Difference between revisions of "Sandbox"

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* '''Description:''' deoxyguanosine kinase <br/><br/>
+
* '''Description:''' general stress protein, survival of ethanol  stress, [[SafA]]-dependent protein of the inner spore coat, spore cortex lytic protein <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'''
−
|''dgk''
+
|''yaaH''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaG ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' sleL''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || deoxyguanosine kinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || N-acetylglucosaminidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || purine salvage and interconversion
+
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of ethanol  stress, protection of the spore
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00150 dgk]
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00160 yaaH]
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/purines_salvage_pathways.html Purine salvage], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.618 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 5.783 
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1281 bp, 427 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 621 bp, 207 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dgk]]'', ''[[yaaI]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dck]]'', ''[[yaaH]]''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00160 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00160 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00160 DNA_with_flanks]
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00150 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00150 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00150 DNA_with_flanks]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaH_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dgk_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>
 
|-
 
|-
−
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dgk_23146_23769_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:dgk_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00150]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaH_23868_25151_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaH_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00160]]
 
|-
 
|-
 
|}
 
|}
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<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
 
<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 =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}}
+
{{SubtiWiki category|[[sporulation proteins]]}},
 +
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
 
+
{{SubtiWiki regulon|[[SigB regulon]]}},
 +
{{SubtiWiki regulon|[[SigE regulon]]}},
 +
{{SubtiWiki regulon|[[SpoIIID regulon]]}}
  
 
=The gene=
 
=The gene=
Line 53: Line 50:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00150
+
* '''Locus tag:''' BSU00160
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dgk-dck.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaH.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10079]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10080]
  
 
=== Additional information===
 
=== Additional information===
−
 
−
 
  
  
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* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''[[Localization]]:'''
+
* '''[[Localization]]:'''  
 +
** inner spore coat, localization depends on [[SafA]] {{PubMed|19933362,22171814}}
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37530 P37530]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37531 P37531]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00150]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00160]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
 +
 +
required for survival of ethanol stress [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[dgk]]-[[dck]]''
+
* '''Operon:''' ''yaaH'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed]
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dgk_23146_23769_-1 dgk] {{PubMed|22383849}}
+
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaH_23868_25151_-1 yaaH] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigE]] {{PubMed|15699190,10419957}}, [[SigB]] {{PubMed|15805528}}
  
−
* '''Regulation:'''  
+
* '''Regulation:'''
 +
** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 +
** expressed during sporulation in the mother cell ([[SigE]], [[SpoIIID]]) {{PubMed|15383836,10419957}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[SpoIIID]]: transcription repression {{PubMed|15383836}}
  
−
* '''Additional information:'''
+
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
−
<pubmed>11078735 </pubmed>
+
 
 +
<pubmed>19087206,12884008,10419957,15805528 11964120, 19933362 22171814 15383836 22343356 18835992 </pubmed>
 +
 
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:54, 11 November 2013

  • Description: general stress protein, survival of ethanol stress, SafA-dependent protein of the inner spore coat, spore cortex lytic protein

Gene name yaaH
Synonyms sleL
Essential no
Product N-acetylglucosaminidase
Function survival of ethanol stress, protection of the spore
Gene expression levels in SubtiExpress: yaaH
MW, pI 48 kDa, 5.618
Gene length, protein length 1281 bp, 427 aa
Immediate neighbours dgk, yaaI
Sequences Protein DNA DNA_with_flanks
Genetic context
YaaH context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YaaH expression.png















Categories containing this gene/protein

sporulation proteins, general stress proteins (controlled by SigB)

This gene is a member of the following regulons

SigB regulon, SigE regulon, SpoIIID regulon

The gene

Basic information

  • Locus tag: BSU00160

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:

Database entries

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

Additional information

required for survival of ethanol stress PubMed

Expression and regulation

  • Additional information: the mRNA is very stable (half-life > 15 min) PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Emily A Lambert, Nora Sherry, David L Popham
In vitro and in vivo analyses of the Bacillus anthracis spore cortex lytic protein SleL.
Microbiology (Reading): 2012, 158(Pt 5);1359-1368
[PubMed:22343356] [WorldCat.org] [DOI] (I p)

Peter T McKenney, Patrick Eichenberger
Dynamics of spore coat morphogenesis in Bacillus subtilis.
Mol Microbiol: 2012, 83(2);245-60
[PubMed:22171814] [WorldCat.org] [DOI] (I p)

Daisuke Imamura, Ritsuko Kuwana, Hiromu Takamatsu, Kazuhito Watabe
Localization of proteins to different layers and regions of Bacillus subtilis spore coats.
J Bacteriol: 2010, 192(2);518-24
[PubMed:19933362] [WorldCat.org] [DOI] (I p)

Takashi Inaoka, Takenori Satomura, Yasutaro Fujita, Kozo Ochi
Novel gene regulation mediated by overproduction of secondary metabolite neotrehalosadiamine in Bacillus subtilis.
FEMS Microbiol Lett: 2009, 291(2);151-6
[PubMed:19087206] [WorldCat.org] [DOI] (I p)

Emily A Lambert, David L Popham
The Bacillus anthracis SleL (YaaH) protein is an N-acetylglucosaminidase involved in spore cortex depolymerization.
J Bacteriol: 2008, 190(23);7601-7
[PubMed:18835992] [WorldCat.org] [DOI] (I p)

Dirk Höper, Uwe Völker, Michael Hecker
Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of Bacillus subtilis.
J Bacteriol: 2005, 187(8);2810-26
[PubMed:15805528] [WorldCat.org] [DOI] (P p)

Patrick Eichenberger, Masaya Fujita, Shane T Jensen, Erin M Conlon, David Z Rudner, Stephanie T Wang, Caitlin Ferguson, Koki Haga, Tsutomu Sato, Jun S Liu, Richard Losick
The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis.
PLoS Biol: 2004, 2(10);e328
[PubMed:15383836] [WorldCat.org] [DOI] (I p)

G Hambraeus, C von Wachenfeldt, L Hederstedt
Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs.
Mol Genet Genomics: 2003, 269(5);706-14
[PubMed:12884008] [WorldCat.org] [DOI] (P p)

A Aronson
Sporulation and delta-endotoxin synthesis by Bacillus thuringiensis.
Cell Mol Life Sci: 2002, 59(3);417-25
[PubMed:11964120] [WorldCat.org] [DOI] (P p)

T Kodama, H Takamatsu, K Asai, K Kobayashi, N Ogasawara, K Watabe
The Bacillus subtilis yaaH gene is transcribed by SigE RNA polymerase during sporulation, and its product is involved in germination of spores.
J Bacteriol: 1999, 181(15);4584-91
[PubMed:10419957] [WorldCat.org] [DOI] (P p)

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