BSGatlas

pnpA

BSGatlas-gene-1962

BSGatlas

Description	Information
Coordinates	1739383..1741500
Genomic Size	2118 bp
Name	pnpA
Outside Links	SubtiWiki
	BsubCyc
Strand	+
Type	CDS

SubtiWiki

Description	Information
Alternative Name	comR
	pnpA
	pnpA
Category	SW 3 Information processing
	SW 3.1 Genetics
	SW 3.1.5 DNA repair/ recombination
	SW 3.1.5.6 Other proteins
	SW 3.1.7 Genetic competence
	SW 3.2 RNA synthesis and degradation
	SW 3.2.4 RNases
	SW 3.2.4.1 Exoribonucleases
	SW 4 Lifestyles
	SW 4.1 Exponential and early post-exponential lifestyles
	SW 4.1.3 Genetic competence
Description	polynucleotide phosphorylase, RNase, involved in double-strand break repair
Enzyme Classifications	EC 2.7.7.8: polyribonucleotide nucleotidyltransferase
Function	DNA repair, competence development, RNA degradation
Is essential?	no
Isoelectric point	4.89
Locus Tag	BSU_16690
Molecular weight	77.2803
Name	pnpA
Product	polynucleotide phosphorylase (PNPase)

RefSeq

Description	Information
Alternative Locus Tag	BSU16690
Description	Evidence 1a: Function from experimental evidencesin the studied strain; PubMedId: 8636041, 8825779,9179491, 10572137, 15805522, 19215769, 19433509, 20659169,21859751, 22568516, 25099370, 27708634; Product type e:enzyme
Enzyme Classifications	EC 2.7.7.8: polyribonucleotide nucleotidyltransferase
	EC 3.1.13.1: exoribonuclease II
Functions	16.11: Scavenge (Catabolism)
	16.2: Construct biomass (Anabolism)
	16.3: Control
Locus Tag	BSU_16690
Name	pnpA
Title	polynucleotide phosphorylase (PNPase)
Type	CDS

BsubCyc

Description	Information
Alternative Name	comR
Citation	Cardenas PP;Carzaniga T;Zangrossi S;Briani F;Garcia-Tirado E;Deho G;Alonso JC Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins. Nucleic Acids Res 39(21);9250-61 (2011) PUBMED: 21859751
	Cascante-Estepa N;Gunka K;Stulke J Localization of Components of the RNA-Degrading Machine in Bacillus subtilis. Front Microbiol 7;1492 (2016) PUBMED: 27708634
	Cruz Hernandez A;Millan ES;de Jesus Romero Gomez S;Antonio Cervantes Chavez J;Garcia Martinez R;Pastrana Martinez X;Gomez JL;Jones GH;Guillen JC Exposure of Bacillus subtilis to mercury induces accumulation of shorter tRNA(Cys) species. Metallomics 5(4);398-403 (2013) PUBMED: 23529473
	Gerwig J;Stulke J Caught in the act: RNA-Seq provides novel insights into mRNA degradation. Mol Microbiol 94(1);5-8 (2014) PUBMED: 25155548
	Liu B;Deikus G;Bree A;Durand S;Kearns DB;Bechhofer DH Global analysis of mRNA decay intermediates in Bacillus subtilis wild-type and polynucleotide phosphorylase-deletion strains. Mol Microbiol 94(1);41-55 (2014) PUBMED: 25099370
	Liu B;Kearns DB;Bechhofer DH Expression of multiple Bacillus subtilis genes is controlled by decay of slrA mRNA from Rho-dependent 3' ends. Nucleic Acids Res 44(7);3364-72 (2016) PUBMED: 26857544
	Salvo E;Alabi S;Liu B;Schlessinger A;Bechhofer DH Interaction of Bacillus subtilis Polynucleotide Phosphorylase and RNase Y: STRUCTURAL MAPPING AND EFFECT ON mRNA TURNOVER. J Biol Chem 291(13);6655-63 (2016) PUBMED: 26797123
Comment	16.3: Control 16.2: Construct biomass (Anabolism) 16.11: Scavenge (Catabolism)
Description	polynucleotide phosphorylase (PNPase)
Enzyme Classifications	EC 2.7.7.8: polyribonucleotide nucleotidyltransferase
Gene Ontology	GO:0000175 3'-5'-exoribonuclease activity
	GO:0000287 magnesium ion binding
	GO:0003723 RNA binding
	GO:0004654 polyribonucleotide nucleotidyltransferase activity
	GO:0005515 protein binding
	GO:0005737 cytoplasm
	GO:0006396 RNA processing
	GO:0006402 mRNA catabolic process
	GO:0016740 transferase activity
	GO:0016779 nucleotidyltransferase activity
	GO:0030420 establishment of competence for transformation
	GO:0046872 metal ion binding
	GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic
Locus Tag	BSU16690
Molecular weight	77.464
Name	pnpA

Nicolas et al. predictions

Description	Information
Expression neg. correlated with	new_3072287_3072400, BSU30020, BSU15100, BSU29110, BSU31340, BSU30270, BSU36580, BSU19840, BSU14230, BSU29100
Expression pos. correlated with	BSU14770, BSU16600, BSU37060, BSU16610, new_3574247_3574338_c, BSU16620, BSU18120, new_2854627_2854844_c, BSU16630, BSU41050
Highly expressed condition	(C30) Cellsgrown overnight on LB agar plates at 30°Cwere harvested and used to inoculate pre-warmed minimal medium at OD600 of 0.5 (D. Dubnau, R. Davidoff-Abelson, J Mol Biol 56, 209, Mar 14, 1971). After growth at 37°C with vigorous shaking, cells were diluted ten times in fresh pre-warmed minimal medium and samples were harvested after a period of 30 minutes [C30] , i.e. before maximal induction of competence, and after a period of 90 minutes [C90], i.e. when competence induction was maximal.
	(Cold) Cells were grown in a synthetic medium (J. Stülke, R. Hanschke, M. Hecker, J Gen Microbiol 139, 2041, Sep, 1993) with 0.2 % glucose as carbon source (Belitsky Minimal Medium/BMM) at 37 °C with vigorous shaking. Stress was applied to exponentially growing cultures at OD500nm of 0.4. Samples were harvested before stress [BMM]; after a rapid temperature up-shift from 37 °C to 48 °C [Heat]; after a temperature down-shift from 37 °C to 18 °C [Cold]. Ethanol stress was imposed by adding ethanol to a final concentration of 4 % (v/v) and cells were harvested 10 minutes after ethanol addition [Etha].
	(G135) Purified spores were obtained by growing cells in DSM medium (P. Schaeffer, J. Millet, J. P. Aubert, Proc Natl Acad Sci U S A 54, 704, Sep, 1965) at 37°C for 48 hours after which they were washed ten times in ice cold distilled waterover a period of 5 days. Purified spores were heat activated at 70°C in Tris 10 mM pH8.4 and germination was initiated by the addition of L-alanine 10 mM (A. Moir, J Bacteriol 146, 1106, Jun, 1981). After incubation for one hour at 37°C, the culture was diluted with an equal volume of 2X LBmedium and germinating cells were harvested at 135, 150 or 180 minutes after addition of L-alanine [G135, G150 and G180].
	(G150) Purified spores were obtained by growing cells in DSM medium (P. Schaeffer, J. Millet, J. P. Aubert, Proc Natl Acad Sci U S A 54, 704, Sep, 1965) at 37°C for 48 hours after which they were washed ten times in ice cold distilled waterover a period of 5 days. Purified spores were heat activated at 70°C in Tris 10 mM pH8.4 and germination was initiated by the addition of L-alanine 10 mM (A. Moir, J Bacteriol 146, 1106, Jun, 1981). After incubation for one hour at 37°C, the culture was diluted with an equal volume of 2X LBmedium and germinating cells were harvested at 135, 150 or 180 minutes after addition of L-alanine [G135, G150 and G180].
	(G180) Purified spores were obtained by growing cells in DSM medium (P. Schaeffer, J. Millet, J. P. Aubert, Proc Natl Acad Sci U S A 54, 704, Sep, 1965) at 37°C for 48 hours after which they were washed ten times in ice cold distilled waterover a period of 5 days. Purified spores were heat activated at 70°C in Tris 10 mM pH8.4 and germination was initiated by the addition of L-alanine 10 mM (A. Moir, J Bacteriol 146, 1106, Jun, 1981). After incubation for one hour at 37°C, the culture was diluted with an equal volume of 2X LBmedium and germinating cells were harvested at 135, 150 or 180 minutes after addition of L-alanine [G135, G150 and G180].
	(H2O2) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition
	(LoTm) Cells were grown in Spizizen’s minimal medium (SMM) (C. Anagnostopoulos, J. Spizizen, J Bacteriol 81, 741, May, 1961) with vigorous agitation. The control culture was grown at 37 °C [SMMPr]. For growth at high or low temperatures, pre-cultures were grown at 37 °C, diluted to an OD578nm of 0.1 and subsequently transferred to 51 °C [HiTm] and 16 °C [LoTm], respectively. For the growth at high salinity, the salinity of the medium was adjusted by adding NaCl (5 M stock solution) to produce a final concentration of 1.2 M [HiOs].
	(LPh) Cells were harvested (i) during exponential growth in high phosphate defined medium [HPh]; (ii) during exponential growth in low phosphate defined medium [LPh] (J. P. Muller, Z. An, T. Merad, I. C. Hancock, C. R. Harwood, Microbiology 143, 947, Mar, 1997);and (iii) at three hours after the outset of the phosphate-limitation induced stationary phase [LPhT].
	(Oxctl) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition
	(Paraq) Cells were grown in LB medium at 37°C. At OD540 of 0.3, the culture were divided into four subcultures and diamide 0.6 mM [Diami], paraquat 0.4 mM [Paraq], H2O2 0.1mM [H2O2] or no oxidative drug [Oxctl] were added to the medium. Samples were taken 10 minutes after addition
Lowely expressed condition	(dia5) Diamide was added to an exponentially growing culture (OD600 approx. 0.6) at a sub-lethal concentration(0.5 mM) and growth continued at 37°C with vigorous shaking. Samples were collected 0, 5 and 15 minutes after diamide addition [dia0, dia5 and dia15].
	(LBGstat) Cells were grown in Luria-Bertani medium (Sigma) supplemented with glucose 0.3 % [LBG] at 37°C with vigorous shaking in flasks. Overnight cultures were diluted 2000-fold in fresh pre-warmed medium and samples were collected during the exponential [exp], transition [tran] and stationary [stat] phases of the growth cycle .
	(LPhT) Cells were harvested (i) during exponential growth in high phosphate defined medium [HPh]; (ii) during exponential growth in low phosphate defined medium [LPh] (J. P. Muller, Z. An, T. Merad, I. C. Hancock, C. R. Harwood, Microbiology 143, 947, Mar, 1997);and (iii) at three hours after the outset of the phosphate-limitation induced stationary phase [LPhT].
	(M40t90) Cells were grown in LB medium at 37°C with vigorous shaking. An exponentially growing culture (O.D.600 approx. 0.25) was divided: one culture acted as the control [no mitomycin C , M0] while mitomycin was added to the second culture to a final concentration of 40 ng/ml [mitomycin, M40]. Samples were harvested at 0, 45 and 90 minutes after mitomycin addition [t0, t45 and t90].
	(M9stat) Cells were grown in M9 supplemented with glucose (0.3 %) at 37°C with vigorous shaking. The composition of the M9 minimal medium is (per liter): 8.5 g Na2HPO4.2H20, 3 g KH2PO4, 1 g NH4Cl and 0.5 g NaCl. The following solutions were individually sterilized and added (volumes per liter of medium): 1 ml 0.1 M CaCl2.2H2O, 1 ml 1 M MgSO4.7H2O, 1 ml 50 mM Fe-Citrate. Also added was 10 ml of a trace salts solution containing (per liter): 170 mg ZnCl2, 100 mg MnCl2.4H2O, 60 mg CoCl2.6H2O, 60 mg Na2MoO4.2H2O and 43 mg CuCl2.2H2O. Overnight cultures were diluted 2000-fold in pre-warmed M9 medium and samples were harvested during exponential growth [M9exp], at the transition phase [M9tran] and during stationary phase [M9stat].
	(S6) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(S7) Cells were grown in CH medium at 37°C and sporulation was induced by resuspension in warm sporulation medium as described by Sterlini and Mandelstam (J. M. Sterlini, J. Mandelstam, Biochem J 113, 29, Jun, 1969). The initiation of sporulation was designated T0, the time of resuspension. Samples were harvested at hourly intervals for 6 hours [S0 to S6] for the first set of experiments and for 8 hours [S0 to S8] for a second set of experiments.
	(T0.30H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
	(T1.0H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
	(T1.30H) Anon-sporulating B. subtilis strain was grown in a modified M9 medium in batch culture (T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, M. Siemann-Herzberg, J Biotechnol 132, 359, Dec 1, 2007). Glucose was exhausted when the culture reached an OD600 of approx. 10 and this was designated T0 [T0.0H]. 7 samples were harvested at various times before glucose exhaustion [T-5.40H to T-0.40H] and 10 samples at various times after glucose exhaustion [T0.30H to T5.0H].
Name	pnpA

KEGG Pathways

Description	Information
Pathway	RNA degradation (ko03018)

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