Difference between revisions of "Sandbox"

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* '''Description:''' trigger enzyme: glutamate dehydrogenase (cryptic in 168 and derivatives)<br/><br/>
+
* '''Description:''' transcription activator of the ''[[gutB]]-[[gutP]]'' operon <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'''
−
|''gudB''
+
|''gutR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypcA ''
+
|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''' || glutamate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription activator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate utilization, control of [[GltC]] activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of glucitol utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 5.582  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 94 kDa, 6.113  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1278 bp, 426 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2487 bp, 829 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ypdA]]'', ''[[ypbH]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydjC]]'', ''[[gutB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14212&#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:CAB12433&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gudB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gutR_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU22960
+
* '''Locus tag:''' BSU06140
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
The gene is cryptic. If ''gudB'' is activated (''gudB1'' mutation), the bacteria are able to utilize glutamate as the only carbon source. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gudB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gutR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11435]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10178]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' L-glutamate + H<sub>2</sub>O + NAD<sup>+</sup> = 2-oxoglutarate + NH<sub>3</sub> + NADH (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family (according to Swiss-Prot)
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[RocG]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 80: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P50735 P50735]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39143 P39143]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU22960]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU06140]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2 1.4.1.2]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''gudB'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9829940 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9829940 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' constitutively expressed
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' GudB is 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]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP691 (cat), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
 
          
 
          
−
* '''lacZ fusion:''' pGP651 (in [[pAC5]]), available in [[Stülke]] lab
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
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* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' antibody against [[RocG]] recognizes GudB, available in [[Stülke]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
 
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
−
 
−
The GudB protein is active in other legacy ''B. subtilis'' strains (e.g. strain 122). Thus, it can be speculated that the ancestral ''gudB'' gene was not cryptic, but became so as a product of the "domestication" of ''B. subtilis'' 168 in the lab. [http://www.ncbi.nlm.nih.gov/pubmed/18723616 PubMed]
 
  
 
=References=
 
=References=
  
−
<pubmed>17183217 18723616, </pubmed>
+
<pubmed>8195087 8195086 11118449, </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/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9829940 PubMed]
+
# Ye R, Rehemtulla SN, Wong SL. (1994) Glucitol induction in Bacillus subtilis is mediated by a regulatory factor, GutR. ''J Bacteriol.'' '''Jun;176(11):''' 3321-7. [http://www.ncbi.nlm.nih.gov/sites/entrez/8195087 PubMed]
−
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
+
# Ye R, Wong SL. (1994) Transcriptional regulation of the Bacillus subtilis glucitol dehydrogenase gene. ''J Bacteriol.'' '''Jun;176(11):''' 3314-20. [http://www.ncbi.nlm.nih.gov/sites/entrez/8195086 PubMed]
−
# Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in Bacillus subtilis: Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]
+
# Poon KK, Chen CL, Wong SL. (2001) Roles of glucitol in the GutR-mediated transcription activation process in Bacillus subtilis: tight binding of GutR to tis binding site. ''J Biol Chem. '' '''Mar 30;276(13):''' 9620-5 [http://www.ncbi.nlm.nih.gov/sites/entrez/11118449 PubMed]
−
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
−
# Zeigler DR, Prágai Z, Rodriguez S, Chevreux B, Muffler A, Albert T, Bai R, Wyss M, Perkins JB (2008) The origins of 168, W23, and other ''Bacillus subtilis'' legacy strains. J Bacteriol 190(21):6983-95 [http://www.ncbi.nlm.nih.gov/pubmed/18723616 PubMed]
 
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 13:20, 8 June 2009

  • Description: transcription activator of the gutB-gutP operon

Gene name gutR
Synonyms
Essential no
Product transcription activator
Function regulation of glucitol utilization
MW, pI 94 kDa, 6.113
Gene length, protein length 2487 bp, 829 aa
Immediate neighbours ydjC, gutB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GutR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU06140

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

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

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

K K Poon, C L Chen, S L Wong
Roles of glucitol in the GutR-mediated transcription activation process in Bacillus subtilis: tight binding of GutR to tis binding site.
J Biol Chem: 2001, 276(13);9620-5
[PubMed:11118449] [WorldCat.org] [DOI] (P p)

R Ye, S N Rehemtulla, S L Wong
Glucitol induction in Bacillus subtilis is mediated by a regulatory factor, GutR.
J Bacteriol: 1994, 176(11);3321-7
[PubMed:8195087] [WorldCat.org] [DOI] (P p)

R Ye, S L Wong
Transcriptional regulation of the Bacillus subtilis glucitol dehydrogenase gene.
J Bacteriol: 1994, 176(11);3314-20
[PubMed:8195086] [WorldCat.org] [DOI] (P p)

  1. Ye R, Rehemtulla SN, Wong SL. (1994) Glucitol induction in Bacillus subtilis is mediated by a regulatory factor, GutR. J Bacteriol. Jun;176(11): 3321-7. PubMed
  2. Ye R, Wong SL. (1994) Transcriptional regulation of the Bacillus subtilis glucitol dehydrogenase gene. J Bacteriol. Jun;176(11): 3314-20. PubMed
  3. Poon KK, Chen CL, Wong SL. (2001) Roles of glucitol in the GutR-mediated transcription activation process in Bacillus subtilis: tight binding of GutR to tis binding site. J Biol Chem. Mar 30;276(13): 9620-5 PubMed
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