|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 [Xu95]. 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, Li94a]. 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 [Zhou97].
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 [Liou02].
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
|MultiFun Terms:||information transfer → RNA related → RNA degradation|
|metabolism → degradation of macromolecules → RNA|
Enzymatic reaction of: polynucleotide phosporylase (polynucleotide phosphorylase)
EC Number: 188.8.131.52a 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
Enzymatic reaction of: polynucleotide phosphorylase
EC Number: 184.108.40.206(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.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 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
|Protein-Segment||77 -> 80|
|Mutagenesis-Variant||79 -> 80|
|Protein-Segment||327 -> 331|
|Mutagenesis-Variant||398 -> 399|
|Conserved-Region||553 -> 612|
|Conserved-Region||622 -> 690|
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.
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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
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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
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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
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
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
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
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
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
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
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
Liou02: 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
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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
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
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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
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
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
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
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
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
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