Difference between revisions of "Sandbox"

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==Mycoplasmas as minimal organisms==
+
* '''Description:''' glutamine-fructose-6-phosphate transaminase <br/><br/>
−
<pubmed> 17183222 19965468 20097688 </pubmed>
 
  
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==Identification of a minimal gene set==
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{| align="right" border="1" cellpadding="2"
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<pubmed>19943949 </pubmed>
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|-
 +
|style="background:#ABCDEF;" align="center"|'''Gene name''' glaube ich oder nicht
 +
|''glmS''
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gcaA, ybxD ''
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamine-fructose-6-phosphate transaminase
 +
|-
 +
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
 +
|-
 +
|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]'''
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796 
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 aa
 +
|-
 +
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glmM]]'', ''[[ybbU]]''
 +
|-
 +
|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]]
 +
|-
 +
|}
  
−
==Steps on the way to an artificial organism==
+
__TOC__
−
<pubmed> 19696314 17600181 18218864 20488990 </pubmed>
+
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
  
−
==Metabolism==
 
−
<pubmed>19762644 19193632 19266023 16924101 9334244 19561621  20933603 </pubmed>
 
  
−
==Systematics==
+
<br/><br/>
−
<pubmed>19693078 19656368 17370266 16138096 </pubmed>
 
  
−
==Mareike Kunze==
+
= [[Categories]] containing this gene/protein =
−
<pubmed>20515935 19965476  </pubmed>
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{{SubtiWiki category|[[cell wall synthesis]]}},
−
Außerdem das MPN420-Paper
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{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
 +
{{SubtiWiki category|[[essential genes]]}}
  
−
==Felix Mehne==
+
= This gene is a member of the following [[regulons]] =
−
<pubmed> 19917605 15369672 </pubmed>
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{{SubtiWiki regulon|[[glmS ribozyme]]}}
−
außerdem das NAR-Paper
 
  
−
==Jan Latz==
+
=The gene=
−
<pubmed> 18757537 17142398 18628769 </pubmed>
 
  
−
==Marcus Richter==
+
=== Basic information ===
−
<pubmed> 19054118 20351052 </pubmed>
 
−
Außerdem das YmdB-Paper
 
  
−
==Sebastian Sieglin==
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* '''Locus tag:''' BSU01780
−
<pubmed> 15231785 20933603 17122393 </pubmed>
 
  
−
==Dominik Tödter {{PubMed|20572937,20709848,14991003 }}==
+
===Phenotypes of a mutant ===
 +
 
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 +
 
 +
=== Database entries ===
 +
* '''BsubCyc:''' [HELLO BSU00100]
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T"]
 +
 
 +
* '''DBTBS entry:''' no entry
 +
 
 +
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10948]
 +
 
 +
=== 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:'''
 +
 
 +
* '''[[SubtInteract|Interactions]]:'''
 +
 
 +
* '''[[Localization]]:'''
 +
** cytoplasm (according to Swiss-Prot)
 +
 
 +
=== 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'')
 +
 
 +
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39754 P39754]
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01780]
 +
 
 +
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.6.1.16 2.6.1.16]
 +
 
 +
=== 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=
 +
 
 +
* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 glmS] {{PubMed|22383849}}
 +
 
 +
* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}
 +
 
 +
* '''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 =
 +
 
 +
* '''Mutant:'''
 +
 
 +
* '''Expression vector:'''
 +
       
 +
* '''lacZ fusion:'''
 +
 
 +
* '''GFP fusion:'''
 +
 
 +
* '''two-hybrid system:'''
 +
 
 +
* '''Antibody:'''
 +
 
 +
=Labs working on this gene/protein=
 +
 
 +
[[Wade Winkler]], University of Texas, USA, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage]
 +
 
 +
=Your additional remarks=
 +
 
 +
=References=
 +
==Reviews==
 +
<pubmed> 18279655 </pubmed>
 +
 
 +
==The ''glmS'' Ribozyme==
 +
<pubmed>18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 </pubmed>
 +
 
 +
==Other Original Publications==
 +
'''Additional publications:''' {{PubMed|22211522}}
 +
<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


Other Original Publications

Additional publications: PubMed

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