Difference between revisions of "Sandbox"

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−
* '''Description:''' similar to deacetylase <br/><br/>
+
* '''Description:''' polynucleotide phosphorylase <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'''
−
|''ylxY''
+
|''pnpA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymxI ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''comR ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || polynucleotide phosphorylase (PNPase) (EC 2.7.7.8)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || necessary for competence development
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 9.364  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 77 kDa, 4.89  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2115 bp, 705 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pnpA]]'', ''[[mlpA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpsO]]'', ''[[ylxY]]''
 
|-
 
|-
 
|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:ylxY_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pnpA_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 43: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11492]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11491]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 70: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PnpA]]-[[RnjA]], [[PnpA]]-[[PfkA]], [[PnpA]]-[[Rny]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 76: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3CDI 3CDI] (protein from ''E. coli'')
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16700]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16690]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
 +
 +
required for the expression of late competence genes [[comG]] and [[comK]], requirement bypassed by a [[mecA]] disruption; may be necessary for modification of the [[srfA]] transcript (stabilization or translation activation)
  
 
=Expression and regulation=
 
=Expression and regulation=
Line 92: Line 94:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' [[RelA]] dependent downregulation (Class I) during stringent response [http://www.ncbi.nlm.nih.gov/sites/entrez/11948165 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 108: Line 110:
 
* '''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=
 +
 +
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 122:
 
=References=
 
=References=
  
 +
# Bechhofer, D. H. & Wang, W. (1998). Decay of ''ermC'' mRNA in a polynucleotide phosphorylase mutant of ''Bacillus subtilis''. J Bacteriol 180:5968-5977. [http://www.ncbi.nlm.nih.gov/sites/entrez/9811656 PubMed]
 +
# Campos-Guillen, J., Bralley, P., Jones, G. H., Bechhofer, D. H. & Olmedo-Alvarez, G. (2005). Addition of poly(A) and heteropolymeric 3´ ends in ''Bacillus subtilis'' wild-type and polynucleotide phosphorylase-deficient strains. J Bacteriol 187:4698-4706.  [http://www.ncbi.nlm.nih.gov/sites/entrez/15995184 PubMed]
 +
# Deutscher, M. P. & Reuven, N. B. (1991). Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in ''Escherichia coli'' and Bacillus subtilis. Proc Natl Acad Sci U S A 88:3277-3280. [http://www.ncbi.nlm.nih.gov/sites/entrez/xxx PubMed]
 +
# Mitra, S., Hue, K. & Bechhofer, D. H. (1996). ''In vitro'' processing activity of ''Bacillus subtilis'' polynucleotide phosphorylase. Mol Microbiol 19:329-342. [http://www.ncbi.nlm.nih.gov/sites/entrez/8825778 PubMed]
 +
# Wang, W. & Bechhofer, D. H. (1996). Properties of a ''Bacillus subtilis'' polynucleotide phosphorylase deletion strain. J Bacteriol 178:2375-2382. [http://www.ncbi.nlm.nih.gov/sites/entrez/8636041 PubMed]
 +
# Oussenko, I. A., Abe, T., Ujiie, H., Muto, A. & Bechhofer, D. H. (2005). Participation of 3'-to-5' exoribonucleases in the turnover of ''Bacillus subtilis'' mRNA. J Bacteriol 187:2758-2767. [http://www.ncbi.nlm.nih.gov/sites/entrez/15805522 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 19:46, 15 April 2009

  • Description: polynucleotide phosphorylase

Gene name pnpA
Synonyms comR
Essential no
Product polynucleotide phosphorylase (PNPase) (EC 2.7.7.8)
Function necessary for competence development
MW, pI 77 kDa, 4.89
Gene length, protein length 2115 bp, 705 aa
Immediate neighbours rpsO, ylxY
Hier soll was neues rein
Genetic context
PnpA 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: 3'-5' exoribonuclease
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure: 3CDI (protein from E. coli)
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

required for the expression of late competence genes comG and comK, requirement bypassed by a mecA disruption; may be necessary for modification of the srfA transcript (stabilization or translation activation)

Expression and regulation

  • Operon:
  • Regulation: RelA dependent downregulation (Class I) during stringent response PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • 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

David Bechhofer, Mount Sinai School, New York, USA Homepage

Your additional remarks

References

  1. Bechhofer, D. H. & Wang, W. (1998). Decay of ermC mRNA in a polynucleotide phosphorylase mutant of Bacillus subtilis. J Bacteriol 180:5968-5977. PubMed
  2. Campos-Guillen, J., Bralley, P., Jones, G. H., Bechhofer, D. H. & Olmedo-Alvarez, G. (2005). Addition of poly(A) and heteropolymeric 3´ ends in Bacillus subtilis wild-type and polynucleotide phosphorylase-deficient strains. J Bacteriol 187:4698-4706. PubMed
  3. Deutscher, M. P. & Reuven, N. B. (1991). Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A 88:3277-3280. PubMed
  4. Mitra, S., Hue, K. & Bechhofer, D. H. (1996). In vitro processing activity of Bacillus subtilis polynucleotide phosphorylase. Mol Microbiol 19:329-342. PubMed
  5. Wang, W. & Bechhofer, D. H. (1996). Properties of a Bacillus subtilis polynucleotide phosphorylase deletion strain. J Bacteriol 178:2375-2382. PubMed
  6. Oussenko, I. A., Abe, T., Ujiie, H., Muto, A. & Bechhofer, D. H. (2005). Participation of 3'-to-5' exoribonucleases in the turnover of Bacillus subtilis mRNA. J Bacteriol 187:2758-2767. PubMed
  7. 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
  8. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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