Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store

MetaCyc Enzyme: polynucleotide phosphorylase

Gene: pnp Accession Numbers: EG10743 (MetaCyc), b3164, ECK3152

Synonyms: bfl, PNPase

Species: Escherichia coli K-12 substr. MG1655

Component of: degradosome (extended summary available)

Subunit composition of polynucleotide phosphorylase = [Pnp]3
         polynucleotide phosphorylase monomer = Pnp

Polynucleotide phosphorylase (PNPase) is a 3' to 5' exonuclease and a 3'-terminal oligonucleotide polymerase. It degrades various mRNAs, is involved in cold shock regulation, is a part of tRNA maturation and degradation, adds heteropolymeric tails to some RNAs and is a component of the degradosome, a multienzyme complex that carries out RNA degradation.

PNPase is involved in general mRNA degradation. Loss of PNPase leads to an increase in steady-state levels of mRNA, as well as increasing mRNA half lives in the absence of the 3' exonuclease RNase II [Mohanty03, Kinscherf75]. PNPase also has a role in mRNA degradation during carbon starvation, where it may be required for breakdown of small rRNA fragments produced by other RNases [Kaplan74, Kaplan75].

A number of specific PNPase substrates have been identified. PNPase is involved in degradation of lac mRNA, rnb mRNA, mRNA coding for ribosomal protein S20, and the RNA-OUT antisense RNA [HarEl79, Pepe94, Mackie89, Zilhao96]. It also degrades sok antisense RNA and thrS and rpsO mRNA following cleavage by RNase E [Dam97, Nogueira01, Braun96, Hajnsdorf94]. PNPase binds to but does not degrade RNA containing 8-oxoguanine [Hayakawa01].

PNPase-mediated degradation is required for regulation of the cold shock response. PNPase degrades a number of mRNAs induced by cold shock, including those coding for CspA, RbfA, CsdA, RpoE, RseA, Rnr and many others [Yamanaka01, Cairrao03, Polissi03]. The isolated PNPase S1 RNA-binding domain can complement a deletion in four cold-shock genes [Xia01].

The 3' to 5' processive cleavage of RNA by PNPase depends on the composition and structure of the 3' end of the substrate [Plamann90, Cisneros96]. RhlB and poly(A) polymerase I (PAP I) in concert with the degradosome are required for PNPase-mediated degradation of cistrons with 3' REP-stabilizers [Khemici04].

Binding of the protein Hfq to poly(A) tracts prevents PNPase degradation of these tails in vitro [Folichon03]. RNA with 3' stem-loops are resistant to degradation by pure PNPase or whole degradosome in vitro, but addition of even a short poly(A) or mixed nucleotide tail overcomes this block [Causton94, Blum99, Lisitsky99]. Polyadenylation similarly destabilizes rpsO mRNA against degradation by RNase E, RNase II and PNPase, and is required for sok RNA degradation [Hajnsdorf95, Hajnsdorf96, Dam97]. Both 3' adenylation and 5' phosphorylation affect the rate of degradation of RNA I [Xu95a]. PNPase itself modulates polyadenylation of several RNAs [Mohanty00].

PNPase is involved in tRNA processing and maintenance. Though purified PNPase is incapable of completely processing tRNA in vitro, it is effective, along with RNase II, in trimming long 3' trailing sequences to yield 2-4 nucleotide intermediates which will be trimmed by RNases T and PH [Deutscher88, Li94]. PNPase is also partially required for repair of 3'-terminal CCA sequences in tRNAs in the absence of tRNA nucleotidyltransferase [Reuven97]. PNPase is also involved in the degradation of mutant tRNA, in a process that is enhanced by polyadenylation by PAP I [Li02].

PNPase also catalyzes the "reverse" reaction, converting nucleoside diphosphates into polyribonucleotides [Littauer57, Gillam78, Gillam80]. PNPase generates heteropolymeric tails on RNA and is responsible for residual polyadenylation detected in PAP I deficient strains [Mohanty00a]. Hfq, which binds to the 3' end of RNA and prevents PNPase-mediated degradation, also prevents PNPase-mediated addition of nucleosides to bound RNA, while promoting PAP I activity [Folichon05].

PNPase is a trimer of Pnp monomers [Portier75, Soreq77]. Each Pnp monomer has two RNA-binding sites, KH and S1, that are dispensible for strict catalytic function but are required for Pnp autoregulation, growth at low temperature, and the generation of oligonucleotides [Jarrige02, MatusOrtega07, Guissani76]. The S1 domain is a five-stranded antiparallel β barrel with conserved residues on one face forming the RNA binding site [Bycroft97].

PNPase binds the signaling molecule c-di-GMP; binding enhances several PNPase activities, including ADP/Pi phosphoryl exchange and poly(A) synthesis [Tuckerman11].

PNPase is subject to autoregulation at the mRNA level. RNase III cleaves a stem-loop in the pnp mRNA leader sequence, following which PNPase binds and degrades the 5' half of the cleaved duplex [Portier87, Takata89, Jarrige01, RobertLe92, Takata87, Carzaniga09]. PNPase autoregulation also decreases as general RNA polyadenylation increases and following a shift to cold temperatures [Mohanty02, Mathy01, Zangrossi00, Beran01].

Strains lacking both PNPase and RNase II activity are inviable and collect mRNA fragments 100-1,500 nucleotides long [Donovan86]. In a triple mutant in pnp, rnb and rne, mRNA degradation slows three- to fourfold and the length and number of poly(A) tails increases [Arraiano88, OHara95]. In a pnp mutant lacking RNase PH function, the 50S ribosomal subunit and 23S rRNA is degraded [Zhou97b].

Even in the absence of the degradosome scaffold RNase E, PNPase and the helicase RhlB interact. In vitro, RhlB unwinding of dsRNA allows PNPase degradation to occur [Liou02a].

PNPase is required to prevent phage P4 superinfection. This prevention requires binding of CI antisense RNA to sequences on nascent P4 transcripts; PNPase processes CI RNA [Piazza96].

pnp shows differential codon adaptation, resulting in differential translation efficiency signatures, in thermophilic microbes. It was therefore predicted to play a role in the heat shock response. A pnp deletion mutant was shown to be more sensitive than wild-type specifically to heat shock, but not other stresses [Krisko14].

Locations: cytosol, membrane

Map Position: [3,307,055 <- 3,309,190]

Molecular Weight of Polypeptide: 77.101 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010397, CGSC:379, DIP:DIP-10522N, EchoBASE:EB0736, EcoGene:EG10743, EcoliWiki:b3164, Mint:MINT-244786, ModBase:P05055, OU-Microarray:b3164, PortEco:pnp, PR:PRO_000023561, Pride:P05055, Protein Model Portal:P05055, RefSeq:NP_417633, RegulonDB:EG10743, SMR:P05055, String:511145.b3164, UniProt:P05055

Relationship Links: InterPro:IN-FAMILY:IPR001247, InterPro:IN-FAMILY:IPR003029, InterPro:IN-FAMILY:IPR004087, InterPro:IN-FAMILY:IPR004088, InterPro:IN-FAMILY:IPR012162, InterPro:IN-FAMILY:IPR012340, InterPro:IN-FAMILY:IPR015847, InterPro:IN-FAMILY:IPR015848, InterPro:IN-FAMILY:IPR020568, InterPro:IN-FAMILY:IPR022967, InterPro:IN-FAMILY:IPR027408, Panther:IN-FAMILY:PTHR11252, PDB:Structure:1SRO, PDB:Structure:3CDI, PDB:Structure:3CDJ, PDB:Structure:3GCM, PDB:Structure:3GLL, PDB:Structure:3GME, PDB:Structure:3H1C, Pfam:IN-FAMILY:PF00013, Pfam:IN-FAMILY:PF00575, Pfam:IN-FAMILY:PF01138, Pfam:IN-FAMILY:PF03725, Pfam:IN-FAMILY:PF03726, Prosite:IN-FAMILY:PS50084, Prosite:IN-FAMILY:PS50126, Smart:IN-FAMILY:SM00316, Smart:IN-FAMILY:SM00322

Gene-Reaction Schematic

Gene-Reaction Schematic

GO Terms:
Biological Process:
Inferred from experimentGO:0009408 - response to heat [Krisko14]
Inferred from experimentInferred by computational analysisGO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic [GOA01a, Li94]
Inferred by computational analysisGO:0006396 - RNA processing [GOA01a]
Inferred by computational analysisGO:0006402 - mRNA catabolic process [GOA06, GOA01a]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0000175 - 3'-5'-exoribonuclease activity [GOA01a, Li94]
Inferred from experimentInferred by computational analysisGO:0004654 - polyribonucleotide nucleotidyltransferase activity [GOA06, GOA01, GOA01a, Littauer57]
Inferred from experimentGO:0005515 - protein binding [Erce10, AitBara10, Regonesi06, Butland05, Callaghan04]
Inferred from experimentGO:0035438 - cyclic-di-GMP binding [Tuckerman11]
Inferred from experimentGO:0042802 - identical protein binding [Lasserre06, Callaghan04]
Inferred by computational analysisGO:0000287 - magnesium ion binding [GOA06]
Inferred by computational analysisGO:0003676 - nucleic acid binding [GOA01a]
Inferred by computational analysisGO:0003723 - RNA binding [UniProtGOA11a, GOA06, GOA01a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016779 - nucleotidyltransferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, Zhang07, LopezCampistrou05, Lasserre06]
Inferred from experimentGO:0016020 - membrane [Lasserre06]
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: information transferRNA relatedRNA degradation
metabolismdegradation of macromoleculesRNA

Imported from EcoCyc 30-Sep-2015 by Paley S, SRI International

Enzymatic reaction of: polynucleotide phosporylase (polynucleotide phosphorylase)

Inferred from experiment

EC Number:

a tRNA precursor with a 5' extension and a long 3' trailer + n H2O → a tRNA precursor with a 5' extension and a short 3' extension + n a nucleoside 5'-monophosphate

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is irreversible in the direction shown.

In Pathways: tRNA processing

Imported from EcoCyc 30-Sep-2015 by Paley S, SRI International

Enzymatic reaction of: polynucleotide phosphorylase

Inferred from experiment

EC Number:

(ribonucleotides)(n) + phosphate ⇄ (ribonucleotides)(n-1) + a nucleoside diphosphate

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

Imported from EcoCyc 30-Sep-2015 by Paley S, SRI International

Cofactors or Prosthetic Groups: Mg2+ [Kimhi68, Littauer57]

Inhibitors (Unknown Mechanism): 6-azauridine diphosphate [Skoda59]

Subunit of: degradosome

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of degradosome = [(Ppk)2][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2]
         polyphosphate kinase = (Ppk)2 (extended summary available)
         ribonuclease E = (Rne)4 (extended summary available)
                 RNase E = Rne
         RhlB, ATP-dependent RNA helicase of the RNA degradosome = (RhlB)2 (extended summary available)
         polynucleotide phosphorylase = (Pnp)3 (extended summary available)
                 polynucleotide phosphorylase monomer = Pnp
         enolase = (Eno)2 (extended summary available)

The degradosome is a large, multiprotein complex involved in RNA degradation. It consists of the RNA degradation enzymes RNase E and PNPase, as well as the ATP-dependent RNA helicase RhlB and the metabolic enzyme enolase [Py94, Carpousis94, Py96]. Polyphosphate kinase and the chaperone protein DnaK are also associated with and may be components of the degradosome [Blum97, Miczak96]. A "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible for this test case, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur [Coburn99]. Based on immunogold labeling studies, RhlB and RNase E are present in equimolar quantities in the degradosome, which is tethered to the cytoplasmic membrane via the amino-terminus of RNase E [Liou01].

RNase E provides the organizational structure for the degradosome. Its carboxy-terminal half binds PNPase, RhlB and enolase, and the loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I [Kido96, Vanzo98, Morita04]. This scaffold region is flexible, with isolated segments of increased structure that may be involved in binding other degradosome constituents [Callaghan04]. RNase E binding to partner proteins can be selectively disrupted. Loss of RhlB and enolase binding results in reduced degradosome activity. Conversely, disrupted PNPase binding yields increased activity. Strains any alteration in RNase E binding do not grow as well as wild type [Leroy02]. The amino-terminal half of RNase E contains sequences involved in oligomerization [Vanzo98].

In vitro purified degradosome generates 147-nucleotide RNase E cleavage intermediates from rpsT mRNA. Continuous cycles of polyadenylation and PNPase cleavage are necessary and sufficient to break down these intermediates, though RNase II can block this second degradation step [Coburn98]. RNAs with 3' REP stabilizers or stem loops must be polyadenylated to allow breakdown by the degradosome [Khemici04, Blum99]. Poly(G) and poly(U) tails do not allow degradation, though addition of a stretch of mixed nucleotides copied from within a coding region has stimulated degradation of a test substrate [Blum99].

The degradosome copurifies with fragments from its RNA substrates, including rRNA fragments derived from cleavage of 16S and 23S rRNA by RNase E, 5S rRNA and ssrA RNA [Bessarab98, LinChao99].

The DEAD-box helicases SrmB, RhlE and CsdA bind RNase E in vitro at a different site than RhlB. RhlE and CsdA can both replace RhlB in promoting PNPase activity in vitro [Khemici04a]. CsdA is induced by cold shock, and following a shift to 15 degrees C it copurifies with the degradosome [PrudhommeGenere04].

At least two poly(A)-binding proteins interact with the degradosome. The cold-shock protein CspE inhibits internal cleavage and breakdown of polyadenylated RNA by RNase E and PNPase by blocking digestion through the poly(A) tail. S1, a component of the 30S ribosome, binds to RNase E and PNPase without apparent effect on their activities [Feng01].

The global effects of mutations in degradeosome constituents on mRNA levels have been evaluated using microarrays [Bernstein04].

Locations: inner membrane

GO Terms:
Cellular Component:
GO:0005886 - plasma membrane [Liou01]

Imported from EcoCyc 30-Sep-2015 by Paley S, SRI International

Sequence Features

Feature Class Location Citations Comment
Protein-Segment 77 -> 80
Author statement[UniProt15]
UniProt: FFRR loop; important for RNA binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 79 -> 80
Inferred from experiment[Shi08]
UniProt: Strongly reduces RNA binding. Reduces RNA degradation.
Mutagenesis-Variant 83
Inferred from experiment[Shi08]
UniProt: No effect on RNA-binding. No effect on degradation of long RNA molecules. Impairs degradation of short RNA molecules.
Mutagenesis-Variant 100
Inferred from experiment[Jarrige02]
UniProt: Abolishes enzyme activity.
Acetylation-Modification 302
Inferred from experiment[Yu08]
Mutagenesis-Variant 319
Inferred from experiment[Jarrige02]
UniProt: Abolishes enzyme activity.
Protein-Segment 327 -> 331
Author statement[UniProt15]
UniProt: Interaction with RNase E; Sequence Annotation Type: region of interest.
Sequence-Conflict 357
Inferred by curator[Regnier87, UniProt15]
UniProt: (in Ref. 1; AAA83905).
Mutagenesis-Variant 398 -> 399
Author statement[UniProt15]
UniProt: Abolishes enzyme activity.
Mutagenesis-Variant 428
Inferred from experiment[Jarrige02]
UniProt: Abolishes enzyme activity.
Mutagenesis-Variant 444
Inferred from experiment[Jarrige02]
UniProt: Abolishes enzyme activity.
Sequence-Conflict 450
Inferred by curator[Regnier87, UniProt15]
UniProt: (in Ref. 1; AAA83905).
Metal-Binding-Site 486
Author statement[UniProt15]
UniProt: Magnesium.
Mutagenesis-Variant 492
Inferred from experiment[Jarrige02]
UniProt: Abolishes enzyme activity.
Metal-Binding-Site 492
Author statement[UniProt15]
UniProt: Magnesium.
Conserved-Region 553 -> 612
Inferred by computational analysis[UniProt15]
UniProt: KH.
Conserved-Region 622 -> 690
Inferred by computational analysis[UniProt15]
UniProt: S1 motif.

Ingrid Keseler on Fri Jun 8, 2007:
Corrected start site based on [Link97].
10/20/97 Gene b3164 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10743; confirmed by SwissProt match.


AitBara10: Ait-Bara S, Carpousis AJ (2010). "Characterization of the RNA degradosome of Pseudoalteromonas haloplanktis: conservation of the RNase E-RhlB interaction in the gammaproteobacteria." J Bacteriol 192(20);5413-23. PMID: 20729366

Arraiano88: Arraiano CM, Yancey SD, Kushner SR (1988). "Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12." J Bacteriol 170(10);4625-33. PMID: 2459106

Beran01: Beran RK, Simons RW (2001). "Cold-temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation." Mol Microbiol 39(1);112-25. PMID: 11123693

Bernstein04: Bernstein JA, Lin PH, Cohen SN, Lin-Chao S (2004). "Global analysis of Escherichia coli RNA degradosome function using DNA microarrays." Proc Natl Acad Sci U S A 101(9);2758-63. PMID: 14981237

Bessarab98: Bessarab DA, Kaberdin VR, Wei CL, Liou GG, Lin-Chao S (1998). "RNA components of Escherichia coli degradosome: evidence for rRNA decay." Proc Natl Acad Sci U S A 95(6);3157-61. PMID: 9501232

Blum97: Blum E, Py B, Carpousis AJ, Higgins CF (1997). "Polyphosphate kinase is a component of the Escherichia coli RNA degradosome." Mol Microbiol 1997;26(2);387-98. PMID: 9383162

Blum99: Blum E, Carpousis AJ, Higgins CF (1999). "Polyadenylation promotes degradation of 3'-structured RNA by the Escherichia coli mRNA degradosome in vitro." J Biol Chem 274(7);4009-16. PMID: 9933592

Braun96: Braun F, Hajnsdorf E, Regnier P (1996). "Polynucleotide phosphorylase is required for the rapid degradation of the RNase E-processed rpsO mRNA of Escherichia coli devoid of its 3' hairpin." Mol Microbiol 19(5);997-1005. PMID: 8830280

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Bycroft97: Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG (1997). "The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold." Cell 88(2);235-42. PMID: 9008164

Cairrao03: Cairrao F, Cruz A, Mori H, Arraiano CM (2003). "Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA." Mol Microbiol 50(4);1349-60. PMID: 14622421

Callaghan04: Callaghan AJ, Aurikko JP, Ilag LL, Gunter Grossmann J, Chandran V, Kuhnel K, Poljak L, Carpousis AJ, Robinson CV, Symmons MF, Luisi BF (2004). "Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E." J Mol Biol 340(5);965-79. PMID: 15236960

Carpousis94: Carpousis AJ, Van Houwe G, Ehretsmann C, Krisch HM (1994). "Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation." Cell 76(5);889-900. PMID: 7510217

Carzaniga09: Carzaniga T, Briani F, Zangrossi S, Merlino G, Marchi P, Deho G (2009). "Autogenous regulation of Escherichia coli polynucleotide phosphorylase expression revisited." J Bacteriol 191(6);1738-48. PMID: 19136586

Causton94: Causton H, Py B, McLaren RS, Higgins CF (1994). "mRNA degradation in Escherichia coli: a novel factor which impedes the exoribonucleolytic activity of PNPase at stem-loop structures." Mol Microbiol 14(4);731-41. PMID: 7534370

Cisneros96: Cisneros B, Court D, Sanchez A, Montanez C (1996). "Point mutations in a transcription terminator, lambda tI, that affect both transcription termination and RNA stability." Gene 181(1-2);127-33. PMID: 8973320

Coburn98: Coburn GA, Mackie GA (1998). "Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes." J Mol Biol 279(5);1061-74. PMID: 9642084

Coburn99: Coburn GA, Miao X, Briant DJ, Mackie GA (1999). "Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3' exonuclease and a DEAD-box RNA helicase." Genes Dev 13(19);2594-603. PMID: 10521403

Dam97: Dam Mikkelsen N, Gerdes K (1997). "Sok antisense RNA from plasmid R1 is functionally inactivated by RNase E and polyadenylated by poly(A) polymerase I." Mol Microbiol 26(2);311-20. PMID: 9383156

Deutscher88: Deutscher MP, Marshall GT, Cudny H (1988). "RNase PH: an Escherichia coli phosphate-dependent nuclease distinct from polynucleotide phosphorylase." Proc Natl Acad Sci U S A 85(13);4710-4. PMID: 2455297

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Donovan86: Donovan WP, Kushner SR (1986). "Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12." Proc Natl Acad Sci U S A 83(1);120-4. PMID: 2417233

Erce10: Erce MA, Low JK, Wilkins MR (2010). "Analysis of the RNA degradosome complex in Vibrio angustum S14." FEBS J 277(24);5161-73. PMID: 21126315

Feng01: Feng Y, Huang H, Liao J, Cohen SN (2001). "Escherichia coli poly(A)-binding proteins that interact with components of degradosomes or impede RNA decay mediated by polynucleotide phosphorylase and RNase E." J Biol Chem 276(34);31651-6. PMID: 11390393

Folichon03: Folichon M, Arluison V, Pellegrini O, Huntzinger E, Regnier P, Hajnsdorf E (2003). "The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation." Nucleic Acids Res 31(24);7302-10. PMID: 14654705

Folichon05: Folichon M, Allemand F, Regnier P, Hajnsdorf E (2005). "Stimulation of poly(A) synthesis by Escherichia coli poly(A)polymerase I is correlated with Hfq binding to poly(A) tails." FEBS J 272(2);454-63. PMID: 15654883

Gillam78: Gillam S, Jahnke P, Smith M (1978). "Enzymatic synthesis of oligodeoxyribonucleotides of defined sequence." J Biol Chem 253(8);2532-9. PMID: 632285

Gillam80: Gillam S, Smith M (1980). "Use of E. coli polynucleotide phosphorylase for the synthesis of oligodeoxyribonucleotides of defined sequence." Methods Enzymol 65(1);687-701. PMID: 6990191

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Guissani76: Guissani A, Portier C (1976). "Study on the structure-function relationship of polynucleotide phosphorylase: model of a proteolytic degraded polynucleotide phosphorylase." Nucleic Acids Res 3(11);3015-24. PMID: 794831

Hajnsdorf94: Hajnsdorf E, Steier O, Coscoy L, Teysset L, Regnier P (1994). "Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant." EMBO J 13(14);3368-77. PMID: 7519147

Hajnsdorf95: Hajnsdorf E, Braun F, Haugel-Nielsen J, Regnier P (1995). "Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli." Proc Natl Acad Sci U S A 92(9);3973-7. PMID: 7732015

Hajnsdorf96: Hajnsdorf E, Braun F, Haugel-Nielsen J, Le Derout J, Regnier P (1996). "Multiple degradation pathways of the rpsO mRNA of Escherichia coli. RNase E interacts with the 5' and 3' extremities of the primary transcript." Biochimie 78(6);416-24. PMID: 8915531

HarEl79: Har-El R, Silberstein A, Kuhn J, Tal M (1979). "Synthesis and degradation of lac mRNA in E. coli depleted of 30S ribosomal subunits." Mol Gen Genet 173(2);135-44. PMID: 386032

Hayakawa01: Hayakawa H, Kuwano M, Sekiguchi M (2001). "Specific binding of 8-oxoguanine-containing RNA to polynucleotide phosphorylase protein." Biochemistry 40(33);9977-82. PMID: 11502194

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jarrige01: Jarrige AC, Mathy N, Portier C (2001). "PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader." EMBO J 20(23);6845-55. PMID: 11726520

Jarrige02: Jarrige A, Brechemier-Baey D, Mathy N, Duche O, Portier C (2002). "Mutational analysis of polynucleotide phosphorylase from Escherichia coli." J Mol Biol 321(3);397-409. PMID: 12162954

Kaplan74: Kaplan R, Apirion D (1974). "The involvement of ribonuclease I, ribonuclease II, and polynucleotide phosphorylase in the degradation of stable ribonucleic acid during carbon starvation in Escherichia coli." J Biol Chem 249(1);149-51. PMID: 4358625

Kaplan75: Kaplan R, Apirion D (1975). "Decay of ribosomal ribonucleic acid in Escherichia coli cells starved for various nutrients." J Biol Chem 250(8);3174-8. PMID: 1091648

Khemici04: Khemici V, Carpousis AJ (2004). "The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers." Mol Microbiol 51(3);777-90. PMID: 14731278

Khemici04a: Khemici V, Toesca I, Poljak L, Vanzo NF, Carpousis AJ (2004). "The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: functional replacement of RhlB by RhlE." Mol Microbiol 54(5);1422-30. PMID: 15554979

Kido96: Kido M, Yamanaka K, Mitani T, Niki H, Ogura T, Hiraga S (1996). "RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli." J Bacteriol 178(13);3917-25. PMID: 8682798

Kimhi68: Kimhi Y, Littauer UZ (1968). "Purification and properties of polynucleotide phosphorylase from Escherichia coli." J Biol Chem 243(2);231-40. PMID: 4866865

Kinscherf75: Kinscherf TG, Apirion D (1975). "Polynucleotide phosphorylase can participate in decay of mRNA in Escherichia coli in the absence of ribonuclease II." Mol Gen Genet 139(4);357-62. PMID: 1102947

Krisko14: Kri Ko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Leroy02: Leroy A, Vanzo NF, Sousa S, Dreyfus M, Carpousis AJ (2002). "Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA." Mol Microbiol 45(5);1231-43. PMID: 12207692

Li02: Li Z, Reimers S, Pandit S, Deutscher MP (2002). "RNA quality control: degradation of defective transfer RNA." EMBO J 21(5);1132-8. PMID: 11867541

Li94: Li Z, Deutscher MP (1994). "The role of individual exoribonucleases in processing at the 3' end of Escherichia coli tRNA precursors." J Biol Chem 269(8);6064-71. PMID: 7509797

LinChao99: Lin-Chao S, Wei CL, Lin YT (1999). "RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity." Proc Natl Acad Sci U S A 96(22);12406-11. PMID: 10535935

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Liou01: Liou GG, Jane WN, Cohen SN, Lin NS, Lin-Chao S (2001). "RNA degradosomes exist in vivo in Escherichia coli as multicomponent complexes associated with the cytoplasmic membrane via the N-terminal region of ribonuclease E." Proc Natl Acad Sci U S A 98(1);63-8. PMID: 11134527

Liou02a: Liou GG, Chang HY, Lin CS, Lin-Chao S (2002). "DEAD box RhlB RNA helicase physically associates with exoribonuclease PNPase to degrade double-stranded RNA independent of the degradosome-assembling region of RNase E." J Biol Chem 277(43);41157-62. PMID: 12181321

Lisitsky99: Lisitsky I, Schuster G (1999). "Preferential degradation of polyadenylated and polyuridinylated RNAs by the bacterial exoribonuclease polynucleotide phosphorylase." Eur J Biochem 261(2);468-74. PMID: 10215858

Littauer57: Littauer UZ, Kornberg A (1957). "Reversible synthesis of polyribonucleotides with an enzyme from Escherichia coli." J Biol Chem 226(2);1077-92. PMID: 13438894

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Mackie89: Mackie GA (1989). "Stabilization of the 3' one-third of Escherichia coli ribosomal protein S20 mRNA in mutants lacking polynucleotide phosphorylase." J Bacteriol 171(8);4112-20. PMID: 2666387

Mathy01: Mathy N, Jarrige AC, Robert-Le Meur M, Portier C (2001). "Increased expression of Escherichia coli polynucleotide phosphorylase at low temperatures is linked to a decrease in the efficiency of autocontrol." J Bacteriol 183(13);3848-54. PMID: 11395447

MatusOrtega07: Matus-Ortega ME, Regonesi ME, Pina-Escobedo A, Tortora P, Deho G, Garcia-Mena J (2007). "The KH and S1 domains of Escherichia coli polynucleotide phosphorylase are necessary for autoregulation and growth at low temperature." Biochim Biophys Acta 1769(3);194-203. PMID: 17337072

Miczak96: Miczak A, Kaberdin VR, Wei CL, Lin-Chao S (1996). "Proteins associated with RNase E in a multicomponent ribonucleolytic complex." Proc Natl Acad Sci U S A 93(9);3865-9. PMID: 8632981

Mohanty00: Mohanty BK, Kushner SR (2000). "Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli." Mol Microbiol 36(4);982-94. PMID: 10844684

Mohanty00a: Mohanty BK, Kushner SR (2000). "Polynucleotide phosphorylase functions both as a 3' right-arrow 5' exonuclease and a poly(A) polymerase in Escherichia coli." Proc Natl Acad Sci U S A 97(22);11966-71. PMID: 11035800

Mohanty02: Mohanty BK, Kushner SR (2002). "Polyadenylation of Escherichia coli transcripts plays an integral role in regulating intracellular levels of polynucleotide phosphorylase and RNase E." Mol Microbiol 45(5);1315-24. PMID: 12207699

Mohanty03: Mohanty BK, Kushner SR (2003). "Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay." Mol Microbiol 50(2);645-58. PMID: 14617186

Morita04: Morita T, Kawamoto H, Mizota T, Inada T, Aiba H (2004). "Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli." Mol Microbiol 54(4);1063-75. PMID: 15522087

Nogueira01: Nogueira T, de Smit M, Graffe M, Springer M (2001). "The relationship between translational control and mRNA degradation for the Escherichia coli threonyl-tRNA synthetase gene." J Mol Biol 310(4);709-22. PMID: 11453682

OHara95: O'Hara EB, Chekanova JA, Ingle CA, Kushner ZR, Peters E, Kushner SR (1995). "Polyadenylylation helps regulate mRNA decay in Escherichia coli." Proc Natl Acad Sci U S A 92(6);1807-11. PMID: 7534403

Pepe94: Pepe CM, Maslesa-Galic S, Simons RW (1994). "Decay of the IS10 antisense RNA by 3' exoribonucleases: evidence that RNase II stabilizes RNA-OUT against PNPase attack." Mol Microbiol 13(6);1133-42. PMID: 7531807

Piazza96: Piazza F, Zappone M, Sana M, Briani F, Deho G (1996). "Polynucleotide phosphorylase of Escherichia coli is required for the establishment of bacteriophage P4 immunity." J Bacteriol 178(18);5513-21. PMID: 8808944

Plamann90: Plamann MD, Stauffer GV (1990). "Escherichia coli glyA mRNA decay: the role of 3' secondary structure and the effects of the pnp and rnb mutations." Mol Gen Genet 220(2);301-6. PMID: 1691434

Polissi03: Polissi A, De Laurentis W, Zangrossi S, Briani F, Longhi V, Pesole G, Deho G (2003). "Changes in Escherichia coli transcriptome during acclimatization at low temperature." Res Microbiol 154(8);573-80. PMID: 14527658

Portier75: Portier C (1975). "Quaternary structure of Escherichia coli polynucleotide phosphorylase: new evidence for a trimeric structure." FEBS Lett 50(1);79-81. PMID: 1089072

Portier87: Portier C, Dondon L, Grunberg-Manago M, Regnier P (1987). "The first step in the functional inactivation of the Escherichia coli polynucleotide phosphorylase messenger is a ribonuclease III processing at the 5' end." EMBO J 6(7);2165-70. PMID: 3308454

PrudhommeGenere04: Prud'homme-Genereux A, Beran RK, Iost I, Ramey CS, Mackie GA, Simons RW (2004). "Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'." Mol Microbiol 54(5);1409-21. PMID: 15554978

Py94: Py B, Causton H, Mudd EA, Higgins CF (1994). "A protein complex mediating mRNA degradation in Escherichia coli." Mol Microbiol 14(4);717-29. PMID: 7891559

Py96: Py B, Higgins CF, Krisch HM, Carpousis AJ (1996). "A DEAD-box RNA helicase in the Escherichia coli RNA degradosome." Nature 381(6578);169-72. PMID: 8610017

Regnier87: Regnier P, Grunberg-Manago M, Portier C (1987). "Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1." J Biol Chem 262(1);63-8. PMID: 2432069

Regonesi06: Regonesi ME, Del Favero M, Basilico F, Briani F, Benazzi L, Tortora P, Mauri P, Deho G (2006). "Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach." Biochimie 88(2);151-61. PMID: 16139413

Reuven97: Reuven NB, Zhou Z, Deutscher MP (1997). "Functional overlap of tRNA nucleotidyltransferase, poly(A) polymerase I, and polynucleotide phosphorylase." J Biol Chem 272(52);33255-9. PMID: 9407115

RobertLe92: Robert-Le Meur M, Portier C (1992). "E.coli polynucleotide phosphorylase expression is autoregulated through an RNase III-dependent mechanism." EMBO J 11(7);2633-41. PMID: 1628624

Shi08: Shi Z, Yang WZ, Lin-Chao S, Chak KF, Yuan HS (2008). "Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation." RNA 14(11);2361-71. PMID: 18812438

Skoda59: Skoda J, Kara J, Sormova Z, Sorm F (1959). "Inhibition of Escherichia coli polynucleotide phosphorylase by 6-azauridine diphosphate." Biochim Biophys Acta 33(2);579-80. PMID: 13670940

Soreq77: Soreq H, Littauer UZ (1977). "Purification and characterization of polynucleotide phosphorylase from Escherichia coli. Probe for the analysis of 3' sequences of RNA." J Biol Chem 252(19);6885-8. PMID: 330538

Takata87: Takata R, Mukai T, Hori K (1987). "RNA processing by RNase III is involved in the synthesis of Escherichia coli polynucleotide phosphorylase." Mol Gen Genet 209(1);28-32. PMID: 2823071

Takata89: Takata R, Izuhara M, Hori K (1989). "Differential degradation of the Escherichia coli polynucleotide phosphorylase mRNA." Nucleic Acids Res 17(18);7441-51. PMID: 2477797

Tuckerman11: Tuckerman JR, Gonzalez G, Gilles-Gonzalez MA (2011). "Cyclic di-GMP activation of polynucleotide phosphorylase signal-dependent RNA processing." J Mol Biol 407(5);633-9. PMID: 21320509

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Vanzo98: Vanzo NF, Li YS, Py B, Blum E, Higgins CF, Raynal LC, Krisch HM, Carpousis AJ (1998). "Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome." Genes Dev 12(17);2770-81. PMID: 9732274

Xia01: Xia B, Ke H, Inouye M (2001). "Acquirement of cold sensitivity by quadruple deletion of the cspA family and its suppression by PNPase S1 domain in Escherichia coli." Mol Microbiol 40(1);179-88. PMID: 11298285

Xu95a: Xu F, Cohen SN (1995). "RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation." Nature 374(6518);180-3. PMID: 7533264

Yamanaka01: Yamanaka K, Inouye M (2001). "Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli." J Bacteriol 183(9);2808-16. PMID: 11292800

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Zangrossi00: Zangrossi S, Briani F, Ghisotti D, Regonesi ME, Tortora P, Deho G (2000). "Transcriptional and post-transcriptional control of polynucleotide phosphorylase during cold acclimation in Escherichia coli." Mol Microbiol 36(6);1470-80. PMID: 10931296

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Zhou97b: Zhou Z, Deutscher MP (1997). "An essential function for the phosphate-dependent exoribonucleases RNase PH and polynucleotide phosphorylase." J Bacteriol 179(13);4391-5. PMID: 9209058

Zilhao96: Zilhao R, Cairrao F, Regnier P, Arraiano CM (1996). "PNPase modulates RNase II expression in Escherichia coli: implications for mRNA decay and cell metabolism." Mol Microbiol 20(5);1033-42. PMID: 8809756

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by Pathway Tools version 19.5 (software by SRI International) on Sat Apr 30, 2016, biocyc14.