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
Sequences	Protein DNA DNA_with_flanks
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, most abundant proteins

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

• BsubCyc: BSU16690

• 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:

• Cofactors:

• 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

• BsubCyc: BSU16690

• 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:
  • belongs to the 100 most abundant proteins PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 3793 PubMed
  • number of protein molecules per cell (complex medium with amino acids, without glucose): 8647 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 2302 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2327 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 2689 PubMed

Biological materials

• Mutant: GP584 (aphA3), available in Jörg Stülke's 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) PubMed, available in Jörg Stülke's lab
  • GP1076 (ermC) PubMed, available in Jörg Stülke's lab

• Antibody:

Labs working on this gene/protein

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

References

Reviews

Jan Gerwig, Jörg Stülke
Caught in the act: RNA-Seq provides novel insights into mRNA degradation.
Mol Microbiol: 2014, 94(1);5-8
[PubMed:25155548] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Richard J Lewis, Ulrike Mäder, Jörg Stülke
RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases.
Mol Microbiol: 2012, 84(6);1005-17
[PubMed:22568516] [WorldCat.org] [DOI] (I p)

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)

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)