PnpA

• Description: polynucleotide phosphorylase, RNase, involved in double-strand break repair
  
  

Gene name	pnpA
Synonyms	comR
Essential	no
Product	polynucleotide phosphorylase (PNPase) (EC 2.7.7.8)
Function	DNA repair, competence development, RNA degradation
Gene expression levels in SubtiExpress: pnpA
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 This image was kindly provided by SubtiList
Expression at a glance   PubMed

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]

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:

• Interactions:
  • part of the RNA degradosome PubMed
  • PnpA-RnjA PubMed, K(D) of the interaction: 250 nM PubMed
  • PnpA-PfkA PubMed
  • PnpA-Rny PubMed, K(D) of the interaction: 5 nM PubMed
  • PnpA-CshA PubMed

• Localization:

Database entries

• Structure: 3CDI (protein from E. coli), 3GCM (protein from E. coli, PNPase/RNase E micro-domain/RNA tetragonal crystal form )

• UniProt: P50849

• 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:

• Expression browser: pnpA PubMed

• Sigma factor:

• 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 Jörg Stülke's lab
  • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1342, available in Jörg Stülke's lab
  • for chromosomal expression of PnpA-Strep (cat): GP1002, available in Jörg Stülke's lab
  • for chromosomal expression of PnpA-Strep (spc): GP1038, 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 Jörg Stülke's lab

• FLAG-tag construct:
  • GP1021 (spc, based on pGP1331), available in Jörg Stülke's lab
  • GP1076 (ermC), available in Jörg Stülke's lab

• Antibody:

Labs working on this gene/protein

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

References

Reviews

Lehnik-Habrink M, Lewis RJ, Mäder U, Stülke J    
RNA degradation in Bacillus subtilis: an interplay of
essential endo- and exoribonucleases. 
Mol Microbiol.: 2012, 84(6) 1005-1017. 
PubMed:22568516

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

Additional publications: PubMed

PNPase in E. coli

Salima Nurmohamed, Helen A Vincent, Christopher M Titman, Vidya Chandran, Michael R Pears, Dijun Du, Julian L Griffin, Anastasia J Callaghan, Ben F Luisi
Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli.
J Biol Chem: 2011, 286(16);14315-23
[PubMed:21324911] [WorldCat.org] [DOI] (I p)

Salima Nurmohamed, Bhamini Vaidialingam, Anastasia J Callaghan, Ben F Luisi
Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.
J Mol Biol: 2009, 389(1);17-33
[PubMed:19327365] [WorldCat.org] [DOI] (I p)

Marta Del Favero, Elisa Mazzantini, Federica Briani, Sandro Zangrossi, Paolo Tortora, Gianni Dehò
Regulation of Escherichia coli polynucleotide phosphorylase by ATP.
J Biol Chem: 2008, 283(41);27355-27359
[PubMed:18650428] [WorldCat.org] [DOI] (P p)