Difference between revisions of "PnpA"

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= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
 
{{SubtiWiki category|[[genetic competence]]}},
 
{{SubtiWiki category|[[genetic competence]]}},
 +
{{SubtiWiki category|[[DNA repair/ recombination]]}},
 
{{SubtiWiki category|[[Rnases]]}}
 
{{SubtiWiki category|[[Rnases]]}}
  
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease, [[RNase]], PNPase degrades the trp mRNA from the RNA-TRAP complex
+
* '''Catalyzed reaction/ biological activity:'''  
 +
** 3'-5' exoribonuclease, [[RNase]]
 +
** PNPase degrades the trp mRNA from the RNA-TRAP complex
 +
** involved in double-strand break (DSB) repair via homologous recombination (HR) or non-homologous end-joining (NHEJ) {{PubMed|21859751}}
 +
** degrades ssDNA (3' --> 5') (stimulated by [[RecA]], inhibited by [[SsbA]])  {{PubMed|21859751}}
 +
** can polymerize ssDNA at a free 3' OH end, stimulated by [[RecN]] {{PubMed|21859751}}
  
 
* '''Protein family:'''
 
* '''Protein family:'''
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<pubmed>10087930 19215773 17514363 16733069 </pubmed>
 
<pubmed>10087930 19215773 17514363 16733069 </pubmed>
 
==Original publications==
 
==Original publications==
−
<pubmed>11948165,10572137 ,8825779,19433509, 9811656, 14976255,19433509, 15995184, 8825778, 8636041, 15805522, 19193632, 1707536  19633085 19638340 20360175 20418391 20572937 ,21803996</pubmed>
+
<pubmed>11948165,10572137 ,8825779,19433509, 9811656, 14976255,19433509, 15995184, 8825778, 8636041, 15805522, 19193632, 1707536  19633085 19638340 20360175 20418391 20572937 ,21803996 21859751</pubmed>
 
==PNPase in ''E. coli''==
 
==PNPase in ''E. coli''==
 
<pubmed>19327365, 21324911 18650428 </pubmed>
 
<pubmed>19327365, 21324911 18650428 </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 13:53, 24 August 2011

  • Description: polynucleotide phosphorylase, RNase

Gene name pnpA
Synonyms comR
Essential no
Product polynucleotide phosphorylase (PNPase) (EC 2.7.7.8)
Function necessary for competence development
Interactions involving this protein in SubtInteract: PnpA
MW, pI 77 kDa, 4.89
Gene length, protein length 2115 bp, 705 aa
Immediate neighbours rpsO, ylxY
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PnpA context.gif
This image was kindly provided by SubtiList



Categories containing this gene/protein

genetic competence, DNA repair/ recombination, Rnases

This gene is a member of the following regulons

stringent response

The gene

Basic information

  • Locus tag: BSU16690

Phenotypes of a mutant

  • The pnpA mutant is cold sensitive and sensitive to tetracyclin, it shows multiseptate filamentous growth. PubMed
  • The mutant is deficient in genetic competence (no expression of the late competence genes) PubMed
  • The mutant overexpresses the trp and putB-putC-putP operons.

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
    • 3'-5' exoribonuclease, RNase
    • PNPase degrades the trp mRNA from the RNA-TRAP complex
    • involved in double-strand break (DSB) repair via homologous recombination (HR) or non-homologous end-joining (NHEJ) PubMed
    • degrades ssDNA (3' --> 5') (stimulated by RecA, inhibited by SsbA) PubMed
    • can polymerize ssDNA at a free 3' OH end, stimulated by RecN PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure: 3CDI (protein from E. coli), 3GCM (protein from E. coli, PNPase/RNase E micro-domain/RNA tetragonal crystal form )
  • KEGG entry: [2]
  • E.C. number:

Additional information

required for the expression of late competence genes comGA and comK, requirement bypassed by a mecA disruption; may be necessary for modification of the srfAA 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: GP584 (aphA3), available in Stülke lab
  • Expression vector:
    • for expression, purification in E. coli with N-terminal His-tag, in pWH844: pGP838, available in Stülke lab
    • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1342, available in Stülke lab
    • for chromosomal expression of PnpA-Strep (cat): GP1002, available in Jörg Stülke's lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • FLAG-tag construct: GP1021 (spc, based on pGP1331), available in the Stülke lab
  • Antibody:

Labs working on this gene/protein

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

Your additional remarks

References

Reviews

José M Andrade, Vânia Pobre, Inês J Silva, Susana Domingues, Cecília M Arraiano
The role of 3'-5' exoribonucleases in RNA degradation.
Prog Mol Biol Transl Sci: 2009, 85;187-229
[PubMed:19215773] [WorldCat.org] [DOI] (P p)

Sue Lin-Chao, Ni-Ting Chiou, Gadi Schuster
The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines.
J Biomed Sci: 2007, 14(4);523-32
[PubMed:17514363] [WorldCat.org] [DOI] (P p)

Devanand Sarkar, Paul B Fisher
Polynucleotide phosphorylase: an evolutionary conserved gene with an expanding repertoire of functions.
Pharmacol Ther: 2006, 112(1);243-63
[PubMed:16733069] [WorldCat.org] [DOI] (P p)

A J Carpousis, N F Vanzo, L C Raynal
mRNA degradation. A tale of poly(A) and multiprotein machines.
Trends Genet: 1999, 15(1);24-8
[PubMed:10087930] [WorldCat.org] [DOI] (P p)

Original publications

Paula P Cardenas, Thomas Carzaniga, Sandro Zangrossi, Federica Briani, Esther Garcia-Tirado, Gianni Dehò, Juan C Alonso
Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins.
Nucleic Acids Res: 2011, 39(21);9250-61
[PubMed:21859751] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Joseph Newman, Fabian M Rothe, Alexandra S Solovyova, Cecilia Rodrigues, Christina Herzberg, Fabian M Commichau, Richard J Lewis, Jörg Stülke
RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli.
J Bacteriol: 2011, 193(19);5431-41
[PubMed:21803996] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Henrike Pförtner, Leonie Rempeters, Nico Pietack, Christina Herzberg, Jörg Stülke
The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex.
Mol Microbiol: 2010, 77(4);958-71
[PubMed:20572937] [WorldCat.org] [DOI] (I p)

Shiyi Yao, David H Bechhofer
Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y.
J Bacteriol: 2010, 192(13);3279-86
[PubMed:20418391] [WorldCat.org] [DOI] (I p)

Juan Campos-Guillén, Jackeline Lizzeta Arvizu-Gómez, George H Jones, Gabriela Olmedo-Alvarez
Characterization of tRNA(Cys) processing in a conditional Bacillus subtilis CCase mutant reveals the participation of RNase R in its quality control.
Microbiology (Reading): 2010, 156(Pt 7);2102-2111
[PubMed:20360175] [WorldCat.org] [DOI] (I p)

Gintaras Deikus, David H Bechhofer
Bacillus subtilis trp Leader RNA: RNase J1 endonuclease cleavage specificity and PNPase processing.
J Biol Chem: 2009, 284(39);26394-401
[PubMed:19638340] [WorldCat.org] [DOI] (I p)

Shiyi Yao, David H Bechhofer
Processing and stability of inducibly expressed rpsO mRNA derivatives in Bacillus subtilis.
J Bacteriol: 2009, 191(18);5680-9
[PubMed:19633085] [WorldCat.org] [DOI] (I p)

Paula P Cardenas, Begoña Carrasco, Humberto Sanchez, Gintaras Deikus, David H Bechhofer, Juan C Alonso
Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair.
Nucleic Acids Res: 2009, 37(12);4157-69
[PubMed:19433509] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Fabian M Rothe, Christina Herzberg, Eva Wagner, Daniel Hellwig, Martin Lehnik-Habrink, Elke Hammer, Uwe Völker, Jörg Stülke
Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing.
Mol Cell Proteomics: 2009, 8(6);1350-60
[PubMed:19193632] [WorldCat.org] [DOI] (I p)

Juan Campos-Guillén, Patricia Bralley, George H Jones, David H Bechhofer, Gabriela Olmedo-Alvarez
Addition of poly(A) and heteropolymeric 3' ends in Bacillus subtilis wild-type and polynucleotide phosphorylase-deficient strains.
J Bacteriol: 2005, 187(14);4698-706
[PubMed:15995184] [WorldCat.org] [DOI] (P p)

Irina A Oussenko, Teppei Abe, Hiromi Ujiie, Akira Muto, David H Bechhofer
Participation of 3'-to-5' exoribonucleases in the turnover of Bacillus subtilis mRNA.
J Bacteriol: 2005, 187(8);2758-67
[PubMed:15805522] [WorldCat.org] [DOI] (P p)

Gintaras Deikus, Paul Babitzke, David H Bechhofer
Recycling of a regulatory protein by degradation of the RNA to which it binds.
Proc Natl Acad Sci U S A: 2004, 101(9);2747-51
[PubMed:14976255] [WorldCat.org] [DOI] (P p)

Christine Eymann, Georg Homuth, Christian Scharf, Michael Hecker
Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis.
J Bacteriol: 2002, 184(9);2500-20
[PubMed:11948165] [WorldCat.org] [DOI] (P p)

G A Farr, I A Oussenko, D H Bechhofer
Protection against 3'-to-5' RNA decay in Bacillus subtilis.
J Bacteriol: 1999, 181(23);7323-30
[PubMed:10572137] [WorldCat.org] [DOI] (P p)

D H Bechhofer, W Wang
Decay of ermC mRNA in a polynucleotide phosphorylase mutant of Bacillus subtilis.
J Bacteriol: 1998, 180(22);5968-77
[PubMed:9811656] [WorldCat.org] [DOI] (P p)

W Wang, D H Bechhofer
Properties of a Bacillus subtilis polynucleotide phosphorylase deletion strain.
J Bacteriol: 1996, 178(8);2375-82
[PubMed:8636041] [WorldCat.org] [DOI] (P p)

A Luttinger, J Hahn, D Dubnau
Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis.
Mol Microbiol: 1996, 19(2);343-56
[PubMed:8825779] [WorldCat.org] [DOI] (P p)

S Mitra, K Hue, D H Bechhofer
In vitro processing activity of Bacillus subtilis polynucleotide phosphorylase.
Mol Microbiol: 1996, 19(2);329-42
[PubMed:8825778] [WorldCat.org] [DOI] (P p)

M P Deutscher, N B Reuven
Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis.
Proc Natl Acad Sci U S A: 1991, 88(8);3277-80
[PubMed:1707536] [WorldCat.org] [DOI] (P p)

PNPase in E. coli

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