB]]'','' [[pckA]]'') and of ''[[sr1]]''
+
|style="background:#ABCDEF;" align="center"|'''Function''' || glucose transport and phosphorylation, control of [[GlcT]] activity
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23.4 kDa, 7.22
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 75,3 kDa, 5.40
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2097 bp, 699 amino acids
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfL]]'', ''[[glyS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glcT]]'', ''[[ptsH]]''
 
|-
 
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpN_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsG_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpN_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsG_protein.txt Protein sequence]'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:yqzB_context.gif]]
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ptsG_context.gif]]
 
|-
 
|-
 
|}
 
|}
Line 30: Line 32:
  
 
<br/><br/>
 
<br/><br/>
 
  
 
=The gene=
 
=The gene=
Line 36: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
* '''Coordinates:''' 2604195 - 2604830
+
* '''Coordinates:''' 1456496 - 1458592
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Impaired growth on glucose due to re-routing of carbon from glycolysis to the pentose phosphate pathway [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpN-yqfL.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ptsGHI.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13768]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10198]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' transcription repression of the ''[[gapB]]'', ''[[pckA]]'', and ''[[sr1]]'' genes in the presence of glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
+
* '''Catalyzed reaction/ biological activity:''' transport and phosphorylation of glucose, receives a phosphate from [[PtsH |HPr]] at the IIA domain (His-620), the phosphate group is then transferred to the IIB domain (Cys-461) an finally to the incoming glucose. In the absence of glucose, PtsG phosphorylates and thereby inactivates the transcriptional antiterminator [[GlcT]].
  
* '''Protein family:'''
+
* '''Protein family:''' PTS enzyme II, glucose family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 64: Line 64:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
 +
** 11x transmembrane domain (16–36, 89–109, 139–159, 180–200, 233–253, 283–303, 313–333, 338–358, 365–385, 388–408)
 +
** PTS EIIC domain (  1-424)
 +
** PTS EIIB domain (439–520)
 +
** PTS EIIA domain (568–672)
  
* '''Modification:'''
+
* '''Modification:''' transient  phosphorylation ([[PtsH |HPr]]-dependent) on His-620, then internal phosphotransfer from His-620 to Cys-461
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
* '''Effectors of protein activity:'''  
+
* '''Effectors of protein activity:'''
** [[YqfL]] (negative effector of CcpN activity) [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
 
** ATP enhances CcpN-dependent repression, ADP counteracts the repressing activity of CcpN [http://www.ncbi.nlm.nih.gov/sites/entrez/18511073 PubMed]
 
  
* '''Interactions:'''
+
* '''Interactions:''' PtsG-[[PtsH |HPr]], PtsG-[[GlcT]] (for phosphorylation of [[GlcT]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14527945 PubMed]
  
* '''Localization:'''
+
* '''Localization:''' membrane protein [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 NCBI]
  
 
=== Database entries ===
 
=== Database entries ===
 +
 +
* '''Structure:''' IIA domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=56258 NCBI], NMR IIA domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=55395 NCBI]
  
* '''Structure:'''
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P20166]
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34994]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13890]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25250]
+
* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?2.7.1.69]
  
 
=== Additional information===
 
=== Additional information===
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[ccpN]]''-''[[yqfL]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
* '''Operon:'''  
 +
**''[[ptsG]]-[[ptsH]]-[[ptsI]]''  
 +
**''[[ptsH]]-[[ptsI]]''
  
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11902727 PubMed]
  
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
* '''Regulation:''' induction by glucose
  
 +
* '''Regulatory mechanism:''' transcriptional antitermination via the [[GlcT]]-dependent RNA-switch [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9765562 PubMed]
 
* '''Additional Fips riecht nach faulen Eiern '''
 
* '''Additional Fips riecht nach faulen Eiern '''
  
 
=Biological materials =
 
=Biological materials =
  
* '''Mutant:''' DB104 ''ccpN''::[[cat]], available in [[Sabine Brantl]] lab
+
* '''Mutant:''' GP474 (cat), QB5436 (spc), QB5445 (erm), available in [[Stülke]] lab
  
* '''Expression vector:'''
+
* '''Expression vector:''' pGP123 (domains BA, in [[pWH844]]), pGP123 (domains BA, mut: H620D, in [[pWH844]]), pGP428 (EIIB, in [[pWH844]]), pGP437(EIIA in [[pWH844]], with thrombin cleavage site), available in [[Stülke]] lab
 
 
* '''lacZ fusion:'''
+
* '''lacZ fusion:''' pGP34 ([[pAC5]]), pGP66 ([[pAC7]]), pGP606 (mutant terminator, [[pAC6]]), pGP532 ([[pAC7]]), series of promoter deletions are available in [[pAC5]] and [[pAC6]], series of RAT mutants are available in [[pAC6]], available in [[Stülke]] lab
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
* '''Antibody:''' available in [[Sabine Brantl]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
+
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
+
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
[[Sabine Brantl |Sabine Brantl]], Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany [http://www.uni-jena.de/AG_Bakteriengenetik_(_Doz__Dr__Sabine_Brantl_).html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 125:
 
=References=
 
=References=
  
 
+
# Stülke J, Martin-Verstraete I, Zagorec M (1997) Induction of the ''Bacillus subtilis ptsGHI'' operon by glucose is controlled by a novel antiterminator, ''GlcT Mol Microbiol.''  '''25:''' 65-78. [http://www.ncbi.nlm.nih.gov/sites/entrez/11902727 PubMed]
# Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of ''Bacillus subtilis'' gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
# Bachem S, Stülke J. (1998)   Regulation of the ''Bacillus subtilis'' GlcT antiterminator protein by components of the phosphotransferase system. ''J Bacteriol.'' '''180:''' 5319-26 [http://www.ncbi.nlm.nih.gov/sites/entrez/9765562 PubMed]
# Licht et al. (2005) Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in ''Bacillus subtilis''. Mol. Microbiol. 58: 189-206. [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
+
# Bachem, S., Faires, N., & Stülke, J. (1997) Characterization of the presumptive phosphorylation sites of the ''Bacillus subtilis'' glucose permease by site-directed mutagenesis: Implication in glucose transport and catabolite repression. FEMS Microbiol. L. 156: 233-238. [http://www.ncbi.nlm.nih.gov/sites/entrez/9513271 PubMed]
# Licht & Brantl (2006) Transcriptional repressor CcpN from ''Bacillus subtilis'' compensates asymmetric contact distribution by cooperative binding. J. Mol. Biol. 364: 434-448. [http://www.ncbi.nlm.nih.gov/sites/entrez/17011578 PubMed]
+
# Gonzy-Tréboul, G., de Waard, J. H., Zagorec, M., and Postma, P.W. (1991). The glucose permease of the phosphotransferase system of ''Bacillus subtilis'': Evidence for IIGlc and IIIGlc domains. Mol. Microbiol. 5, 1241-1249. [http://www.ncbi.nlm.nih.gov/sites/entrez/1956301 PubMed]
# Licht et al. (2008) Identification of ligands affecting the activity of the transcriptional repressor CcpN from ''Bacillus subtilis''. J. Mol. Biol. 380: 17-30. [http://www.ncbi.nlm.nih.gov/sites/entrez/18511073 PubMed]
+
# Langbein, I., Bachem, S. & Stülke, J. (1999) Specific interaction of the RNA binding domain of the ''Bacillus subtilis'' transcriptional antiterminator GlcT with its RNA target, RAT. J. Mol. Biol. 293: 795-805. [http://www.ncbi.nlm.nih.gov/sites/entrez/10543968 PubMed]
# Tännler et al. (2008) CcpN controls central carbon fluxes in ''Bacillus subtilis''. J. Bacteriol. 190: 6178-6187. [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]
+
# Schilling, O., Herzberg, C., Hertrich, T., Vörsmann, H., Jessen, D., Hübner, S., Titgemeyer, F. & Stülke, J. (2006) Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA-protein couples. Nucl. Acids Res. 34: 6102-6115. [http://www.ncbi.nlm.nih.gov/sites/entrez/17074746 PubMed]
 +
# Schilling, O., Langbein, I., Müller, M., Schmalisch, M. & Stülke, J. (2004) A protein-dependent riboswitch controlling ''ptsGHI'' operon expression in ''Bacillus subtilis'': RNA structure rather than sequence provides interaction specificity. Nucl. Acids Res. 32: 2853-2864. [http://www.ncbi.nlm.nih.gov/sites/entrez/15155854 PubMed]
 +
# Schmalisch, M., Bachem, S. & Stülke, J. (2003) Control of the ''Bacillus subtilis'' antiterminator protein GlcT by phosphorylation: Elucidation of the phosphorylation chain leading to inactivation of GlcT. J. Biol. Chem. 278: 51108-51115. [http://www.ncbi.nlm.nih.gov/sites/entrez/14527945 PubMed]
 +
# Zagorec, M. & Postma, P. (1992). Cloning and nucleotide sequence of the ''ptsG'' gene of ''Bacillus subtilis''. Mol Gen Genet 234, 325-328. [http://www.ncbi.nlm.nih.gov/sites/entrez/1508157 PubMed]
 +
# Sutrina, S. L., Reddy, P., Saier, M. H., Jr & Reizer, J. (1990). The glucose permease of ''Bacillus subtilis'' is a single polypeptide chain that functions to energize the sucrose permease. J Biol Chem 265, 18581-18589. [http://www.ncbi.nlm.nih.gov/sites/entrez/2120236 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 15:33, 18 March 2009

  • Description: trigger enzyme: major glucose permease of the PTS, EIICBA(Glc)

Gene name ptsG
Synonyms ptsX, crr
Essential no
Product glucose-specific enzyme IICBA component
Function glucose transport and phosphorylation, control of GlcT activity
MW, pI 75,3 kDa, 5.40
Gene length, protein length 2097 bp, 699 amino acids
Immediate neighbours glcT, ptsH
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
PtsG context.gif



The gene

Basic information

  • Coordinates: 1456496 - 1458592

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transport and phosphorylation of glucose, receives a phosphate from HPr at the IIA domain (His-620), the phosphate group is then transferred to the IIB domain (Cys-461) an finally to the incoming glucose. In the absence of glucose, PtsG phosphorylates and thereby inactivates the transcriptional antiterminator GlcT.
  • Protein family: PTS enzyme II, glucose family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic Fips riecht nach faulen Eiern
  • Domains:
    • 11x transmembrane domain (16–36, 89–109, 139–159, 180–200, 233–253, 283–303, 313–333, 338–358, 365–385, 388–408)
    • PTS EIIC domain ( 1-424)
    • PTS EIIB domain (439–520)
    • PTS EIIA domain (568–672)
  • Modification: transient phosphorylation (HPr-dependent) on His-620, then internal phosphotransfer from His-620 to Cys-461
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: membrane protein NCBI

Database entries

  • Structure: IIA domain NCBI, NMR IIA domain NCBI
  • Swiss prot entry: [3]
  • KEGG entry: [4]
  • E.C. number: [5]

Additional information

Expression and regulation

  • Regulation: induction by glucose
  • Regulatory mechanism: transcriptional antitermination via the GlcT-dependent RNA-switch PubMed
  • Additional Fips riecht nach faulen Eiern

Biological materials

  • Mutant: GP474 (cat), QB5436 (spc), QB5445 (erm), available in Stülke lab
  • Expression vector: pGP123 (domains BA, in pWH844), pGP123 (domains BA, mut: H620D, in pWH844), pGP428 (EIIB, in pWH844), pGP437(EIIA in pWH844, with thrombin cleavage site), available in Stülke lab
  • lacZ fusion: pGP34 (pAC5), pGP66 (pAC7), pGP606 (mutant terminator, pAC6), pGP532 (pAC7), series of promoter deletions are available in pAC5 and pAC6, series of RAT mutants are available in pAC6, available in Stülke lab
  • GFP fusion:
  • Antibody:

Labs working on this gene/protein

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

  1. Stülke J, Martin-Verstraete I, Zagorec M (1997) Induction of the Bacillus subtilis ptsGHI operon by glucose is controlled by a novel antiterminator, GlcT Mol Microbiol. 25: 65-78. PubMed
  2. Bachem S, Stülke J. (1998) Regulation of the Bacillus subtilis GlcT antiterminator protein by components of the phosphotransferase system. J Bacteriol. 180: 5319-26 PubMed
  3. Bachem, S., Faires, N., & Stülke, J. (1997) Characterization of the presumptive phosphorylation sites of the Bacillus subtilis glucose permease by site-directed mutagenesis: Implication in glucose transport and catabolite repression. FEMS Microbiol. L. 156: 233-238. PubMed
  4. Gonzy-Tréboul, G., de Waard, J. H., Zagorec, M., and Postma, P.W. (1991). The glucose permease of the phosphotransferase system of Bacillus subtilis: Evidence for IIGlc and IIIGlc domains. Mol. Microbiol. 5, 1241-1249. PubMed
  5. Langbein, I., Bachem, S. & Stülke, J. (1999) Specific interaction of the RNA binding domain of the Bacillus subtilis transcriptional antiterminator GlcT with its RNA target, RAT. J. Mol. Biol. 293: 795-805. PubMed
  6. Schilling, O., Herzberg, C., Hertrich, T., Vörsmann, H., Jessen, D., Hübner, S., Titgemeyer, F. & Stülke, J. (2006) Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA-protein couples. Nucl. Acids Res. 34: 6102-6115. PubMed
  7. Schilling, O., Langbein, I., Müller, M., Schmalisch, M. & Stülke, J. (2004) A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity. Nucl. Acids Res. 32: 2853-2864. PubMed
  8. Schmalisch, M., Bachem, S. & Stülke, J. (2003) Control of the Bacillus subtilis antiterminator protein GlcT by phosphorylation: Elucidation of the phosphorylation chain leading to inactivation of GlcT. J. Biol. Chem. 278: 51108-51115. PubMed
  9. Zagorec, M. & Postma, P. (1992). Cloning and nucleotide sequence of the ptsG gene of Bacillus subtilis. Mol Gen Genet 234, 325-328. PubMed
  10. Sutrina, S. L., Reddy, P., Saier, M. H., Jr & Reizer, J. (1990). The glucose permease of Bacillus subtilis is a single polypeptide chain that functions to energize the sucrose permease. J Biol Chem 265, 18581-18589. PubMed
  11. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed