PnpA

• 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
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

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.
• The mutant is deficient in genetic competence (no expression of the late competence genes)
• The mutant overexpresses the trp and ycgM-ycgN-ycgO 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

• Protein family:

• Paralogous protein(s):

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:

• Cofactor(s):

• Effectors of protein activity:

• Interactions: PnpA-RnjA, PnpA-PfkA, PnpA-Rny 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:

• 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 Stülke lab
  • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1342, available in Stülke 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

References

Reviews

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

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)

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)

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)