Genomes and Genes
Gene Symbol: pnp
Description: polynucleotide phosphorylase/polyadenylase
Alias: ECK3152, JW5851, bfl
Species: Escherichia coli str. K-12 substr. MG1655
- Mohanty B, Kushner S. The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells. Nucleic Acids Res. 2006;34:5695-704 pubmed..The data presented here demonstrates that polyadenylation in E.coli occurs much more frequently than previously envisioned. ..
- Tuckerman J, Gonzalez G, Gilles Gonzalez M. Cyclic di-GMP activation of polynucleotide phosphorylase signal-dependent RNA processing. J Mol Biol. 2011;407:633-9 pubmed publisher..We conclude that c-di-GMP can mediate signal-dependent RNA processing and that macromolecular complexes can compartmentalize c-di-GMP signaling. ..
- Mohanty B, Kushner S. Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Mol Microbiol. 2003;50:645-58 pubmed..coli transcripts using deletion mutations in either rnb or pnp. The data show that, in exponentially growing cells, inactivation of PNPase leads to an increase in the steady-..
- Vanzo N, Li Y, Py B, Blum E, Higgins C, Raynal L, et al. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 1998;12:2770-81 pubmed
- Nurmohamed S, Vincent H, Titman C, Chandran V, Pears M, Du D, et al. Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli. J Biol Chem. 2011;286:14315-23 pubmed publisher..This communication appears to be part of a feedback network that may contribute to global regulation of metabolism and cellular energy efficiency. ..
- Mohanty B, Kushner S. Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli. Mol Microbiol. 2000;36:982-94 pubmed..Conversely, toxicity is significantly reduced in the presence of excess RNase II. Overproduction of RNase E leads to increased polyadenylation and no reduction in toxicity. ..
- Yamanaka K, Inouye M. Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli. J Bacteriol. 2001;183:2808-16 pubmed..A pnp mutant, upon cold shock, maintained a high level of CSPs even after 24 h...
- Nurmohamed S, Vaidialingam B, Callaghan A, Luisi B. 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;389:17-33 pubmed publisher..We discuss the implications of these structural observations for the catalytic mechanism of PNPase, its processive mode of action, and its assembly into the RNA degradosome. ..
- Bernstein J, Lin P, Cohen S, Lin Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc Natl Acad Sci U S A. 2004;101:2758-63 pubmed
- Mohanty B, Kushner S. 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. 2000;97:11966-71 pubmed..In addition, the enzyme is responsible for adding the C and U residues that are found in poly(A) tails in exponentially growing cultures of wild type E. coli. ..
- Liou G, Jane W, Cohen S, Lin N, Lin Chao S. 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. 2001;98:63-8 pubmed..Our findings, which establish the existence and cellular location of RNase E-based degradosomes in vivo in E. coli, also suggest that RNA processing and decay may occur at specific sites within cells. ..
- Regonesi M, Del Favero M, Basilico F, Briani F, Benazzi L, Tortora P, et al. Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach. Biochimie. 2006;88:151-61 pubmed..In addition, we show that normalized score values obtain by MudPIT analysis may be taken as quantitative estimates of the relative protein abundance in different degradosome preparations. ..
- Jarrige A, Mathy N, Portier C. PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader. EMBO J. 2001;20:6845-55 pubmed..RNase III cleaves a long stem-loop in the pnp leader, which triggers pnp mRNA instability, resulting in a decrease in the synthesis of polynucleotide ..
- De Lay N, Gottesman S. Role of polynucleotide phosphorylase in sRNA function in Escherichia coli. RNA. 2011;17:1172-89 pubmed publisher..In our combined genetic selection and screen, we isolated hfq mutants and mutants in pnp, encoding polynucleotide phosphorylase (PNPase)...
- Callaghan A, Aurikko J, Ilag L, Günter Grossmann J, Chandran V, Kühnel K, et al. Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J Mol Biol. 2004;340:965-79 pubmed..The carboxy-terminal domain of RNase E may thus act as a flexible tether of the degradosome components. The implications of these and other observations for the organization of the RNA degradosome are discussed. ..
- Khemici V, Toesca I, Poljak L, Vanzo N, Carpousis A. 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. 2004;54:1422-30 pubmed..Thus, RhlE can replace the function of RhlB in vitro. The results in the accompanying article show that CsdA can also replace RhlB in vitro. Thus, RhlB, RhlE and CsdA are interchangeable in in vitro RNA degradation assays. ..
- Awano N, Inouye M, Phadtare S. RNase activity of polynucleotide phosphorylase is critical at low temperature in Escherichia coli and is complemented by RNase II. J Bacteriol. 2008;190:5924-33 pubmed publisher..different targets of these enzymes and stabilization of some of the PNPase-sensitive mRNAs, like fis, in the Delta pnp cells has consequences, such as accumulation of ribosomal subunits in the Delta pnp cells, which may play a role in ..
- Donovan W, Kushner S. 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. 1986;83:120-4 pubmed..Double-mutant strains carrying the pnp-7 and rnb-500 alleles (PNPase deficient and RNase II thermolabile) ceased growing in Luria broth within 30 min ..
- Carpousis A. The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol. 2007;61:71-87 pubmed
- Briani F, Del Favero M, Capizzuto R, Consonni C, Zangrossi S, Greco C, et al. Genetic analysis of polynucleotide phosphorylase structure and functions. Biochimie. 2007;89:145-57 pubmed..PNPase negatively controls its own gene (pnp) expression by destabilizing pnp mRNA...
- Jarrige A, Brechemier Baey D, Mathy N, Duché O, Portier C. Mutational analysis of polynucleotide phosphorylase from Escherichia coli. J Mol Biol. 2002;321:397-409 pubmed..We introduced about 30 mutations in the pnp gene by site-directed mutagenesis, most of them in phylogenetically conserved residues, and determined their ..
- Mohanty B, Kushner S. Polyadenylation of Escherichia coli transcripts plays an integral role in regulating intracellular levels of polynucleotide phosphorylase and RNase E. Mol Microbiol. 2002;45:1315-24 pubmed..However, transiently increasing intracellular poly(A) levels has also been shown to stabilize the pnp and rne transcripts, leading to increased polynucleotide phosphorylase (PNPase) and RNase E levels respectively...
- McLaren R, Newbury S, Dance G, Causton H, Higgins C. mRNA degradation by processive 3'-5' exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J Mol Biol. 1991;221:81-95 pubmed..These data suggest that an additional factor, such as a stem-loop binding protein, is required for stabilization of mRNA by stem-loop structures in vivo. The implications for the regulation of mRNA stability are discussed. ..
- Viegas S, Pfeiffer V, Sittka A, Silva I, Vogel J, Arraiano C. Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res. 2007;35:7651-64 pubmed..Taken together, the results of this study provide initial insight into the mechanisms of sRNA decay in Salmonella, and indicate specific contributions of the RNA decay machinery components to the turnover of individual sRNAs. ..
- Spickler C, Mackie G. Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure. J Bacteriol. 2000;182:2422-7 pubmed..Our data provide a clear mechanistic explanation for the previous observation that RNase II and PNPase behave as functionally redundant. ..
- Amblar M, Barbas A, Gomez Puertas P, Arraiano C. The role of the S1 domain in exoribonucleolytic activity: substrate specificity and multimerization. RNA. 2007;13:317-27 pubmed..In addition, we show that the S1 domain from PNPase is able to induce the trimerization of the RNaseII-PNP hybrid protein, indicating that this domain can have a role in the biogenesis of multimers.
- Zangrossi S, Briani F, Ghisotti D, Regonesi M, Tortora P, Deho G. Transcriptional and post-transcriptional control of polynucleotide phosphorylase during cold acclimation in Escherichia coli. Mol Microbiol. 2000;36:1470-80 pubmed..7.7.8) is one of the cold shock-induced proteins in Escherichia coli and pnp, the gene encoding it, is essential for growth at low temperatures...
- R gnier P, Grunberg Manago M, Portier C. 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. 1987;262:63-8 pubmedThe pnp gene is located at 69 min on the Escherichia coli chromosome adjacent to the rpsO gene which encodes the ribosomal protein S15...
- Xu F, Cohen S. RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation. Nature. 1995;374:180-3 pubmed..the 3' exonuclease, polynucleotide phosphorylase; conversely, mutation of the polynucleotide phosphorylase-encoding pnp gene affects ribonuclease acting at the 5' end...
- Andrade J, Arraiano C. PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins. RNA. 2008;14:543-51 pubmed publisher..RybB was also destabilized by PNPase. This work highlights a new role for PNPase in the degradation of small noncoding RNAs and opens the way to evaluate striking similarities between bacteria and eukaryotes. ..
- Carzaniga T, Briani F, Zangrossi S, Merlino G, Marchi P, Dehò G. Autogenous regulation of Escherichia coli polynucleotide phosphorylase expression revisited. J Bacteriol. 2009;191:1738-48 pubmed publisherThe Escherichia coli polynucleotide phosphorylase (PNPase; encoded by pnp), a phosphorolytic exoribonuclease, posttranscriptionally regulates its own expression at the level of mRNA stability and translation...
- O Hara E, Chekanova J, Ingle C, Kushner Z, Peters E, Kushner S. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc Natl Acad Sci U S A. 1995;92:1807-11 pubmed..The half-lives of individual mRNAs were increased in both a delta pcnB single mutant and a delta pcnB pnp-7 rnb-500 rne-1 multiple mutant...
- Morita T, Kawamoto H, Mizota T, Inada T, Aiba H. 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. 2004;54:1063-75 pubmed..We also demonstrate that the depletion of enolase but not the disruption of pnp or rhlB eliminates the rapid degradation of ptsG mRNA...
- Leroy A, Vanzo N, Sousa S, Dreyfus M, Carpousis A. Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA. Mol Microbiol. 2002;45:1231-43 pubmed..Although the catalytic domain of RNase E is sufficient for viability, our work demonstrates that elements in the non-catalytic part are necessary for normal activity in vivo. ..
- Coburn G, Mackie G. Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes. J Mol Biol. 1998;279:1061-74 pubmed..Moreover, decay of a model mRNA can be reconstituted in vitro by a small number of purified components in a process which is more dynamic and ATP-dependent than previously imagined. ..
- Briani F, Curti S, Rossi F, Carzaniga T, Mauri P, Dehò G. Polynucleotide phosphorylase hinders mRNA degradation upon ribosomal protein S1 overexpression in Escherichia coli. RNA. 2008;14:2417-29 pubmed publisherThe exoribonuclease polynucleotide phosphorylase (PNPase, encoded by pnp) is a major player in bacterial RNA decay. In Escherichia coli, PNPase expression is post-transcriptionally regulated at the level of mRNA stability...
- Miczak A, Kaberdin V, Wei C, Lin Chao S. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc Natl Acad Sci U S A. 1996;93:3865-9 pubmed..The FLAG-Rne complex has RNase E activity in vivo and in vitro. The relative amount of proteins associated with wild-type and Rne-3071 expressed at an elevated temperature differed. ..
- Bae W, Xia B, Inouye M, Severinov K. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc Natl Acad Sci U S A. 2000;97:7784-9 pubmed..and CspE at 37 degrees C was sufficient to induce transcription of the metY-rpsO operon genes nusA, infB, rbfA, and pnp located downstream of multiple transcription terminators...
- Del Favero M, Mazzantini E, Briani F, Zangrossi S, Tortora P, Dehò G. Regulation of Escherichia coli polynucleotide phosphorylase by ATP. J Biol Chem. 2008;283:27355-9 pubmed publisher..These findings connect RNA turnover with the energy charge of the cell and highlight unforeseen metabolic roles of PNPase. ..
- Py B, Higgins C, Krisch H, Carpousis A. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature. 1996;381:169-72 pubmed..These results suggest that RhlB acts by unwinding RNA structures that impede the processive activity of PNPase. RhlB is thus an important enzyme in mRNA turnover. ..
- Carpousis A, Van Houwe G, Ehretsmann C, Krisch H. Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell. 1994;76:889-900 pubmed..The discovery of a specific association between RNAase E and PNPase raises the intriguing possibility that these enzymes act cooperatively in the processing and degradation of RNA. ..
- Garcia Mena J, Das A, Sánchez Trujillo A, Portier C, Montanez C. A novel mutation in the KH domain of polynucleotide phosphorylase affects autoregulation and mRNA decay in Escherichia coli. Mol Microbiol. 1999;33:235-48 pubmed..Genetic and molecular analysis of one such mutant revealed that it contains a mutation in the pnp gene, which encodes the PNPase catalytic subunit alpha...
- Shi Z, Yang W, Lin Chao S, Chak K, Yuan H. Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation. RNA. 2008;14:2361-71 pubmed publisher..Taking these results together, we conclude that the constricted central channel and the basic-charged residues in the channel necks of PNPase play crucial roles in trapping RNA for processive exonucleolytic degradation. ..
- Dam Mikkelsen N, Gerdes K. Sok antisense RNA from plasmid R1 is functionally inactivated by RNase E and polyadenylated by poly(A) polymerase I. Mol Microbiol. 1997;26:311-20 pubmed..We also show that Sok RNA is polyadenylated by poly(A) polymerase I (PAP I), and that the poly(A)-tailing is prerequisite for the rapid 3'-exonucleolytic degradation by PNPase. ..
- Zilhao R, Cairrao F, Regnier P, Arraiano C. PNPase modulates RNase II expression in Escherichia coli: implications for mRNA decay and cell metabolism. Mol Microbiol. 1996;20:1033-42 pubmed..These observations suggest that the two main exonucleases are inter-regulated through a fine tuning mechanism. We discuss the implications of these results with regard to mRNA degradation and cell metabolism. ..
- Cheng Z, Deutscher M. An important role for RNase R in mRNA decay. Mol Cell. 2005;17:313-8 pubmed..These data demonstrate that RNase R, which is widespread in prokaryotes and eukaryotes, is an important participant in mRNA decay. ..
- Stickney L, Hankins J, Miao X, Mackie G. Function of the conserved S1 and KH domains in polynucleotide phosphorylase. J Bacteriol. 2005;187:7214-21 pubmed..The present data as well as prior observations can be rationalized by a two-step model for substrate binding. ..
- Li Z, Reimers S, Pandit S, Deutscher M. RNA quality control: degradation of defective transfer RNA. EMBO J. 2002;21:1132-8 pubmed..These data indicate that quality control of stable RNA metabolism in many ways resembles normal turnover of unstable RNA. ..
- Piazza F, Zappone M, Sana M, Briani F, Deho G. Polynucleotide phosphorylase of Escherichia coli is required for the establishment of bacteriophage P4 immunity. J Bacteriol. 1996;178:5513-21 pubmed..By physical mapping and genetic analysis we show that bfl-1 is allelic to pnp, which codes for polynucleotide phosphorylase, a 3'-to-5' exonucleolytic enzyme...
- Arraiano C, Yancey S, Kushner S. Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12. J Bacteriol. 1988;170:4625-33 pubmed..By constructing a series of multiple mutants containing the pnp-7 (polynucleotide phosphorylase), rnb-500 (RNase II), and ams-1 (altered message stability) alleles, it was ..
- Liou G, Chang H, Lin C, Lin Chao S. 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. 2002;277:41157-62 pubmed
- Marcaida M, DePristo M, Chandran V, Carpousis A, Luisi B. The RNA degradosome: life in the fast lane of adaptive molecular evolution. Trends Biochem Sci. 2006;31:359-65 pubmed
- Coburn G, Miao X, Briant D, Mackie G. Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3' exonuclease and a DEAD-box RNA helicase. Genes Dev. 1999;13:2594-603 pubmed..A model for degradosome-mediated degradation of structured RNA is presented with its implications for mRNA decay in Escherichia coli...
- Cairrao F, Cruz A, Mori H, Arraiano C. Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA. Mol Microbiol. 2003;50:1349-60 pubmed..The wide biological significance of RNase R regarding adaptation to cold shock and its involvement in RNA surveillance, protein quality control and pathogenesis is discussed. ..
- Rath D, Mangoli S, Pagedar A, Jawali N. Involvement of pnp in survival of UV radiation in Escherichia coli K-12. Microbiology. 2012;158:1196-205 pubmed publisher..Consequently, uvrA pnp, uvrB pnp and uvrC pnp strains show hypersensitivity to UV radiation...
- Matus Ortega M, Regonesi M, Piña Escobedo A, Tortora P, Dehò G, Garcia Mena J. The KH and S1 domains of Escherichia coli polynucleotide phosphorylase are necessary for autoregulation and growth at low temperature. Biochim Biophys Acta. 2007;1769:194-203 pubmed..behavior of both phosphorolysis and polymerization activities of the enzyme, in particular for the double mutant Pnp-DeltaKHS1-H...
- Blum E, Carpousis A, Higgins C. Polyadenylation promotes degradation of 3'-structured RNA by the Escherichia coli mRNA degradosome in vitro. J Biol Chem. 1999;274:4009-16 pubmed..The inaccessibility of 3'-oligo(U) sequences is likely to have a role in stabilization of RNA molecules generated by Rho-independent terminators...
- Hajnsdorf E, Braun F, Haugel Nielsen J, Regnier P. Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli. Proc Natl Acad Sci U S A. 1995;92:3973-7 pubmed..In contrast polyadenylylation does not significantly modify the stability of rpsO mRNA undergoing RNase E-mediated degradation. ..
- Robert Le Meur M, Portier C. E.coli polynucleotide phosphorylase expression is autoregulated through an RNase III-dependent mechanism. EMBO J. 1992;11:2633-41 pubmedIt has been previously shown that the pnp messenger RNAs are cleaved by RNase III at the 5' end and that these cleavages induce a rapid decay of these messengers...
- Feng Y, Huang H, Liao J, Cohen S. 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. 2001;276:31651-6 pubmed..Our findings raise the prospect that E. coli proteins that bind to poly(A) tails may link the functions of degradosomes and ribosomes. ..
- Seki E, Matsuda N, Kigawa T. Multiple inhibitory factor removal from an Escherichia coli cell extract improves cell-free protein synthesis. J Biosci Bioeng. 2009;108:30-5 pubmed publisher..Using this strategy to remove multiple inhibitory factors in a cell extract will be widely applicable to improve cell-free protein synthesis. ..
- Takata R, Mukai T, Hori K. Attenuation and processing of RNA from the rpsO-pnp transcription unit of Escherichia coli. Nucleic Acids Res. 1985;13:7289-97 pubmedRibosomal protein S15 and polynucleotide phosphorylase of E. coli are encoded by two adjacent genes, rpsO and pnp, respectively. Analysis of in vivo transcripts from these two genes shows that they are within the same operon (S15 operon)...
- Regnier P, Portier C. Initiation, attenuation and RNase III processing of transcripts from the Escherichia coli operon encoding ribosomal protein S15 and polynucleotide phosphorylase. J Mol Biol. 1986;187:23-32 pubmed..It is adjacent to the pnp gene, which encodes polynucleotide phosphorylase...
- Soreq H, Littauer U. Purification and characterization of polynucleotide phosphorylase from Escherichia coli. Probe for the analysis of 3' sequences of RNA. J Biol Chem. 1977;252:6885-8 pubmed..An advantageous method was developed for synchronous phosphorolysis of RNA molecules using a molar excess of polynucleotide phosphorylase immobilized onto Sepharose. ..
- Nogueira T, de Smit M, Graffe M, Springer M. The relationship between translational control and mRNA degradation for the Escherichia coli threonyl-tRNA synthetase gene. J Mol Biol. 2001;310:709-22 pubmed..Although mRNA degradation was suspected to increase the efficiency of translational control based on several considerations, our results indicate that inhibition of mRNA degradation has no effect on the level of repression by ThrRS. ..
- Reuven N, Zhou Z, Deutscher M. Functional overlap of tRNA nucleotidyltransferase, poly(A) polymerase I, and polynucleotide phosphorylase. J Biol Chem. 1997;272:33255-9 pubmed..These data show that poly(A) polymerase I and PNPase participate in the end repair process and are required to maintain functional tRNA levels when tRNA nucleotidyltransferase is absent. ..