SubtiBank SubtiBank
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polynucleotide phosphorylase, RNase, involved in double-strand break repair
77.28 kDa
protein length
705 aa Sequence Blast
gene length
2118 bp Sequence Blast
DNA repair, competence development, RNA degradation
polynucleotide phosphorylase (PNPase)

Genomic Context



  • [category|SW 3|Information processing] → [category|SW 3.1|Genetics] → [category|SW 3.1.5|DNA repair/ recombination]
  • [category|SW 3|Information processing] → [category|SW 3.1|Genetics] → [category|SW 3.1.5|DNA repair/ recombination] → [category|SW|Other proteins]
  • [category|SW 3|Information processing] → [category|SW 3.1|Genetics] → [category|SW 3.1.7|Genetic competence]
  • [category|SW 3|Information processing] → [category|SW 3.2|RNA synthesis and degradation] → [category|SW 3.2.4|RNases] → [category|SW|Exoribonucleases]
  • [category|SW 4|Lifestyles] → [category|SW 4.1|Exponential and early post-exponential lifestyles] → [category|SW 4.1.3|Genetic competence]
  • Gene

    1,739,383 1,741,500

    Phenotypes of a mutant

  • The [gene|64C6D783FF3F41C81B216F798A1DC8071345B1ED|pnpA] mutant is cold sensitive and sensitive to tetracyclin, it shows multiseptate filamentous growth [Pubmed|8636041]
  • The mutant is deficient in genetic competence (no expression of the late competence genes) [Pubmed|8825779]
  • The [gene|64C6D783FF3F41C81B216F798A1DC8071345B1ED|pnpA] mutant exhibits reduced motility and reduced expression of the [SW|fla-che operon] resulting from accumulation of [gene|C17C296F3EB2E106C380E3B5D784F3FA63F4C9B7|slrA] mRNA [Pubmed|26857544]
  • The mutant overexpresses the ''trp'' and ''[gene|1F548515402950572E7212901729B2480432D1B9|putB]-[gene|2042F691CB37B1BAFE2CF3906A9F7F47457C3995|putC]-[gene|B3DF99B747D0A7472E3878920BF3CE7CE954B0BE|putP]'' operons.
  • The protein

    Catalyzed reaction/ biological activity

  • 3'-5' exoribonuclease, [SW|RNase]
  • PNPase degrades the trp mRNA from RNA-TRAP complex
  • degradation of the [protein|C17C296F3EB2E106C380E3B5D784F3FA63F4C9B7|SlrA] mRNA from the 3' end, through the [protein|7CD46C64BE69EDADF58B634DC50C3F61BFFEC5B5|Rho]-dependent terminator [Pubmed|26857544]
  • 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 [protein|A44D4677FB70BE8F554BF1001A500F817C7DA95F|RecA], inhibited by [protein|8DE39680CA7663803A107066FBE9AFFCC77DB72A|SsbA]) [Pubmed|21859751]
  • can polymerize ssDNA at a free 3' OH end, stimulated by [protein|5680A06A74D3EC6310EF8677795511C75DB3059E|RecN] [Pubmed|21859751]
  • phosphate + RNA(n+1) --> ribonucleoside 5'-diphosphate + RNA(n) (according to UniProt)
  • Protein family

  • polyribonucleotide nucleotidyltransferase family (single member, according to UniProt)
  • [SW|Domains]

  • [SW|KH domain] (aa 554-613) (according to UniProt)
  • [SW|S1 domain] (aa 623-691) (according to UniProt)
  • Structure

  • [PDB|5YJJ] (protein from ''Staphylococcus aureus'') [pubmed|29242153]
  • [PDB|3GCM] (protein from ''E. coli'', PNPase/RNase E micro-domain/RNA tetragonal crystal form )
  • [SW|Localization]

  • cytoplasm (homogeneous) [Pubmed|27708634]
  • Additional information

  • required for the expression of late competence genes ''[gene|41DFEF8A6BC7E34A6681C26D92F2B08DC120A957|comGA]'' and ''[gene|08CFA2C72931A75532D4289BC1D18A826DE9F9CA|comK]'', requirement bypassed by a ''[gene|331993A875907C10C77105FD8DDD86D4412CE405|mecA]'' disruption; may be necessary for modification of the ''[gene|81845F44CE2C601555066E31E87384FF5D7B4139|srfAA]'' transcript (stabilization or translation activation)
  • belongs to the 100 [SW|most abundant proteins] [PubMed|15378759]
  • Expression and Regulation



    regulatory mechanism

  • [regulon|stringent response|stringent response]: negative regulation, in [regulon|stringent response|stringent response]
  • regulation

  • [protein|CEE73284EFC0DBE8870CE0B474922DED79475A57|RelA] dependent downregulation (Class I) during stringent response [Pubmed|11948165]
  • view in new tab

    Biological materials


  • GP1748 ([gene|64C6D783FF3F41C81B216F798A1DC8071345B1ED|pnpA]::aphA3), available in [SW|Jörg Stülke]'s lab, [Pubmed|27708634]
  • BKE16690 ([gene|64C6D783FF3F41C81B216F798A1DC8071345B1ED|pnpA]::erm trpC2) available at [ BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATACAATTACGAACTCCTC, downstream forward: _UP4_TAAATGAAAACATAAAAGGA
  • BKK16690 ([gene|64C6D783FF3F41C81B216F798A1DC8071345B1ED|pnpA]::kan trpC2) available at [ BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATACAATTACGAACTCCTC, downstream forward: _UP4_TAAATGAAAACATAAAAGGA
  • Expression vectors

  • for expression, purification in ''E. coli'' with N-terminal His-tag, in [SW|pWH844]: pGP838, available in [SW|Jörg Stülke]'s lab
  • for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [SW|SPINE], in [SW|pGP380]: pGP1342, available in [SW|Jörg Stülke]'s lab
  • for chromosomal expression of PnpA-Strep (cat): GP1002, available in [SW|Jörg Stülke]'s lab
  • for chromosomal expression of PnpA-Strep (spc): GP1038, available in [SW|Jörg Stülke]'s lab
  • pGP1439: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, in [SW|pGP172], available in [SW|Jörg Stülke]'s lab
  • GFP fusion

  • GP1698 (in [SW|pBP43]), expression of '' pnpA-GFP''::''spc'' under the native promoter, available in [SW|Jörg Stülke]'s lab [Pubmed|27708634]
  • two-hybrid system

  • B. pertussis adenylate cyclase-based bacterial two hybrid system ([SW|BACTH]), available in [SW|Jörg Stülke]'s lab, [pubmed|19193632]
  • FLAG-tag construct

  • GP1021 (spc, based on [SW|pGP1331]) [Pubmed|21803996], available in [SW|Jörg Stülke]'s lab
  • GP1076 (ermC) [Pubmed|21803996], available in [SW|Jörg Stülke]'s lab
  • labs

  • [SW|David Bechhofer], Mount Sinai School, New York, USA [ Laboratories and Programs/Bechhofer Laboratory?citype=Physician&ciid=Bechhofer David H 1255565 Homepage]
  • References


  • 10087930,19215773,17514363,16733069,22568516,25155548,25292357,25878039,28117687,29651979,30340785,31464530
  • Original publications

  • 11948165,10572137,8825779,19433509,9811656,14976255,15995184,8825778,8636041,15805522,19193632,1707536,19633085,19638340,20360175,20418391,20572937,21803996,21862575,22198292,23529473,21859751,15378759,25099370,26797123,26857544,27708634,28238534,28334892,28516784,29242153,31041723
  • PNPase in ''E. coli

  • 19327365,21324911,18650428