Molecular and functional characterization of polynucleotide phosphorylase from the antarctic eubacterium pseudoalteromonas haloplanktis

Protein and Peptide Letters

Volumn 16, Issue 9, 2009, Pages 999-1005

  Evangelista, G ^a   Falasca, P ^a   Ruggiero, I ^b,c   Masullo, M ^b,c   Raimo, G ^a,b,c  

^a Dipartimento di Scienze e Tecnologie Ambiente e Territorio   (Italy)

^b Dipartimento di Biochimica e Biotecnologie Mediche   (Italy)

^c UNIVERSITY MAGNA GRAECIA OF CATANZARO   (Italy)

Author keywords

Activity stability relationship; Cold adapted enzymes; RNA metabolism

Indexed keywords

POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; ENZYME STABILITY; ENZYMOLOGY; METABOLISM; MOLECULAR GENETICS; MOLECULAR WEIGHT; PSEUDOALTEROMONAS; SEQUENCE ALIGNMENT; TEMPERATURE;

AMINO ACID SEQUENCE; ENZYME STABILITY; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; PSEUDOALTEROMONAS; SEQUENCE ALIGNMENT; TEMPERATURE;

PSEUDOALTEROMONAS; PSEUDOALTEROMONAS HALOPLANKTIS;

EID: 69549127735     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986609789055296     Document Type: Article

References (56)

1. Grunberg-Manago, M.; Oritz, P.J.; Ochoa, S.Enzymatic synthesis of nucleic acid like polynucleotides.Science, 1955, 122, 907-910.
2. Symmons, M.F.; Williams, M.G.; Luisi, B.F.; Jones, G.H.; Carpousis,A.J.Running rings around RNA: a superfamily of phosphate- dependent RNases.Trends Biochem.Sci., 2002, 27, 11-18.
3. Littauer, U.Z.; Soreq, H.In The Enzymes; Boyer, P., Ed., Academic Press, New York, NY, 1982, Vol.XV, pp.517-553.
4. Coburn, G.A.; Mackie, G.A.Degradation of mRNA in Escherichia coli: an old problem with some new twists.Nucleic Acid Res.Mol.Biol., 1999, 62, 55-108.
5. Cheng, Z.F.; Deutscher, M.P.Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R.Proc.Natl.Acad.Sci.USA, 2003, 100, 6388-6393.
6. Li, Z.; Reimers, S.; Pandit, S.; Deutscher M.P.RNA quality control: degradation of defective transfer RNA.EMBO J., 2002, 21, 1132-1138.
7. Houseley, J.; LaCava, J.; Tollervey, D.RNA-quality control by the exosome.Nat.Rev.Mol.Cell.Biol., 2006, 7, 529-539.
8. Clements, M.O.; Eriksson, S.; Thompson, A.; Lucchini, S.; Hinton, J.C.; Normark, S.; Rhen, M.Polynucleotide phosphorylase is global regulator of virulence and persistency in Salmonella enterica.Proc.Natl.Acad.Sci.USA, 2002, 99, 8784-8789.
9. Perrin, R.; Meyer, E.H.; Zaepfel, M.; Kim, Y.J.; Mache, R.; Grienenberger, J.M.; Gualberto, J.M.; Gagliardi, D.Two exoribonucleases act sequentially to process mature 3'-ends of atp9 mRNAs in Arabidopsis mitochondria.J.Biol.Chem., 2004, 279, 25440- 25446.
10. Mohanty, B.K.; Kushner, S.R.Polynucleotide phosphorylase functions both as a 3′ to 5′ exonuclease and a poly(A) polymerase in Escherichia coli.Proc.Natl.Acad.Sci.USA, 2000, 97, 11966- 11971.
11. Deutscher, M.P.; Li, Z.Exoribonucleases and their multiple roles in RNA metabolism.Prog.Nucl.Acid Res.Mol.Biol., 2001, 66, 67- 105.
12. Carpousis, A.J.The RNA degradosome of Escherichia coli: an mRNA degrading machine assembled on RNase E.Annu.Rev.Microbiol.2007, 61, 71-87.
13. Sarkar, D.; Fisher, P.B.Polynucleotide phosphorylase: an evolutionary conserved gene with an expanding repertoire of functions.Pharmacol.Ther.2006, 112, 243-263.
14. Slomovic, S.; Portnoy, V.; Yehudai-Resheff, S.; Bronshtein, E.; Schuster, G.Polynucleotide phosphorylase and the archaeal exosome as poly(A)-polymerases. Biochim.Biophys.Acta, 2008, 1779, 247-255.
15. Littauer, U.Z.From polynucleotide phosphorylase to neurobiology.J.Biol. Chem., 2005, 280, 38889-38897.
16. Matus-Ortega, M.E.; Regonesi, M.E.; Piña-Escobedo, A.; Tortora, P.; Dehò, G.; García-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.
17. Kelly, K.O.; Deutscher, M.P.Characterization of Escherichia coli RNase PH.J.Biol.Chem.; 1992, 267, 17153-17158.
18. Siomi, H.; Matunis, M.J.; Michael, W.M.; Dreyfuss, G.The premRNA binding K protein contains a novel evolutionarily conserved motif.Nucl.Acids Res., 1993, 21, 1193-1198.
19. Bycroft, M.; Hubbard, T.J.; Proctor, M.; Freund, S.M.; Murzin, A.G.The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.Cell, 1998, 88, 235-242.
20. Symmons, M.F.; Jones, G.H.; Luisi, B.F.A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation.Structure, 2000, 8, 1215-1226.
21. Lorentzen, E.; Walter, P.; Fribourg, S.; Evguenieva-Hackenberg, E.; Klug, G.; Conti, E.The archaeal exosome core is a hexameric ring structure with three catalytic subunits.Nat.Struct.Mol.Biol., 2005, 12, 575-581.
22. Pruijn, G.J.M.Doughnuts dealing with RNA.Nat.Struct.Mol.Biol., 2005, 12, 562-564.
23. Cheng, Z.F.; Zuo, Y.; Li, Z.; Rudd, K.E.; Deutscher, M.P.The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R.J.Biol.Chem., 1998, 273, 14077-14080.
24. Donovan, W.P.; Kushner, S.R.Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12.Proc.Natl.Acad.Sci.USA, 1986, 83, 120-124.
25. Goverde, R.L.; Huis int'Veld, J.H.J.; Kusters, J.G.; Mooi, F.R.The psychrotrophic bacterium Yersinia enterocolitica requires expression of pnp, the gene for polynucleotide phosphorylase, for growth at low temperature (5 degrees C).Mol.Microbiol., 1998, 28, 555- 569.
26. Luttinger, A.; Hahn, J.; Dubnau, D.Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis.Mol.Microbiol.1996, 19, 343-356.
27. 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, 5513-5521.
28. Zangrossi, S.; Briani, F.; Ghisotti, D.; Regonesi, M.E.; Tortora, P.; Dehò, G.Transcriptional and post-transcriptional control of polynucleotide phosphorylase during cold acclimation in Escherichia coli.Mol.Microbiol., 2000, 36, 1470-1480.
29. Jones, P.G.; van Bogelen, R.A.; Neidhardt, F.C.Induction of protein in response to low temperatures in Escherichia coli.J.Bacteriol., 1987, 169, 2092-2095.
30. Goldstein, J.; Pollitt, N.S.; Inouye, M.Major cold shock protein of Escherichia coli.Proc.Natl.Acad.Sci.USA, 1990, 87, 283-287.
31. Favaro, R.; Deh̀, G.Polynucleotide phosphorylase-deficient mutants of Pseudomonas putida.J.Bacteriol., 2003, 185, 5279-5286.
32. Robert-Le Meur, M.; Portier, C.Polynucleotide phosphorylase of Escherichia coli induces the degradation of its RNase III processed messenger by preventing its translation.Nucl.Acids Res., 1994, 22, 397-403.
33. Jarrige, A.C.; Mathy, N.; Portier, C.PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader.EMBO J., 2001, 20, 6845-6855.
34. Jarrige, A.; Brechemier-Baey, D.; Mathy, N.; Duche, O.; Portier, C.Mutational analysis of polynucleotide phosphorylase from Escherichia coli.J.Mol.Biol., 2002, 321, 397-409.
35. Regonesi, M.E.; Briani, F.; Ghetta, A.; Zangrossi, S.; Ghiotti, D.; Tortora, P.; Dehò, G.A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability.Nucl.Acids Res., 2004, 32, 1006-1017.
36. Mathy, N.; Jarrige, A.C.; Robert-Le Meur, M.; Portier, C.Increased expression of Escherichia coli polynucleotide phosphorylase at low temperatures is linked to a decrease in the efficiency of autocontrol.J.Bacteriol., 2001, 183, 3848-3854.
37. Beran, R.K.; Simons, R.W.Cold-temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation.Mol. Microbiol., 2001, 39, 112-125.
38. Gualerzi, C.O.; Giuliodori, A.M.; Pon, C.L.Transcriptional and post-transcriptional control of cold-shock genes.J.Mol.Biol., 2003, 331, 527-539.
39. Purusharth, R.I.; Madhuri, B.; Ray, M.K.Exoribonuclease R in Pseudomonas syringae Is Essential for Growth at Low Temperature and Plays a Novel Role in the 3'End Processing of 16 and 5 Ribosomal RNA.J.Biol.Chem., 2007, 282, 16267-16277.
40. Fontanella, L.; Pozzuolo, S.; Costanzo, A.; Favaro, R.; Deho,G.; Tortora, P.Photometric Assay for Polynucleotide Phosphorylase.Anal.Biochem., 1999, 269, 353-358.
41. Masullo, M.; Arcari, P.; de Paola, B.; Parmeggiani, A.; Bocchini, V.Psychrophilic elongation factor Tu from the Antarctic Pseudoalteromonas haloplanktis sp.TAC II 25.Biochemical characterization and cloning of the encoding gene.Biochemistry, 2000, 39, 15531-15539.
42. Laemmli, U.K.Cleavage of structural proteins during the assembly of the head of bacteriophage T4.Nature, 1970, 227, 680-685.
43. Bradford, M.A rapid and sensitive method for the quantitation of microgram quantities of protein utilyzing the principle of proteindye binding.Anal.Biochem., 1976, 102, 248-254.
44. Myers, E.W.; Miller, W.Description of the alignment method used in program PALIGN.CABIOS, 1988, 4, 11-23.
45. Higgins, D.G.; Sharp, P.M.CLUSTAL: a package for performing multiple alignment on a microcomputer.Gene, 1988, 73, 237-244.
46. Médigue, C.; Krin, E.; Pascal, G.; Barbe, V.; Bernsel, A.; Bertin, P.N.; Cheung, F.; Cruveiller, S.; D'Amico, S.; Duilio, A.; Fang, G.; Feller, G.; Ho, C.; Mangenot, S.; Marino, G.; Nilsson, J.; Parrilli E.; Rocha, E.P.C.; Rouy, Z.; Sekowska, A.; Tutino, M.L.; Vallenet, D.; von Heijne, G.; Danchin, A.Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125.Genome Res., 2005, 15, 1325-1335.
47. De Vendittis, E.; Castellano, I.; Cotugno, R.; Ruocco, M.R.; Raimo, G.; Masullo, M.Adaptation of model proteins from cold to hot environments involve continuous and small adjustments of average parameters related to amino acid composition.J.Theor.Biol., 2008, 250, 156-171.
48. Erickson, R.J.; Grosch, J.C.Isolation and characterization of a polynucleotide phosphorylase from Bacillus amyloliquefaciens.J.Bacteriol., 1977, 130, 869-876.
49. Srimathi, S.; Jayaraman G.; Feller G.; Danielsson B.; Narayanan, P.R.Intrinsic halotolerance of the psychrophilic a-amylase from Pseudoalteromonas haloplanktis.Extremophiles, 2007, 11, 505- 515.
50. Tronelli, D.; Maugini, E.; Bossa, F.; Pascarella, S.Structural adaptation to low temperatures - analysis of the subunit interface of oligomeric psychrophilic enzymes.FEBS J., 2007, 274, 4595-4608.
51. Ruggiero, I.; Raimo, G.; Palma, M.; Arcari, P.; Masullo, M.Molecular and functional properties of the psychrophilic elongation factor G from the Antarctic Eubacterium Pseudoalteromonas haloplanktis TAC 125.Extremophiles, 2007, 11, 699-709.
52. Masullo, M.; Raimo, G.; Bocchini, V.Resistance of archaebacterial aEF-1 alpha·GDP against denaturation by heat and urea.Biochim.Biophys.Acta, 1993, 1162, 35-39.
53. D'Amico, S.; Collins, T.; Marx, J.C.; Feller, G.; Gerday, C.Psychrophilic microrganisms: challenges for life.EMBO Rep., 2006, 7, 385-389.
54. Siddiqui, K.S.; Cavicchioli, R.Cold-adapted enzymes.Ann.Rev.Biochem., 2006, 26, 403-433.
55. Feller, G.; Gerday, C.Psychrophilic enzymes: molecular basis of cold adaptation.Cell.Mol.Life Sci., 1997, 53, 830-841. (Pubitemid 27507534)
56. Zeldovich K.B.; Berezovsky I.N.; Shakhnovich E.I.Protein and DNA sequence determinants of thermophilic adaptation.PLOS Comput.Biol., 2007, 3, 62-72.