polynucleotide phosphorylase, RNase, involved in double-strand break repair
function
DNA repair, competence development, RNA degradation
product
polynucleotide phosphorylase (PNPase)
Genomic Context
categories
[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 3.1.5.6|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 3.2.4.1|Exoribonucleases][category|SW 4|Lifestyles] → [category|SW 4.1|Exponential and early post-exponential lifestyles] → [category|SW 4.1.3|Genetic competence][SW|Categories] containing this gene/protein
[SW|genetic competence], [SW|DNA repair/ recombination], [SW|RNAses], [SW|most abundant proteins]This gene is a member of the following [SW|regulons]
[SW|stringent response]Gene
Coordinates on the chromosome (coding sequence)
1,739,383 -> 1,741,500
Phenotypes of a mutant
The ''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 ''[SW|pnpA]'' mutant exhibits reduced motility and reduced expression of the [SW|fla-che operon] [Pubmed|26857544]The mutant overexpresses the ''trp'' and ''[protein|search|putB]-[protein|search|putC]-[protein|search|putP]'' operons.accumulation of ''[SW|slrA]'' mRNA [Pubmed|26857544]The protein
Catalyzed reaction/ biological activity
3'-5' exoribonuclease, [SW|RNase]PNPase degrades the trp mRNA from the RNA-TRAP complexinvolved 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|search|RecA], inhibited by [protein|search|SsbA]) [Pubmed|21859751]can polymerize ssDNA at a free 3' OH end, stimulated by [protein|search|RecN] [Pubmed|21859751]Structure
[PDB|3CDI] (protein from ''E. coli''), [PDB|3GCM] (protein from ''E. coli'', PNPase/RNase E micro-domain/RNA tetragonal crystal form )[SW|Localization]
cytoplasm (homogeneous) [Pubmed|27708634][SW|Interactions]
part of the [SW|RNA degradosome] [Pubmed|19193632][protein|search|PnpA]-[protein|search|RnjA] [Pubmed|19193632], K(D) of the interaction: 250 nM [Pubmed|22198292][protein|search|PnpA]-[protein|search|PfkA] [Pubmed|19193632][protein|search|PnpA]-[protein|search|Rny] [Pubmed|19193632,21803996,26797123], K(D) of the interaction: 5 nM [Pubmed|22198292][protein|search|PnpA]-[protein|search|CshA] [Pubmed|20572937]Additional information
required for the expression of late competence genes ''[SW|comGA]'' and ''[protein|search|comK]'', requirement bypassed by a ''[protein|search|mecA]'' disruption; may be necessary for modification of the ''[SW|srfAA]'' transcript (stabilization or translation activation)Expression and Regulation
Regulation
[protein|search|RelA] dependent downregulation (Class I) during stringent response [Pubmed|11948165]Additional information
belongs to the 100 [SW|most abundant proteins] [PubMed|15378759]Biological materials
Mutant
GP584 (aphA3), available in [SW|Jörg Stülke]'s labGP1748: ''pnpA::aphA3'', available in [SW|Jörg Stülke]' lab, [Pubmed|27708634]Expression vector
for expression, purification in ''E. coli'' with N-terminal His-tag, in [SW|pWH844]: pGP838, available in [SW|Jörg Stülke]'s labfor expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [SW|SPINE], in [SW|pGP380]: pGP1342, available in [SW|Jörg Stülke]'s labfor chromosomal expression of PnpA-Strep (cat): GP1002, available in [SW|Jörg Stülke]'s labfor chromosomal expression of PnpA-Strep (spc): GP1038, available in [SW|Jörg Stülke]'s labGFP 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 labFLAG-tag construct
GP1021 (spc, based on [SW|pGP1331]) [Pubmed|21803996], available in [SW|Jörg Stülke]'s labGP1076 (ermC) [Pubmed|21803996], available in [SW|Jörg Stülke]'s labLabs working on this gene/protein
[SW|David Bechhofer], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers Laboratories and Programs/Bechhofer Laboratory?citype=Physician&ciid=Bechhofer David H 1255565 Homepage]References
Reviews
10087930,19215773,17514363,16733069,22568516,25155548,25292357,25878039 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 PNPase in ''E. coli
19327365,21324911,18650428 
