Difference between revisions of "Sandbox"

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−
* '''Description:''' required for dehydratation of the spore core and assembly of the coat, mutation increases SigD-dependent gene expression, might act via SinR <br/><br/>
+
* '''Description:''' RNase Y, endoribonuclease, required for the processing of the ''[[gapA]]'' operon mRNA<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'''
−
|''spoVS''
+
|''rny''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymdA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNase Y
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || spore coat assembly, spore core dehydratation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || required for the processing <br/>of the ''[[gapA]]'' operon mRNA
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 6.475 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,7 kDa, 5.39
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 258 bp, 86 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1560 bp, 520 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ymdB]]'', ''[[tdh]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpX]]'', ''[[ymdB]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:spoVS_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:rny_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>
 
|-
 
|-
Line 29: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 1766580 - 1768139
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spoVS.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11245]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13420]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 52: Line 55:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' required for the processing of the ''[[gapA]]'' operon mRNA  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
  
−
* '''Protein family:'''
+
* '''Protein family:''' 2',3' cyclic nucleotide phosphodiesterase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 63: Line 66:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
 +
** transmembrane domain (4–24)
 +
** KH domain (210–273)
 +
** HD domain (336–429)
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' metal-dependent
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[Rny]]-[[PfkA]], [[Rny]]-[[Eno]], [[Rny]]-[[PnpA]], [[Rny]]-[[RnjA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' Single-pass membrane protein [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31774]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16980]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16960]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.4.16 3.1.4.16]
  
 
=== Additional information===
 
=== Additional information===
  
 +
required for the processing of the ''[[gapA]]'' operon mRNA
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[rny]]-[[ymdB]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' constitutive
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' essential!!!!, 4043 (''rny'' under p-spac control), GP193 (''rny'' under p-xyl control), available in [[Stülke]] lab
 +
 
 +
* '''Expression vector:'''
 +
 
 +
N-terminal Strep-tag, expression in ''E. coli'', in [[pGP172]]: pGP441, available in [[Stülke]] lab
  
−
* '''Expression vector:'''
+
N-terminal Strep-tag, for SPINE, expression in ''B. subtilis'', in [[pGP380]]: pGP775 , available in [[Stülke]] lab
−
       
 
−
* '''lacZ fusion:'''
 
  
−
* '''GFP fusion:'''
+
wild type ''rny'', expression in B. subtilis, in [[pBQ200]]: pGP1201, available in [[Stülke]] lab
  
−
* '''two-hybrid system:'''  
+
there is also a series of domain constructs present in [[pBQ200]], all available in [[Stülke]] lab
 +
 +
* '''lacZ fusion:''' pGP459 (in [[pAC7]]), available in [[Stülke]] lab
  
−
* '''Antibody:'''
+
* '''GFP fusion:''' B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in [[Errington]] lab
 +
 
 +
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
 +
 
 +
* '''Antibody:''' available in [[van Dijl]] and [[Stülke]] labs
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]
 +
 +
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 137:
 
=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
 +
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
 +
# Hunt, A., Rawlins, J. P., Thomaides, H. B., and Errington, J. (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895-2907. [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed]

Revision as of 19:45, 15 April 2009

  • Description: RNase Y, endoribonuclease, required for the processing of the gapA operon mRNA

Gene name rny
Synonyms ymdA
Essential yes
Product RNase Y
Function required for the processing
of the gapA operon mRNA
MW, pI 58,7 kDa, 5.39
Gene length, protein length 1560 bp, 520 amino acids
Immediate neighbours pbpX, ymdB
Hier soll was neues rein
Genetic context
Rny context.gif
This image was kindly provided by SubtiList






The gene

Basic information

  • Coordinates: 1766580 - 1768139

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: required for the processing of the gapA operon mRNA PubMed
  • Protein family: 2',3' cyclic nucleotide phosphodiesterase family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
    • transmembrane domain (4–24)
    • KH domain (210–273)
    • HD domain (336–429)
  • Modification:
  • Cofactor(s): metal-dependent
  • Effectors of protein activity:

Database entries

  • Structure:
  • Swiss prot entry: [2]
  • KEGG entry: [3]

Additional information

required for the processing of the gapA operon mRNA

Expression and regulation

  • Sigma factor:
  • Regulation: constitutive
  • Regulatory mechanism:
  • Additional information: there is a terminator between rny and ymdB, most transcripts terminate there

Biological materials

  • Mutant: essential!!!!, 4043 (rny under p-spac control), GP193 (rny under p-xyl control), available in Stülke lab
  • Expression vector:

N-terminal Strep-tag, expression in E. coli, in pGP172: pGP441, available in Stülke lab

N-terminal Strep-tag, for SPINE, expression in B. subtilis, in pGP380: pGP775 , available in Stülke lab

wild type rny, expression in B. subtilis, in pBQ200: pGP1201, available in Stülke lab

there is also a series of domain constructs present in pBQ200, all available in Stülke lab

  • lacZ fusion: pGP459 (in pAC7), available in Stülke lab
  • GFP fusion: B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in Errington lab
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab

Labs working on this gene/protein

Harald Putzer, IBPC Paris, France Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press PubMed
  3. Hunt, A., Rawlins, J. P., Thomaides, H. B., and Errington, J. (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895-2907. PubMed
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