pnp

Summary

Gene Symbol: pnp
Description: polynucleotide phosphorylase/polyadenylase
Alias: ECK3152, JW5851, bfl
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. ncbi Purification and characterization of polynucleotide phosphorylase from Escherichia coli. Probe for the analysis of 3' sequences of RNA
    H Soreq
    J Biol Chem 252:6885-8. 1977
  2. ncbi Polynucleotide phosphorylase is required for the rapid degradation of the RNase E-processed rpsO mRNA of Escherichia coli devoid of its 3' hairpin
    F Braun
    Institut de Biologie Physico Chimique, Paris, France
    Mol Microbiol 19:997-1005. 1996
  3. ncbi mRNA degradation by processive 3'-5' exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo
    R S McLaren
    Imperial Cancer Research Fund Laboratories, Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, U K
    J Mol Biol 221:81-95. 1991
  4. pmc Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12
    W P Donovan
    Proc Natl Acad Sci U S A 83:120-4. 1986
  5. ncbi 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
    P Regnier
    J Biol Chem 262:63-8. 1987
  6. pmc Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12
    C M Arraiano
    Department of Genetics, University of Georgia, Athens 30602
    J Bacteriol 170:4625-33. 1988
  7. ncbi Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation
    A J Carpousis
    Department of Molecular Biology, University of Geneva, Switzerland
    Cell 76:889-900. 1994
  8. ncbi RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation
    F Xu
    Department of Genetics, Stanford University School of Medicine, California 94305
    Nature 374:180-3. 1995
  9. pmc Polyadenylylation helps regulate mRNA decay in Escherichia coli
    E B O'Hara
    Department of Genetics, University of Georgia, Athens 30602 7223
    Proc Natl Acad Sci U S A 92:1807-11. 1995
  10. pmc Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli
    E Hajnsdorf
    Institut de Biologie Physico Chimique, Paris, France
    Proc Natl Acad Sci U S A 92:3973-7. 1995

Research Grants

  1. Purine Analog Anti-Mycobacterial Drug Development
    William Parker; Fiscal Year: 2009

Scientific Experts

  • A J Carpousis
  • Federica Briani
  • Thomas Carzaniga
  • William Parker
  • Hiroshi Hayakawa
  • G H Jones
  • Chaitanya Jain
  • Vladimir R Kaberdin
  • Bijoy K Mohanty
  • Salima Nurmohamed
  • Gianni Dehò
  • Maria Elena Regonesi
  • Ben F Luisi
  • Anastasia J Callaghan
  • Paolo Tortora
  • Sue Lin-Chao
  • Vanessa Khemici
  • Marta Del Favero
  • Cecilia M Arraiano
  • Vidya Chandran
  • George A Mackie
  • Sandro Zangrossi
  • Pei Hsun Lin
  • Devashish Rath
  • C Portier
  • S Lin-Chao
  • Nicholas De Lay
  • Jason R Tuckerman
  • Sidney R Kushner
  • E Blum
  • B K Mohanty
  • Fernando Garza-Sánchez
  • José M Andrade
  • Samantha A Chang
  • Zhonghao Shi
  • Naoki Awano
  • C F Higgins
  • Mónica Amblar
  • G A Coburn
  • Aziz Taghbalout
  • Sandra C Viegas
  • Maura Epifanía Matus-Ortega
  • N Mathy
  • A C Jarrige
  • Hitoshi Suzuki
  • M Inouye
  • B Xia
  • Maria Jose Marcaida
  • B Py
  • Leigh M Stickney
  • G G Liou
  • Zhuan Fen Cheng
  • G A Mackie
  • Leonora Poljak
  • Annie Prud'homme-Généreux
  • Jonathan A Bernstein
  • K Yamanaka
  • Teppei Morita
  • S R Kushner
  • Murray P Deutscher
  • Marc Folichon
  • Nathalie F Vanzo
  • Fatima Cairrao
  • Alessandra Polissi
  • Zhongwei Li
  • E Hajnsdorf
  • Anne Jarrige
  • Anne Leroy
  • Gunn Guang Liou
  • C L Wei
  • P Regnier
  • Suhas H Mangoli
  • T Nogueira
  • R K Beran
  • Narendra Jawali
  • Amruta R Pagedar
  • Helen A Vincent
  • Z Zhou
  • Michael R Pears
  • Susan Gottesman
  • Dijun Du
  • Julian L Griffin
  • Marie Alda Gilles-Gonzalez
  • Gonzalo Gonzalez
  • Christopher M Titman
  • S Zangrossi
  • M P Deutscher
  • W Bae
  • C Spickler
  • Bhamini Vaidialingam

Detail Information

Publications115 found, 100 shown here

  1. ncbi Purification and characterization of polynucleotide phosphorylase from Escherichia coli. Probe for the analysis of 3' sequences of RNA
    H Soreq
    J Biol Chem 252:6885-8. 1977
    ..An advantageous method was developed for synchronous phosphorolysis of RNA molecules using a molar excess of polynucleotide phosphorylase immobilized onto Sepharose...
  2. ncbi Polynucleotide phosphorylase is required for the rapid degradation of the RNase E-processed rpsO mRNA of Escherichia coli devoid of its 3' hairpin
    F Braun
    Institut de Biologie Physico Chimique, Paris, France
    Mol Microbiol 19:997-1005. 1996
    ..Moreover, we show that RNase E cuts in vitro the coding sequence of the rpsO mRNA at several sites which are not detected in vivo...
  3. ncbi mRNA degradation by processive 3'-5' exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo
    R S McLaren
    Imperial Cancer Research Fund Laboratories, Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, U K
    J Mol Biol 221:81-95. 1991
    ..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...
  4. pmc Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12
    W P Donovan
    Proc Natl Acad Sci U S A 83:120-4. 1986
    ..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 ..
  5. ncbi 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
    P Regnier
    J Biol Chem 262:63-8. 1987
    The pnp gene is located at 69 min on the Escherichia coli chromosome adjacent to the rpsO gene which encodes the ribosomal protein S15...
  6. pmc Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12
    C M Arraiano
    Department of Genetics, University of Georgia, Athens 30602
    J Bacteriol 170:4625-33. 1988
    ..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 ..
  7. ncbi Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation
    A J Carpousis
    Department of Molecular Biology, University of Geneva, Switzerland
    Cell 76:889-900. 1994
    ..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...
  8. ncbi RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation
    F Xu
    Department of Genetics, Stanford University School of Medicine, California 94305
    Nature 374:180-3. 1995
    ..the 3' exonuclease, polynucleotide phosphorylase; conversely, mutation of the polynucleotide phosphorylase-encoding pnp gene affects ribonuclease acting at the 5' end...
  9. pmc Polyadenylylation helps regulate mRNA decay in Escherichia coli
    E B O'Hara
    Department of Genetics, University of Georgia, Athens 30602 7223
    Proc Natl Acad Sci U S A 92:1807-11. 1995
    ..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...
  10. pmc Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli
    E Hajnsdorf
    Institut de Biologie Physico Chimique, Paris, France
    Proc Natl Acad Sci U S A 92:3973-7. 1995
    ..In contrast polyadenylylation does not significantly modify the stability of rpsO mRNA undergoing RNase E-mediated degradation...
  11. ncbi A DEAD-box RNA helicase in the Escherichia coli RNA degradosome
    B Py
    Nuffield Department of Clinical Biochemisstry and Imperial Cancer Research Fund Laboratories, Institute of Molecular Medicine, UK
    Nature 381:169-72. 1996
    ..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...
  12. pmc Proteins associated with RNase E in a multicomponent ribonucleolytic complex
    A Miczak
    Institute of Molecular Biology, Academia Sinica, Nankang Taipei, Taiwan, Republic of China
    Proc Natl Acad Sci U S A 93:3865-9. 1996
    ..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...
  13. pmc Polynucleotide phosphorylase of Escherichia coli is required for the establishment of bacteriophage P4 immunity
    F Piazza
    Dipartimento di Genetica e di Biologia dei Microorganismi, Universita degli Studi di Milano, Italy
    J Bacteriol 178:5513-21. 1996
    ..One such mutation, bfl-1, severely reduced P4's lysogenization frequency and delayed both the disappearance of the long transcripts that ..
  14. ncbi Sok antisense RNA from plasmid R1 is functionally inactivated by RNase E and polyadenylated by poly(A) polymerase I
    N Dam Mikkelsen
    Department of Molecular Biology, Odense University, Odense M, Denmark
    Mol Microbiol 26:311-20. 1997
    ..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...
  15. ncbi Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes
    G A Coburn
    D H Copp Building, University of British Columbia, 2146 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3, Canada
    J Mol Biol 279:1061-74. 1998
    ..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...
  16. pmc Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome
    N F Vanzo
    Laboratoire de Microbiologie et Genetique Moleculaire, UPR 9007, Centre National de la Recherche Scientifique CNRS, 31062 Toulouse Cedex, France
    Genes Dev 12:2770-81. 1998
    ....
  17. ncbi Polyadenylation promotes degradation of 3'-structured RNA by the Escherichia coli mRNA degradosome in vitro
    E Blum
    Nuffield Department of Clinical Biochemistry, Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, United Kingdom
    J Biol Chem 274:4009-16. 1999
    ..The inaccessibility of 3'-oligo(U) sequences is likely to have a role in stabilization of RNA molecules generated by Rho-independent terminators...
  18. ncbi A novel mutation in the KH domain of polynucleotide phosphorylase affects autoregulation and mRNA decay in Escherichia coli
    J Garcia-Mena
    Departamento de Genetica y Biologia Molecular, Centro de Investigacion y de Estudios Avanzados del IPN, Apdo Postal 14 740, Mexico DF 07000, Mexico
    Mol Microbiol 33:235-48. 1999
    ..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...
  19. pmc Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3' exonuclease and a DEAD-box RNA helicase
    G A Coburn
    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
    Genes Dev 13:2594-603. 1999
    ..A model for degradosome-mediated degradation of structured RNA is presented with its implications for mRNA decay in Escherichia coli...
  20. ncbi Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli
    B K Mohanty
    Department of Genetics, University of Georgia, Athens, GA 30605, USA
    Mol Microbiol 36:982-94. 2000
    ..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...
  21. pmc Escherichia coli CspA-family RNA chaperones are transcription antiterminators
    W Bae
    Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA
    Proc Natl Acad Sci U S A 97:7784-9. 2000
    ..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...
  22. ncbi Transcriptional and post-transcriptional control of polynucleotide phosphorylase during cold acclimation in Escherichia coli
    S Zangrossi
    Centro di Studio del Consiglio Nazionale delle Ricerche sulla Biologia Cellulare e Molecolare delle Piante, c o Dipartimento di Biologia, Universita degli Studi di Milano, Italy
    Mol Microbiol 36:1470-80. 2000
    ..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...
  23. pmc Polynucleotide phosphorylase functions both as a 3' right-arrow 5' exonuclease and a poly(A) polymerase in Escherichia coli
    B K Mohanty
    Department of Genetics, University of Georgia, Athens, GA 30602 7223, USA
    Proc Natl Acad Sci U S A 97:11966-71. 2000
    ..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...
  24. pmc RNA degradosomes exist in vivo in Escherichia coli as multicomponent complexes associated with the cytoplasmic membrane via the N-terminal region of ribonuclease E
    G G Liou
    Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
    Proc Natl Acad Sci U S A 98:63-8. 2001
    ..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...
  25. pmc PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader
    A C Jarrige
    UPR9073 du CNRS, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
    EMBO J 20:6845-55. 2001
    ..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 ..
  26. ncbi Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay
    Bijoy K Mohanty
    Department of Genetics, University of Georgia, Athens, GA 30602, USA
    Mol Microbiol 50:645-58. 2003
    ..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-..
  27. ncbi Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA
    Fatima Cairrao
    Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apt 127, 2781 901 Oeiras, Portugal
    Mol Microbiol 50:1349-60. 2003
    ..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...
  28. pmc Global analysis of Escherichia coli RNA degradosome function using DNA microarrays
    Jonathan A Bernstein
    Department of Genetics, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:2758-63. 2004
    ....
  29. ncbi Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E
    Anastasia J Callaghan
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    J Mol Biol 340:965-79. 2004
    ..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...
  30. ncbi 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
    Teppei Morita
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 54:1063-75. 2004
    ..We also demonstrate that the depletion of enolase but not the disruption of pnp or rhlB eliminates the rapid degradation of ptsG mRNA...
  31. ncbi The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: functional replacement of RhlB by RhlE
    Vanessa Khemici
    Laboratoire de Microbiologie et Genetique Moleculaires, UMR 5100, Centre National de la Recherche Scientifique CNRS et Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
    Mol Microbiol 54:1422-30. 2004
    ..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...
  32. ncbi An important role for RNase R in mRNA decay
    Zhuan Fen Cheng
    Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, FL 33101, USA
    Mol Cell 17:313-8. 2005
    ..These data demonstrate that RNase R, which is widespread in prokaryotes and eukaryotes, is an important participant in mRNA decay...
  33. ncbi Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach
    Maria Elena Regonesi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
    Biochimie 88:151-61. 2006
    ..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...
  34. pmc Function of the conserved S1 and KH domains in polynucleotide phosphorylase
    Leigh M Stickney
    Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
    J Bacteriol 187:7214-21. 2005
    ..The present data as well as prior observations can be rationalized by a two-step model for substrate binding...
  35. ncbi The RNA degradosome: life in the fast lane of adaptive molecular evolution
    Maria Jose Marcaida
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Trends Biochem Sci 31:359-65. 2006
    ....
  36. pmc The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells
    Bijoy K Mohanty
    Department of Genetics, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 34:5695-704. 2006
    ..The data presented here demonstrates that polyadenylation in E.coli occurs much more frequently than previously envisioned...
  37. ncbi Genetic analysis of polynucleotide phosphorylase structure and functions
    Federica Briani
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
    Biochimie 89:145-57. 2007
    ..PNPase negatively controls its own gene (pnp) expression by destabilizing pnp mRNA...
  38. ncbi The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E
    Agamemnon J Carpousis
    Laboratoire de Microbiologie et Genetique Moleculaires, Unité Mixte de Recherche 5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 31062 Toulouse, France
    Annu Rev Microbiol 61:71-87. 2007
    ....
  39. pmc Characterization of the role of ribonucleases in Salmonella small RNA decay
    Sandra C Viegas
    Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Apartado 127, 2781 901 Oeiras, Portugal
    Nucleic Acids Res 35:7651-64. 2007
    ..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...
  40. pmc PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins
    José M Andrade
    Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, 2781 901 Oeiras, Portugal
    RNA 14:543-51. 2008
    ..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...
  41. pmc RNase activity of polynucleotide phosphorylase is critical at low temperature in Escherichia coli and is complemented by RNase II
    Naoki Awano
    Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA
    J Bacteriol 190:5924-33. 2008
    ..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 ..
  42. doi Regulation of Escherichia coli polynucleotide phosphorylase by ATP
    Marta Del Favero
    Dipartimento di Biotecnologie e Bioscienze, Universita degli Studi di Milano Bicocca, 20126 Milan, Italy
    J Biol Chem 283:27355-9. 2008
    ..These findings connect RNA turnover with the energy charge of the cell and highlight unforeseen metabolic roles of PNPase...
  43. pmc Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation
    Zhonghao Shi
    Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
    RNA 14:2361-71. 2008
    ..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...
  44. pmc Autogenous regulation of Escherichia coli polynucleotide phosphorylase expression revisited
    Thomas Carzaniga
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milan, Italy
    J Bacteriol 191:1738-48. 2009
    The Escherichia coli polynucleotide phosphorylase (PNPase; encoded by pnp), a phosphorolytic exoribonuclease, posttranscriptionally regulates its own expression at the level of mRNA stability and translation...
  45. pmc Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly
    Salima Nurmohamed
    Department of Biochemistry, University of Cambridge, UK
    J Mol Biol 389:17-33. 2009
    ..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...
  46. doi Cyclic di-GMP activation of polynucleotide phosphorylase signal-dependent RNA processing
    Jason R Tuckerman
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    J Mol Biol 407:633-9. 2011
    ..We conclude that c-di-GMP can mediate signal-dependent RNA processing and that macromolecular complexes can compartmentalize c-di-GMP signaling...
  47. pmc Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli
    Salima Nurmohamed
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
    J Biol Chem 286:14315-23. 2011
    ..This communication appears to be part of a feedback network that may contribute to global regulation of metabolism and cellular energy efficiency...
  48. pmc Role of polynucleotide phosphorylase in sRNA function in Escherichia coli
    Nicholas De Lay
    Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA
    RNA 17:1172-89. 2011
    ..In our combined genetic selection and screen, we isolated hfq mutants and mutants in pnp, encoding polynucleotide phosphorylase (PNPase)...
  49. doi Involvement of pnp in survival of UV radiation in Escherichia coli K-12
    Devashish Rath
    Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
    Microbiology 158:1196-205. 2012
    ..Consequently, uvrA pnp, uvrB pnp and uvrC pnp strains show hypersensitivity to UV radiation...
  50. ncbi The role of individual exoribonucleases in processing at the 3' end of Escherichia coli tRNA precursors
    Z Li
    Department of Biochemistry, University of Connecticut Health Center, Farmington 06030 3305
    J Biol Chem 269:6064-71. 1994
    ..These studies provide the first detailed information about the specific role of individual exoribonucleases in tRNA processing, and bring us closer to defining a complete E. coli tRNA maturation pathway...
  51. ncbi Decay of the IS10 antisense RNA by 3' exoribonucleases: evidence that RNase II stabilizes RNA-OUT against PNPase attack
    C M Pepe
    Department of Microbiology and Molecular Genetics, University of California, Los Angeles 90024
    Mol Microbiol 13:1133-42. 1994
    ..We also show that wild-type RNA-OUT stability changes only two-fold across the normal range of physiological growth temperatures (30-44 degrees C) in wild-type cells, which has important implications for IS10 biology...
  52. ncbi PNPase modulates RNase II expression in Escherichia coli: implications for mRNA decay and cell metabolism
    R Zilhao
    Instituto de Technologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
    Mol Microbiol 20:1033-42. 1996
    ..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...
  53. pmc Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure
    C Spickler
    Department of Biochemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
    J Bacteriol 182:2422-7. 2000
    ..Our data provide a clear mechanistic explanation for the previous observation that RNase II and PNPase behave as functionally redundant...
  54. pmc Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli
    K Yamanaka
    Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    J Bacteriol 183:2808-16. 2001
    ..A pnp mutant, upon cold shock, maintained a high level of CSPs even after 24 h...
  55. ncbi DEAD box RhlB RNA helicase physically associates with exoribonuclease PNPase to degrade double-stranded RNA independent of the degradosome-assembling region of RNase E
    Gunn Guang Liou
    Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
    J Biol Chem 277:41157-62. 2002
    ....
  56. ncbi Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA
    Anne Leroy
    Laboratoire de Microbiologie et Génétique Moléculaire CNRS, UMR 5100, Universite Paul Sabatier, 118 rue de Narbonne, 31062 Toulouse, France
    Mol Microbiol 45:1231-43. 2002
    ..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...
  57. ncbi Polyadenylation of Escherichia coli transcripts plays an integral role in regulating intracellular levels of polynucleotide phosphorylase and RNase E
    Bijoy K Mohanty
    Department of Genetics, University of Georgia, Athens, GA 30602, USA
    Mol Microbiol 45:1315-24. 2002
    ..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...
  58. pmc The role of the S1 domain in exoribonucleolytic activity: substrate specificity and multimerization
    Mónica Amblar
    Instituto de Tecnologia Quimica e Biologica Universidade Nova de Lisboa, Oeiras, Portugal
    RNA 13:317-27. 2007
    ..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.
  59. ncbi The KH and S1 domains of Escherichia coli polynucleotide phosphorylase are necessary for autoregulation and growth at low temperature
    Maura Epifanía Matus-Ortega
    Departamento de Genetica y Biologia Molecular, Centro de Investigacion y de Estudios Avanzados, Apartado Postal 14 740, Mexico DF 07360 México, Mexico
    Biochim Biophys Acta 1769:194-203. 2007
    ..behavior of both phosphorolysis and polymerization activities of the enzyme, in particular for the double mutant Pnp-DeltaKHS1-H...
  60. pmc RNA quality control: degradation of defective transfer RNA
    Zhongwei Li
    Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, FL 33101 6129, USA
    EMBO J 21:1132-8. 2002
    ..These data indicate that quality control of stable RNA metabolism in many ways resembles normal turnover of unstable RNA...
  61. ncbi Mutational analysis of polynucleotide phosphorylase from Escherichia coli
    Anne Jarrige
    UPR 9073 du CNRS, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
    J Mol Biol 321:397-409. 2002
    ..We introduced about 30 mutations in the pnp gene by site-directed mutagenesis, most of them in phylogenetically conserved residues, and determined their ..
  62. pmc Polynucleotide phosphorylase hinders mRNA degradation upon ribosomal protein S1 overexpression in Escherichia coli
    Federica Briani
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, 20133 Milano, Italy
    RNA 14:2417-29. 2008
    The 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...
  63. ncbi Quaternary structure of Escherichia coli polynucleotide phosphorylase: new evidence for a trimeric structure
    C Portier
    FEBS Lett 50:79-81. 1975
  64. ncbi Polynucleotide phosphorylase can participate in decay of mRNA in Escherichia coli in the absence of ribonuclease II
    T G Kinscherf
    Mol Gen Genet 139:357-62. 1975
    ..These results allow to unify in a simple model a variety of observations about turnover of RNA in a variety of bacteria...
  65. ncbi Escherichia coli glyA mRNA decay: the role of 3' secondary structure and the effects of the pnp and rnb mutations
    M D Plamann
    Department of Microbiology, University of Iowa, Iowa City 52242
    Mol Gen Genet 220:301-6. 1990
    ..The results support the model of cooperative endonucleolytic and 3' to 5' exonucleolytic activities in mRNA decay...
  66. pmc Attenuation and processing of RNA from the rpsO-pnp transcription unit of Escherichia coli
    R Takata
    Nucleic Acids Res 13:7289-97. 1985
    Ribosomal 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)...
  67. ncbi Cloning of E. coli pnp gene from an episome
    C Portier
    Mol Gen Genet 183:298-305. 1981
    Starting with an F' episome harboring a transposon inserted in the pnp gene (Portier 1980), we were able to identify an EcoRI restriction fragment carrying the pnp and argG genes...
  68. pmc An essential function for the phosphate-dependent exoribonucleases RNase PH and polynucleotide phosphorylase
    Z Zhou
    Department of Biochemistry, University of Connecticut Health Center, Farmington 06030, USA
    J Bacteriol 179:4391-5. 1997
    ..Here we show that the RNase PH-negative, PNP-negative double-mutant strain actually displays a reversible cold-sensitive phenotype and that tRNA biosynthesis is ..
  69. ncbi Acquirement of cold sensitivity by quadruple deletion of the cspA family and its suppression by PNPase S1 domain in Escherichia coli
    B Xia
    Department of Biochemistry, UMDNJ Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA
    Mol Microbiol 40:179-88. 2001
    ....
  70. ncbi Reversible synthesis of polyribonucleotides with an enzyme from Escherichia coli
    U Z Littauer
    J Biol Chem 226:1077-92. 1957
  71. ncbi 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
    Vanessa Khemici
    Laboratoire de Microbiologie et Genetique Moleculaire, CNRS, UMR 5100 and Paul Sabatier Université, 118 route de Narbonne, 31062 Toulouse, France
    Mol Microbiol 51:777-90. 2004
    ....
  72. ncbi Overexpression and purification of untagged polynucleotide phosphorylases
    George H Jones
    Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
    Protein Expr Purif 32:202-9. 2003
    ..The pnp genes from Streptomyces antibioticus, Streptomyces coelicolor, and Escherichia coli were overexpressed using the ..
  73. pmc Kinetics of polynucleotide phosphorylase: comparison of enzymes from Streptomyces and Escherichia coli and effects of nucleoside diphosphates
    Samantha A Chang
    Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA 30319, USA
    J Bacteriol 190:98-106. 2008
    ..Streptomyces antibioticus, and Escherichia coli in phosphorolysis using substrates derived from the rpsO-pnp operon of S. coelicolor. The Streptomyces and E...
  74. ncbi Synthesis and degradation of lac mRNA in E. coli depleted of 30S ribosomal subunits
    R Har-El
    Mol Gen Genet 173:135-44. 1979
    ..2.25 in untreated cells) and chemical stability. The analysis of rna and pnp mutants showed that polynucleotide phosphorylase is involved in lac mRNA degradation in heat treated cells but that ..
  75. pmc Processing in the 5' region of the pnp transcript facilitates the site-specific endonucleolytic cleavages of mRNA
    R Takata
    Department of Biotechnology, College of Agriculture, Ehime University, Japan
    Nucleic Acids Res 20:847-50. 1992
    The primary transcript of pnp, the gene encoding polynucleotide phosphorylase in Escherichia coli, is processed in the 5' end region by ribonuclease III (RNase III)...
  76. pmc RNase PH: an Escherichia coli phosphate-dependent nuclease distinct from polynucleotide phosphorylase
    M P Deutscher
    Department of Biochemistry, University of Connecticut Health Center, Farmington 06032
    Proc Natl Acad Sci U S A 85:4710-4. 1988
    ..RNase PH has a molecular mass of 45-50 kDa and favors tRNA precursors as substrates. The possible physiological role of RNase PH and the advantages of phosphorolytic processing are discussed...
  77. pmc Stabilization of the 3' one-third of Escherichia coli ribosomal protein S20 mRNA in mutants lacking polynucleotide phosphorylase
    G A Mackie
    Department of Biochemistry, University of Western Ontario, London, Canada
    J Bacteriol 171:4112-20. 1989
    ..The 5' two-thirds of S20 mRNAs decays significantly more quickly than the 3' third in this latter mode of mRNA turnover...
  78. pmc Tn5 insertion in the polynucleotide phosphorylase (pnp) gene in Escherichia coli increases susceptibility to antibiotics
    L M McMurry
    J Bacteriol 169:1321-4. 1987
    ..and functionally diverse antibiotics was found to map within the gene for polynucleotide phosphorylase (pnp) and to inactivate this enzyme, which is involved in RNA breakdown...
  79. ncbi Isolation of a recombinant lambda phage carrying nusA and surrounding region of the Escherichia coli K-12 chromosome
    E W Holowachuk
    Mol Gen Genet 187:248-53. 1982
    ..5 Kb DNA fragment from the Escherichia coli chromosome. The locations of the argG, nusA and pnp genes on the 15.5 Kb DNA fragment have been determined...
  80. ncbi Use of E. coli polynucleotide phosphorylase for the synthesis of oligodeoxyribonucleotides of defined sequence
    S Gillam
    Methods Enzymol 65:687-701. 1980
  81. ncbi mRNA degradation in Escherichia coli: a novel factor which impedes the exoribonucleolytic activity of PNPase at stem-loop structures
    H Causton
    Imperial Cancer Research Fund Laboratories, Institute of Molecular Medicine, Oxford, UK
    Mol Microbiol 14:731-41. 1994
    ..Its mechanism of action, and possible role in regulating mRNA degradation, is discussed...
  82. ncbi Point mutations in a transcription terminator, lambda tI, that affect both transcription termination and RNA stability
    B Cisneros
    Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del I P N, Mexico, D F, Mexico
    Gene 181:127-33. 1996
    ..The results show that the intact hairpin of tI is essential for efficient transcription termination and for maintaining mRNA stability by blocking the 3' to 5' exonucleolytic activity of polynucleotide phosphorylase...
  83. ncbi The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold
    M Bycroft
    Department of Chemistry, University of Cambridge, United Kingdom
    Cell 88:235-42. 1997
    ..Enhanced sequence searches reveal hitherto unidentified S1 domains in RNase E, RNase II, NusA, EMB-5, and other proteins...
  84. ncbi Polyphosphate kinase is a component of the Escherichia coli RNA degradosome
    E Blum
    Nuffield Department of Clinical Biochemistry, Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, UK
    Mol Microbiol 26:387-98. 1997
    ..Thus, PPK in the degradosome appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP...
  85. pmc RNA components of Escherichia coli degradosome: evidence for rRNA decay
    D A Bessarab
    Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, Republic of China
    Proc Natl Acad Sci U S A 95:3157-61. 1998
    ..Our results, which provide evidence that decay of mature rRNAs occurs in growing Escherichia coli cells in the RNA degradosome, implicate RNase E in degradosome-mediated decay...
  86. ncbi Preferential degradation of polyadenylated and polyuridinylated RNAs by the bacterial exoribonuclease polynucleotide phosphorylase
    I Lisitsky
    Department of Biology, Israel Institute of Technology, Haifa, Israel
    Eur J Biochem 261:468-74. 1999
    ..The high affinity of PNPase for polyadenylated RNA molecules may be part of the molecular mechanism by which polyadenylated RNA is preferentially degraded in bacterial cells...
  87. pmc RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity
    S Lin-Chao
    Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
    Proc Natl Acad Sci U S A 96:12406-11. 1999
    ..coli, also has the previously unsuspected ability to affect protein degradation through its role in maturation of the 3' end of ssrA RNA...
  88. ncbi Cold-temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation
    R K Beran
    1602 Molecular Science, Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
    Mol Microbiol 39:112-25. 2001
    ..One CSR gene, pnp, encodes polynucleotide phosphorylase (PNPase), a 3'-exoribonuclease and component of the RNA degradosome...
  89. pmc Increased expression of Escherichia coli polynucleotide phosphorylase at low temperatures is linked to a decrease in the efficiency of autocontrol
    N Mathy
    UPR9073 du CNRS, Institut de Biologie PhysicoChimique, 75005 Paris, France
    J Bacteriol 183:3848-54. 2001
    ..To investigate whether this effect was transcriptional or posttranscriptional, the expression of a set of pnp-lacZ transcriptional and translational fusions was analyzed in cells grown at different temperatures...
  90. ncbi The relationship between translational control and mRNA degradation for the Escherichia coli threonyl-tRNA synthetase gene
    T Nogueira
    Institut de Biologie Physico Chimique, UPR9073 du CNRS, 13 rue Pierre et Marie Curie, Paris, 75005, France
    J Mol Biol 310:709-22. 2001
    ..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...
  91. ncbi Specific binding of 8-oxoguanine-containing RNA to polynucleotide phosphorylase protein
    H Hayakawa
    Department of Medical Biochemistry, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812 8582, Japan
    Biochemistry 40:9977-82. 2001
    ..This protein was identified as polynucleotide phosphorylase, encoded by the pnp gene. pnp(-)() mutants are hyperresistant to paraquat, a drug that induces oxidative stress in the cell...
  92. ncbi The Escherichia coli RNA degradosome: structure, function and relationship in other ribonucleolytic multienzyme complexes
    A J Carpousis
    Laboratoire de Microbiologie et Genetique Moleculaire, Centre National de la Recherche Scientifique, UMR 5100, 118 route de Narbonne, 31061 Toulouse Cedex, France
    Biochem Soc Trans 30:150-5. 2002
    ..RhlB in vitro can facilitate the degradation of structured RNA by PNPase. Since the discovery of the RNA degradosome in E. coli, related complexes have been described in other organisms...
  93. pmc The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation
    Marc Folichon
    UPR CNRS no 9073, conventionnée avec l Université Paris 7 Denis Diderot, Institut de Biologie Physico Chimique, 75005 Paris, France
    Nucleic Acids Res 31:7302-10. 2003
    ..In addition, RNase E processing, which occurred close to the U-rich sequence, is impaired by the presence of Hfq. These data suggest that Hfq modulates the sensitivity of RNA to ribonucleases in the cell...
  94. pmc A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability
    Maria Elena Regonesi
    Dipartimento di Biotecnologie e Bioscienze, Universita degli Studi di Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
    Nucleic Acids Res 32:1006-17. 2004
    Polynucleotide phosphorylase (PNPase), a 3' to 5' exonuclease encoded by pnp, plays a key role in Escherichia coli RNA decay...
  95. ncbi Design and evaluation of 5'-modified nucleoside analogs as prodrugs for an E. coli purine nucleoside phosphorylase mutant
    William B Parker
    Southern Research Institute, 2000 Ninth Ave, South, Birmingham, AL 35205, USA
    Nucleosides Nucleotides Nucleic Acids 24:387-92. 2005
    Our studies have led to the identification of an E. coli PNP mutant (M64V) that is able to cleave numerous 5'-modified nucleoside analogs with much greater efficiency than the wild-type enzyme...
  96. pmc RhlB helicase rather than enolase is the beta-subunit of the Escherichia coli polynucleotide phosphorylase (PNPase)-exoribonucleolytic complex
    Pei Hsun Lin
    Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
    Proc Natl Acad Sci U S A 102:16590-5. 2005
    ..coli PNPase complex...
  97. pmc Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing
    Hitoshi Suzuki
    Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1011 NW 15th Street, Miami, FL 33136, USA
    Nucleic Acids Res 34:e63. 2006
    ..Further analysis of the intronic RNA pool from a specific tissue or cell will provide insights into the global profile of alternative splicing...
  98. pmc Identification and characterization of growth suppressors of Escherichia coli strains lacking phosphorolytic ribonucleases
    Chaitanya Jain
    Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
    J Bacteriol 191:5622-7. 2009
    ..These results suggest that the requirement for phosphorolytic RNases for robust cellular growth and efficient ribosome assembly can be bypassed by increased expression of hydrolytic RNases...
  99. pmc RNase II is important for A-site mRNA cleavage during ribosome pausing
    Fernando Garza-Sánchez
    Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106 9610, USA
    Mol Microbiol 73:882-97. 2009
    ..We propose that RNase II degrades mRNA to the downstream border of paused ribosomes, facilitating cleavage of the A-site codon by an unknown RNase...
  100. pmc Study on the structure-function relationship of polynucleotide phosphorylase: model of a proteolytic degraded polynucleotide phosphorylase
    A Guissani
    Nucleic Acids Res 3:3015-24. 1976
    ..The phosphorolysis of polynucleotide, which is quite progressive for the native enzyme, is shown to be only partially progressive for the degraded enzyme, owing to the loss of polymer attachment sites...

Research Grants1

  1. Purine Analog Anti-Mycobacterial Drug Development
    William Parker; Fiscal Year: 2009
    ..tb activity;and (4) design and synthesis of purine and purine nucleoside analogs with selective activity against M. tb. ..