Difference between revisions of "Sandbox"

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* '''Description:''' Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon <br/><br/>
+
* '''Description:''' glutamine-fructose-6-phosphate transaminase <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Gene name'''
+
|style="background:#ABCDEF;" align="center"|'''Gene name''' glaube ich oder nicht
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|''ccpA''
+
|''glmS''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''graR, alsA, amyR''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gcaA, ybxD ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' \|\| YeS
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamine-fructose-6-phosphate transaminase
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || mediates carbon catabolite repression (CCR)
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36,8 kDa, 5.06
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=sandbox sandbox]'''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1002 bp, 334 amino acids
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796 
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[aroA]]'', ''[[motP]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 aa
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glmM]]'', ''[[ybbU]]''
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpA_protein.txt Protein sequence]'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ccpA_context.gif]]
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11954&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:quintos.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 +
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:test.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 +
|-
 +
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:glmS_expression.png|500px]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
  
 
<br/><br/>
 
<br/><br/>
  
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[cell wall synthesis]]}},
 +
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
 +
{{SubtiWiki category|[[essential genes]]}}
 +
 +
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[glmS ribozyme]]}}
  
 
=The gene=
 
=The gene=
Line 36: Line 57:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3043210 - 3044211
+
* '''Locus tag:''' BSU01780
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
Loss of carbon catabolite repression.  
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
−
Loss of PTS-dependent sugar transport due to excessive phosphorylation of [[PtsH |HPr]] by [[HprK]].
 
−
The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.
 
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [HELLO BSU00100]
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T"]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpA-motPS.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10376]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10948]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 77:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcriptional regulator of carbon catabolite repression (CCR)
+
* '''Catalyzed reaction/ biological activity:''' L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot)  
  
−
* '''Protein family:''' LacI family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 67: Line 88:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** HTH lacI-type Domain (1 – 58)
 
−
** DNA binding Domain  (6 – 25)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):''' [[PtsH |HPr]]-Ser46-P, Crh-Ser-46-P
+
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''glucose-6-phosphate, fructose-1,6-bisphosphate [http://www.ncbi.nlm.nih.gov/pubmed/17376479?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Pubmed]
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' CcpA-[[PtsH |HPr]] [http://www.ncbi.nlm.nih.gov/pubmed/15369672?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed], CcpA-[[Crh]] [http://www.ncbi.nlm.nih.gov/pubmed/16316990?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
+
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
 +
** cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [HELLO BSU00100]
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T BSU00240]
 +
 +
* '''Structure:'''
 +
**[http://www.pdb.org/pdb/explore/explore.do?structureId=HIV2 HIV2] (from ''Bacillus subtilis'', 100% identity) {{PubMed|13454352}}
 +
** [http://www.pdb.org/pdb/explore/explore.do?structureId=2VF4 2VF4] (GlmS from ''E. coli'', 39% identity, 58% similarity) {{PubMed|18295797}}
 +
** the ribozyme: [http://www.rcsb.org/pdb/explore.do?structureId=3g8s 3G8S], [http://www.rcsb.org/pdb/explore.do?structureId=3G9C 3G9C], [http://www.rcsb.org/pdb/explore.do?structureId=3g8t 3G8T], [http://www.rcsb.org/pdb/explore.do?structureId=3g95 3G95], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 3G96] (all for the ribozyme from ''Bacillus anthracis''), [http://www.rcsb.org/pdb/explore.do?structureId=2HO7 2HO7] (the ribozyme from ''Thermonanaerobacter tengcongensis'')
  
−
* '''Structure:''' CcpA-Crh-DNA-complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], complex with P-Ser-[[PtsH |HPr]] and sulphate ions [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39857 NCBI]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39754 P39754]
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P25144]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01780]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29740]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.6.1.16 2.6.1.16]
  
 
=== Additional information===
 
=== Additional information===
  
 +
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ccpA]] [[motP]] [[motS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]
+
* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''
  
−
* '''Sigma factor:'''  
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 glmS] {{PubMed|22383849}}
  
−
* '''Regulation:''' constitutively  expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]
+
* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}
  
−
* '''Additional information:''' there are about 3.000 molecules of CcpA per cell [http://www.ncbi.nlm.nih.gov/sites/entrez/8000527 PubMed]
+
* '''Regulation:'''
 +
** repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine {{PubMed|14343123}}
 +
** ''glmS'' is only expressed in the absence of glucosamine 6-phosphate ([[glmS]] [[ribozyme]])
 +
 
 +
* '''Regulatory mechanism:''' ''glmS'' [[ribozyme]]: glucosamine 6-phosphate binds the leader mRNA, and a [[riboswitch]] with [[ribozyme]] activity cleaves off the ''[[glmS]]'' section from the mRNA, resulting in stopp of transcript elongation
 +
 
 +
* '''Additional information:'''  
 +
** subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 +
** A [[ncRNA]] is predicted between ''[[glmM]]'' and ''[[glmS]]'' {{PubMed|20525796}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 2000 {{PubMed|24696501}}
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 4000 {{PubMed|24696501}}
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' QB5407 (spc), GP302 (erm), GP300 (an in frame deletion of ccpA), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP643 (in [[pGP380]], for SPINE, expression in Bacillus subtilis)
+
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''Antibody:''' available in [[Hillen]] and [[Stülke]] labs
+
* '''two-hybrid system:'''
 +
 
 +
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
+
[[Wade Winkler]], University of Texas, USA, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage]
−
 
 
−
[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]
 
−
 
 
−
[[Milton H. Saier]], University of California at San Diego, USA [http://biology.ucsd.edu/faculty/saier.html Homepage]
 
−
 
 
−
[[Yasutaro Fujita]], University of Fukuyama, Japan
 
−
 
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 18279655 </pubmed>
  
−
'''Reviews'''
+
==The ''glmS'' Ribozyme==
−
 
+
<pubmed>18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 </pubmed>
−
# Henkin, T. M. (1996) The role of the CcpA transcriptional regulator in carbon metabolism in Bacillus subtilis. FEMS Microbiol Lett 135: 9-15. [http://www.ncbi.nlm.nih.gov/sites/entrez/8598282 PubMed]
 
−
# Warner, J. B. & Lolkema, J. S. CcpA-dependent carbon catabolite repression in bacteria. Microbiol. Mol. Biol. Rev. 67, 475-490 (2003). [http://www.ncbi.nlm.nih.gov/sites/entrez/14665673 PubMed]
 
−
 
 
−
'''General and physiological studies'''
 
−
 
 
−
# Henkin, T. M., Grundy, F. J., Nicholson, W. L. and Chambliss, G. H. (1991) Catabolite repression of -amylase gene expression in Bacillus subtilis involves a trans-acting gene product homologous to the Escherichia coli lacI and galR repressors. Mol. Microbiol. 5, 575-584. [http://www.ncbi.nlm.nih.gov/sites/entrez/1904524 PubMed]
 
−
# Faires, N., Tobisch, S., Bachem, S., Martin-Verstraete, I., Hecker, M., & Stülke, J. (1999) The catabolite control protein CcpA controls ammonium assimilation in Bacillus subtilis. J. Mol. Microbiol. Biotechnol. 1: 141-148. [http://www.ncbi.nlm.nih.gov/sites/entrez/10941796 PubMed]
 
−
# Ludwig, H., Rebhan, N., Blencke, H.-M., Merzbacher, M. & Stülke, J. (2002) Control of the glycolytic gapA operon by the catabolite control protein A in Bacillus subtilis: a novel mechanism of CcpA-mediated regulation. Mol. Microbiol. 45: 543-553. [http://www.ncbi.nlm.nih.gov/sites/entrez/12123463 PubMed]
 
−
# Miwa, Y., M. Saikawa, and Y. Fujita. 1994. Possible function and some properties of the CcpA protein of Bacillus subtilis. Microbiology 140:2567-2575. [http://www.ncbi.nlm.nih.gov/sites/entrez/8000527 PubMed]
 
−
# Singh, K. D., Schmalisch, M. H., Stülke, J. & Görke, B. (2008) Carbon catabolite repression in Bacillus subtilis: A quantitative analysis of repression exerted by different carbon sources. J. Bacteriol. 190: 7275-7284. [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]
 
−
# Terahara et al. (2006) An intergenic stem-loop mutation in the Bacillus subtilis ccpA-motPS operon increases motPS transcription and the MotPS contribution to motility ''J Bacteriol.'' '''188:''' 2701-2705. [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]
 
−
# Wacker, I., Ludwig, H., Reif, I., Blencke, H.-M., Detsch, C. & Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in Bacillus subtilis: regulation of the gltAB operon by the catabolite control protein CcpA. Microbiology 149:  3001-3009. [http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]
 
−
 
 
−
'''Global analyses (proteome, transcriptome)'''
 
−
 
 
−
# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
 
−
# Moreno MS, Schneider BL, Maile RR, Weyler W, Saier Jr MH: Catabolite repression mediated by CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analysis. Mol Microbiol 2001, 39:1366-1381. [http://www.ncbi.nlm.nih.gov/sites/entrez/11251851 PubMed]
 
−
# Tobisch, S., Zühlke, D., Bernhardt, J., Stülke, J. & Hecker, M. (1999) Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis. J. Bacteriol. 181: 6996-7004. [http://www.ncbi.nlm.nih.gov/sites/entrez/10559165 PubMed]
 
−
# Yoshida, K.-I., Kobayashi, K., Miwa, Y., Kang, C.-M., Matsunaga, M., Yamaguchi, H., Tojo, S., Yamamoto, M., Nishi, R., Ogasawara, N., Nakayama, T. & Fujita, Y. (2001). Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucl Acids Res 29, 6683-6692. [http://www.ncbi.nlm.nih.gov/sites/entrez/11160890 PubMed]
 
−
 
 
−
'''Repression of target genes by CcpA'''
 
−
 
 
−
# Belitsky BR, Sonenshein, AL: CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression. J Bacteriol 2004, 186:3392-3398. [http://www.ncbi.nlm.nih.gov/sites/entrez/15150224 PubMed]
 
−
# Choi SK, Saier MH Jr: 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 2005, 187:6856-6861. [http://www.ncbi.nlm.nih.gov/sites/entrez/16166551 PubMed]
 
−
# Darbon, E., Servant, P., Poncet, S., and Deutscher, J. (2002). Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P~GlpK dephosphorylation control Bacillus subtilis glpFK expression. Mol. Microbiol. 43, 1039-1052. [http://www.ncbi.nlm.nih.gov/sites/entrez/11929549 PubMed]
 
−
# Grundy, F. J., Turinski, A. J., and Henkin, T. M. (1994). Catabolite regulation of Bacillus subtilis acetate and acetoin utilization genes by CcpA. J. Bacteriol. 176, 4527-4533. [http://www.ncbi.nlm.nih.gov/sites/entrez/7913927 PubMed]
 
−
# Inacio, J. M. & de Sá-Nogueira, I. trans-Acting factors and cis-elements involved in glucose repression of arabinan degradation in Bacillus subtilis. J. Bacteriol. 189, 8371-8376 (2007). [http://www.ncbi.nlm.nih.gov/sites/entrez/17827291 PubMed]
 
−
# Kim HJ, Jourlin-Castelli C, Kim SI, Sonenshein AL (2002) Regulation of the Bacillus subtilis ccpC gene by CcpA and CcpC. Mol Microbiol 43:399-410 [http://www.ncbi.nlm.nih.gov/sites/entrez/11985717 PubMed]
 
−
# Kim HJ, Roux A, Sonenshein AL (2002) Direct and indirect roles of CcpA in regulation of Bacillus subtilis Krebs cycle genes. Mol Microbiol 45:179-190 [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
 
−
# Martin-Verstraete, I., Stülke, J., Klier, A. & Rapoport, G. (1995) Two different mechanisms mediate catabolite repression of the Bacillus subtilis levanase operon. J. Bacteriol. 177: 6919-6927. [http://www.ncbi.nlm.nih.gov/sites/entrez/7592486 PubMed]
 
−
 
 
−
'''Positive regulation of gene expression by CcpA'''
 
−
 
 
−
# Grundy FJ, Waters DA, Allen SH, Henkin TM (1993) Regulation of the Bacillus subtilis acetate kinase gene by CcpA. J Bacteriol 175:7348-7355 [http://www.ncbi.nlm.nih.gov/sites/entrez/8226682 PubMed]
 
−
# Ludwig, H., Meinken, C., Matin, A. & Stülke, J. (2002) Insufficient expression of the ilv-leu operon encoding enzymes of branched-chain amino acids biosynthesis limits growth of a Bacillus subtilis ccpA mutant. J. Bacteriol. 184: 5174-5178. [http://www.ncbi.nlm.nih.gov/sites/entrez/12193635 PubMed]
 
−
# Presecan-Siedel, E., Galinier, A., Longin, R., Deutscher, J., Danchin, A., Glaser, P. and Martin-Verstraete, I. (1999) The catabolite regulation of the pta gene as part of carbon flow pathways in Bacillus subtilis. J. Bacteriol. 181, 6889-6897. [http://www.ncbi.nlm.nih.gov/sites/entrez/10559153 PubMed]
 
−
# Shivers, R. P., and Sonenshein, A. L. (2005) Bacillus subtilis ilvB operon: an intersection of global regulons. Mol Microbiol 56: 1549-1559. [http://www.ncbi.nlm.nih.gov/sites/entrez/15916605 PubMed]
 
−
# Turinsky, A. J., Grundy, F. J., Kim, J. H., Chambliss, G. H., and Henkin, T. M. 1998. Transcriptional activation of the Bacillus subtilis ackA gene requires sequences upstream of the promoter. J. Bacteriol. 180: 5961-5967. [http://www.ncbi.nlm.nih.gov/sites/entrez/9811655 PubMed]
 
−
# Turinsky, A. J., Moir-Blais, T. R., Grundy, F. J., and Henkin, T. M. 2000. Bacillus subtilis ccpA gene mutants specifically defective in activation of acetoin synthesis. J. Bacteriol. 182:5611-5614. [http://www.ncbi.nlm.nih.gov/sites/entrez/10986270 PubMed]
 
−
 
 
−
'''Control of CcpA activity'''
 
−
 
 
−
# Deutscher, J., Küster, E., Bergstedt, U., Charrier, V., and Hillen, W. 1995. Protein kinase-dependent HPr/CcpA interaction links glycolytic activity to carbon catabolite repression in Gram-positive bacteria. Mol. Microbiol. 15: 1049-1053. [http://www.ncbi.nlm.nih.gov/sites/entrez/7623661 PubMed]
 
−
# Galinier A, Deutscher J, Martin-Verstraete I: Phosphorylation of either Crh or HPr mediates binding of CcpA to the Bacillus subtilis xyn cre and catabolite repression of the xyn operon. J Mol Biol 1999, 286:307-314. [http://www.ncbi.nlm.nih.gov/sites/entrez/9973552 PubMed]
 
−
# Jones, B. E., Dossonnet, V., Küster, E., Hillen, W., Deutscher, J. & Klevit, R. E. (1997). Binding of the catabolite repressor protein CcpA to its DNA target is regulated by phosphorylation of its corepressor HPr. J Biol Chem 272, 26530-26535. [http://www.ncbi.nlm.nih.gov/sites/entrez/9334231 PubMed]
 
−
 
 
−
'''CcpA-DNA interaction'''
 
−
 
 
−
# Fujita, Y., Miwa, Y., Galinier, A. and Deutscher, J. (1995) Specific recognition of the Bacillus subtilis gnt cis-acting catabolite-responsive element by a protein complex formed between CcpA and seryl-phosphorylated HPr. Mol. Microbiol. 17, 953-960. [http://www.ncbi.nlm.nih.gov/sites/entrez/8596444 PubMed]
 
−
# Miwa, Y., Nakata, A., Ogiwara, A., Yamamota, M., and Fujita, Y. 2000. Evaluation and characterization of catabolite-responsive elements (cre) of Bacillus subtilis. Nucl. Acids Res. 28: 1206-1210. [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]
 
−
# Seidel G, Diel M, Fuchsbauer N, Hillen W: Quantitative interdependence of coeffectors, CcpA and cre in carbon catabolite regulation of Bacillus subtilis. FEBS J 2005, 272:2566-2577. [http://www.ncbi.nlm.nih.gov/sites/entrez/15885105 PubMed]
 
−
 
 
−
'''Functional analysis of CcpA'''
 
−
 
 
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# Küster, E., Hilbich, T., Dahl, M. and Hillen, W. (1999) Mutations in catabolite control protein CcpA separating growth effects from catabolite repression. J. Bacteriol. 181, 4125-4128. [http://www.ncbi.nlm.nih.gov/sites/entrez/10383986 PubMed]
 
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# Küster-Schöck, E., Wagner, A., Völker, U., and Hillen, W. (1999) Mutations in catabolite control protein CcpA showing glucose-independent regulation in Bacillus megaterium. J Bacteriol 181: 7634-7638. [http://www.ncbi.nlm.nih.gov/sites/entrez/10601226 PubMed]
 
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# Ludwig, H. & Stülke, J. (2001) The Bacillus subtilis catabolite control protein CcpA exerts all its regulatory functions by DNA binding. FEMS Microbiol. Lett. 203: 125-129. [http://www.ncbi.nlm.nih.gov/sites/entrez/11557150 PubMed]
 
−
 
 
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'''Structural analyses'''
 
  
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# Schumacher, M. A. et al. Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P. Cell 118, 731-741 (2004). [http://www.ncbi.nlm.nih.gov/sites/entrez/15369672 PubMed]
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==Other Original Publications==
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# Schumacher, M. A., Seidel, G., Hillen, W. & Brennan, R. G. Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation. J. Biol. Chem. 281, 6793-6800 (2006). [http://www.ncbi.nlm.nih.gov/sites/entrez/16316990 PubMed]
+
'''Additional publications:''' {{PubMed|22211522}}
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# Schumacher, M. A., Seidel, G., Hillen, W. & Brennan, R. G. Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors glucose 6-phosphate and fructose 1,6-bisphosphate. J. Mol. Biol. 368, 1042-1050 (2007). [http://www.ncbi.nlm.nih.gov/sites/entrez/17376479 PubMed]
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<pubmed> 14343123 17981983 ,11160890, 18295797 20525796  </pubmed>
 +
[[Category:Protein-coding genes]]

Latest revision as of 13:22, 29 July 2014

  • Description: glutamine-fructose-6-phosphate transaminase

Gene name glaube ich oder nicht glmS
Synonyms gcaA, ybxD
Essential yes PubMed
Product glutamine-fructose-6-phosphate transaminase
Function cell wall synthesis
Metabolic function and regulation of this protein in SubtiPathways:
sandbox
MW, pI 65 kDa, 4.796
Gene length, protein length 1800 bp, 600 aa
Immediate neighbours glmM, ybbU
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
File:Quintos.gif
This image was kindly provided by SubtiList
Genetic context
Test.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
GlmS expression.png
























Categories containing this gene/protein

cell wall synthesis, biosynthesis of cell wall components, essential genes

This gene is a member of the following regulons

glmS ribozyme

The gene

Basic information

  • Locus tag: BSU01780

Phenotypes of a mutant

essential PubMed

Database entries

  • BsubCyc: [HELLO BSU00100]
  • BsubCyc: "
  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot)
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • BsubCyc: [HELLO BSU00100]
  • BsubCyc: BSU00240
  • Structure:
    • HIV2 (from Bacillus subtilis, 100% identity) PubMed
    • 2VF4 (GlmS from E. coli, 39% identity, 58% similarity) PubMed
    • the ribozyme: 3G8S, 3G9C, 3G8T, 3G95, 3G96 (all for the ribozyme from Bacillus anthracis), 2HO7 (the ribozyme from Thermonanaerobacter tengcongensis)
  • KEGG entry: [2]

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation:
    • repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine PubMed
    • glmS is only expressed in the absence of glucosamine 6-phosphate (glmS ribozyme)
  • Regulatory mechanism: glmS ribozyme: glucosamine 6-phosphate binds the leader mRNA, and a riboswitch with ribozyme activity cleaves off the glmS section from the mRNA, resulting in stopp of transcript elongation
  • Additional information:
    • subject to Clp-dependent proteolysis upon glucose starvation PubMed
    • A ncRNA is predicted between glmM and glmS PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 2000 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 4000 PubMed

Biological materials

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

Labs working on this gene/protein

Wade Winkler, University of Texas, USA, Homepage

Your additional remarks

References

Reviews


The glmS Ribozyme

Krista M Brooks, Ken J Hampel
Rapid steps in the glmS ribozyme catalytic pathway: cation and ligand requirements.
Biochemistry: 2011, 50(13);2424-33
[PubMed:21395279] [WorldCat.org] [DOI] (I p)

Peter Y Watson, Martha J Fedor
The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo.
Nat Struct Mol Biol: 2011, 18(3);359-63
[PubMed:21317896] [WorldCat.org] [DOI] (I p)

Jesse C Cochrane, Sarah V Lipchock, Kathryn D Smith, Scott A Strobel
Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme.
Biochemistry: 2009, 48(15);3239-46
[PubMed:19228039] [WorldCat.org] [DOI] (I p)

Jennifer A Collins, Irnov Irnov, Stephanie Baker, Wade C Winkler
Mechanism of mRNA destabilization by the glmS ribozyme.
Genes Dev: 2007, 21(24);3356-68
[PubMed:18079181] [WorldCat.org] [DOI] (P p)

Rebecca A Tinsley, Jennifer R W Furchak, Nils G Walter
Trans-acting glmS catalytic riboswitch: locked and loaded.
RNA: 2007, 13(4);468-77
[PubMed:17283212] [WorldCat.org] [DOI] (P p)

Kenneth Blount, Izabela Puskarz, Robert Penchovsky, Ronald Breaker
Development and application of a high-throughput assay for glmS riboswitch activators.
RNA Biol: 2006, 3(2);77-81
[PubMed:17114942] [WorldCat.org] [DOI] (I p)

Daniel J Klein, Adrian R Ferré-D'Amaré
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.
Science: 2006, 313(5794);1752-6
[PubMed:16990543] [WorldCat.org] [DOI] (I p)

Ken J Hampel, Melissa M Tinsley
Evidence for preorganization of the glmS ribozyme ligand binding pocket.
Biochemistry: 2006, 45(25);7861-71
[PubMed:16784238] [WorldCat.org] [DOI] (P p)

Adam Roth, Ali Nahvi, Mark Lee, Inbal Jona, Ronald R Breaker
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.
RNA: 2006, 12(4);607-19
[PubMed:16484375] [WorldCat.org] [DOI] (P p)

Tom J McCarthy, Melissa A Plog, Shennen A Floy, Joshua A Jansen, Juliane K Soukup, Garrett A Soukup
Ligand requirements for glmS ribozyme self-cleavage.
Chem Biol: 2005, 12(11);1221-6
[PubMed:16298301] [WorldCat.org] [DOI] (P p)

Jeffrey E Barrick, Keith A Corbino, Wade C Winkler, Ali Nahvi, Maumita Mandal, Jennifer Collins, Mark Lee, Adam Roth, Narasimhan Sudarsan, Inbal Jona, J Kenneth Wickiser, Ronald R Breaker
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.
Proc Natl Acad Sci U S A: 2004, 101(17);6421-6
[PubMed:15096624] [WorldCat.org] [DOI] (P p)

Wade C Winkler, Ali Nahvi, Adam Roth, Jennifer A Collins, Ronald R Breaker
Control of gene expression by a natural metabolite-responsive ribozyme.
Nature: 2004, 428(6980);281-6
[PubMed:15029187] [WorldCat.org] [DOI] (I p)


Other Original Publications

Additional publications: PubMed

Irnov Irnov, Cynthia M Sharma, Jörg Vogel, Wade C Winkler
Identification of regulatory RNAs in Bacillus subtilis.
Nucleic Acids Res: 2010, 38(19);6637-51
[PubMed:20525796] [WorldCat.org] [DOI] (I p)

Stéphane Mouilleron, Marie-Ange Badet-Denisot, Béatrice Golinelli-Pimpaneau
Ordering of C-terminal loop and glutaminase domains of glucosamine-6-phosphate synthase promotes sugar ring opening and formation of the ammonia channel.
J Mol Biol: 2008, 377(4);1174-85
[PubMed:18295797] [WorldCat.org] [DOI] (I p)

Ulf Gerth, Holger Kock, Ilja Kusters, Stephan Michalik, Robert L Switzer, Michael Hecker
Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis.
J Bacteriol: 2008, 190(1);321-31
[PubMed:17981983] [WorldCat.org] [DOI] (I p)

K Yoshida, K Kobayashi, Y Miwa, C M Kang, M Matsunaga, H Yamaguchi, S Tojo, M Yamamoto, R Nishi, N Ogasawara, T Nakayama, Y Fujita
Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis.
Nucleic Acids Res: 2001, 29(3);683-92
[PubMed:11160890] [WorldCat.org] [DOI] (I p)

C J BATES, C A PASTERNAK
FURTHER STUDIES ON THE REGULATION OF AMINO SUGAR METABOLISM IN BACILLUS SUBTILIS.
Biochem J: 1965, 96(1);147-54
[PubMed:14343123] [WorldCat.org] [DOI] (P p)

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