Difference between revisions of "Sandbox"

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−
* '''Description:''' signal peptide peptidase required for efficient processing of pre-proteins <br/><br/>
+
* '''Description:''' RNase J2<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'''
−
|''tepA''
+
|''rnjB ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymfB, ylxI ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymfA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || signal peptide peptidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNase J2
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein secretion
+
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA processing and degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 5.575  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 9.18  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 669 bp, 223 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1545 bp, 515 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rnjB]]'', ''[[spoIIIE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dapA]]'', ''[[tepA]]''
 
|-
 
|-
 
|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:tepA_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ymfA_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/>
  
 
=The gene=
 
=The gene=
Line 43: Line 45:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11055]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13422]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' endoribonuclease, involved in processing of ''[[thrS]]'' mRNA
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[RnjA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 70: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[RnjA]]-[[RnjB]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 76: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do;jsessionid=8B071C0C81B11ADEBA3DDC3FF3395811?structureId=3BK1 3BK1] (RNase J from ''Thermus thermophilus'') [http://www.pdb.org/pdb/explore/explore.do?structureId=3BK2 3BK2] (RNase J from ''Thermus thermophilus'', complex with UMP)
−
 
 
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16790]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16780]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 91:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 100: Line 101:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP1120 (spc), available in the [[Stülke]] lab
+
* '''Mutant:''' GP45, GP1113 (spc), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 108: Line 109:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=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]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 121:
 
=References=
 
=References=
  
 +
# Even, S., Pellegrini, O., Zig, L., Labas, V., Vinh, J., Brechemmier-Baey, D., and Putzer, H. (2005) Ribonucleases J1 and J2: Two novel endoribonucleases in B. subtilis with functional  homology to E. coli RNase E. Nucl Acids Res 33, 2141-2152. [http://www.ncbi.nlm.nih.gov/sites/entrez/15831787 PubMed]
 +
# de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. (2008 Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol. 15:206-212. [http://www.ncbi.nlm.nih.gov/sites/entrez/18204464 PubMed]
 +
# Mäder, U., Zig, L., Kretschmer, J., Homuth, G., and Putzer, H. (2008) mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol 70, 183-196. [http://www.ncbi.nlm.nih.gov/sites/entrez/18713320 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]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 15:23, 15 April 2009

  • Description: RNase J2

Gene name rnjB
Synonyms ymfA
Essential no
Product RNase J2
Function RNA processing and degradation
MW, pI 56 kDa, 9.18
Gene length, protein length 1545 bp, 515 aa
Immediate neighbours dapA, tepA
Hier soll was neues rein
Genetic context
YmfA context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: endoribonuclease, involved in processing of thrS mRNA
  • Protein family:
  • Paralogous protein(s): RnjA

Extended information on the protein

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

Database entries

  • Structure: 3BK1 (RNase J from Thermus thermophilus) 3BK2 (RNase J from Thermus thermophilus, complex with UMP)
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

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

Biological materials

  • Mutant: GP45, GP1113 (spc), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • Antibody:

Labs working on this gene/protein

Harald Putzer, IBPC Paris, France Homepage

Your additional remarks

References

  1. Even, S., Pellegrini, O., Zig, L., Labas, V., Vinh, J., Brechemmier-Baey, D., and Putzer, H. (2005) Ribonucleases J1 and J2: Two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucl Acids Res 33, 2141-2152. PubMed
  2. de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. (2008 Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol. 15:206-212. PubMed
  3. Mäder, U., Zig, L., Kretschmer, J., Homuth, G., and Putzer, H. (2008) mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol 70, 183-196. PubMed
  4. 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
  5. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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