Exoribonucleases and their multiple roles in RNA metabolism

Progress in Nucleic Acid Research and Molecular Biology

Volumn 66, Issue , 2000, Pages 67-105

  Deutscher, Murray P ^a   Li, Zhongwei ^a  

^a UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; EXORIBONUCLEASE; FUNGAL PROTEIN; MESSENGER RNA;

CHEMISTRY; CHLOROPLAST; ENZYMOLOGY; METABOLISM; MULTIGENE FAMILY; PHYSIOLOGY; PROTEIN BINDING; REVIEW;

BACTERIAL PROTEINS; CHLOROPLASTS; EXORIBONUCLEASES; FUNGAL PROTEINS; MULTIGENE FAMILY; PROTEIN BINDING; RNA, MESSENGER;

EID: 0035193362     PISSN: 00796603     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0079-6603(00)66027-0     Document Type: Review

References (194)

1. A.W Nicholson Function, mechanism and regulation of bacterial ribonucleases FEMS Microbiol. Rev. 23 1999 371 390
2. G.A Coburn G.A Mackie Degradation of mRNA in Escherichia coli: an old problem with some new twists Prog. Nucleic Acid Res. Mot. Biol. 62 1999 55 108
3. A.J Carpousis N.F Vanzo L.C Raynal mRNA degradation. A tale of poly(A) and multiprotein machines Trends Genet. 15 1999 24 28
4. C.J Decker The exosome: a versatile RNA processing machine Curr. Biol. 8 1998 R238 R240
5. M.P Deutscher Promiscuous exoribonucleases of Escherichia coli J. Bacteriol. 175 1993 4577 4583
6. M Viswanathan S.T Lovett Exonuclease X of Escherichia coli . A novel 3′–5′ DNase and dnaQ superfamily member involved in DNA repair J. Biol. Chem. 274 1999 30094 30100
7. W.P Donovan S.R Kushner Polynucleotide phosphorylase and ribonuclease 11 are required for cell viability and mRNA turnover in Escherichia coli K-12 6th ed. Proc. Natl. Acad. Sci. USA 83 1986 120 124
8. S Ghosh M.P Deutscher Oligoribonuclease is an essential component of the mRNA decay pathway 6th ed. Proc. Natl. Acad. Sci. USA 96 1999 4372 4377
9. Z Li M.P Deutscher Maturation pathways for E. coli tRNA precursors: a random multienzyme process in vivo Cell 86 1996 503 512
10. Z Li S Pandit M.P Deutscher 3′ exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli 6th ed. Proc. Natl. Acad. Sci. USA 95 1998 2856 2861
11. Z Li M.P Deutscher The tRNA processing enzyme RNase T is essential for maturation of 5S RNA Proc. Natl. Acad. Sci. USA 92 1995 6883 6886
12. Z Li S Pandit M.P Deutscher Maturation of 23S ribosomal RNA requires the exoribonuclease RNase T RNA 5 1999 139 146
13. K.O Kelly M.P Deutscher The presence of only one of five exoribonucleases is sufficient to support the growth of Escherichia coli J Bacteriol. 174 1992 6682 6684
14. I.S Mian Comparative sequence analysis of ribonucleases HII, III, II, PH, and D Nucleic Acids Res. 25 1997 3187 3195
15. V Shen D Schlessinger RNase I, II and IV of Escherichia coli 6th ed. P.D Boyer The Enzymes Vol. XV 1982 Academic Press New York 501 515 part B
16. M.P Deutscher N.B Reuven Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis 6th ed. Proc. Natl. Acad. Sci. USA 88 1991 3277 3280
17. Z.F Cheng Y Zuo Z Li K.E Rudd M.P Deutscher The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R J. Biol. Chem. 273 1998 14077 14080
18. G.A Coburn G.A Mackie Overexpression, purification, and properties of Escherichia coli ribonuclease II J. Biol. Chem. 271 1996 1048 1053
19. G Guarneros C Portier Different specificities of ribonuclease II and polynucleotide phosphorylase in TmRNA decay Biochimie 72 1990 771 777
20. V.J Cannistraro D Kennell The processive reaction mechanism of ribonuclease II J. Mol. Biol. 243 1994 930 943
21. V.J Cannistraro D Kennell The reaction mechanism of ribonuclease II and its interaction with nucleic acid secondary structures Biochim. Biophys. Acta 1433 1999 170 187
22. G.A Coburn G.A Mackie Differential sensitivities of portions of the mRNA for ribosomal protein S20 to 3′-exonucleases dependent on oligoadenylation and RNA secondary structure J. Biol. Chem. 271 1996 15776 15781
23. R Zilhao L Camelo C.M Arraiano DNA sequencing and expression of the gene rnb encoding Escherichia coli ribonuclease II Mol. Microbiol. 8 1993 43 51
24. R Zilhao F Cairrao P Regnier C.M Arraiano PNPase modulates RNase II expression in Escherichia coli: implications for mRNA decay and cell metabolism Mol. Microbiol. 20 1996 1033 1042
25. N Nikolaev V Folsom D Schlessinger Escherichia coli mutants deficient in exoribonucleases Biochem. Biophys. Res. Commun. 70 1976 920 924
26. T Kasai R.S Gupta D Schlessinger Exoribonucleases in wild type Escherichia coli and RNase II-deficient mutants J. Biol. Chem. 252 1977 8950 8956
27. M Bycroft T.J Hubbard M Proctor S.M Freund A.G Murzin The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold Cell 88 1997 235 242
28. T Tobe C Sasakawa N Okada Y Houma M Yoshikawa vacB, a novel chromosomal gene required for expression of virulence genes on the large plasmid of Shigella flexneri J. Bacteriol. 174 1992 6359 6367
29. W Wang D.H Bechhofer Properties of a Bacillus subtilis polynucleotide phosphorylase deletion strain J. Bacteriol. 178 1996 2375 2382
30. D.H Bechhofer W Wang Decay of ermC mRNA in a polynucleotide phosphorylase mutant of Bacillus subtilis J. Bacteriol. 180 1998 5968 5977
31. P Mitchell E Petfalski A Shevchenko M Mann D Tollervey The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′→5′ exoribonucleases Cell 91 1997 457 466
32. E Noguchi N Hayashi Y Azuma T Seki M Nakamura N Nakashima M Yanagida X He U Mueller S Sazer T Nishimoto Dis3, implicated in mitotic control, binds directly to Ran and enhances the GEF activity of RCC1 EMBO J. 15 1996 5595 5605
33. H Ohkura Y Adachi N Kinoshita O Niwa T Toda M Yanagida Cold-sensitive and caffeine-supersensitive mutants of the Schizosaccharoinyces pombe dis genes implicated in sister chromatid separation during mitosis EMBO J. 7 1988 1465 1473
34. + gene encodes a 110-kDa essential protein implicated in mitotic control Mol. Cell Biol. 11 1991 5839 5847
35. T Shiomi K Fukushima N Suzuki N Nakashima E Noguchi T Nishimoto Human Dis3p, which binds to either GTP- or GDP-Ran, complements Saccharomyces cerevisiae dis3 J. Biochem. (Tokyo) 123 1998 883 890
36. A Sutton D Immanuel K.T Arndt The SIT4 protein phosphatase functions in late G1 for progression into S phase Mol. Cell Biol. 11 1991 2133 2148
37. R.B Wilson A.A Brenner T.B White M.J Engler J.P Gaughran K Tatchell The Saccharomyces cerevisiae SRKI gene, a suppressor of bcyl and insl, may be involved in protein phosphatase function Mol. Cell Biol. 11 1991 3369 3373
38. Y Uesono A Fujita A Toh-e Y Kikuchi The MCS11SSDIISRKIISSLI gene is involved in stable maintenance of the chromosome in yeast Gene 143 1994 135 138
39. Y Uesono A Toh-e Y Kikuchi Ssdlp of Saccharomyces cerevisiae associates with RNA J. Biol. Chem. 272 1997 16103 16109
40. B.G Luukkonen B Seraphin A conditional U5 snRNA mutation affecting pre-mRNA splicing and nuclear pre-mRNA retention identifies SSDl/SRKI as a general splicing mutant suppressor Nucleic Acids Res. 27 1999 3455 3465
41. J.J Min H.P Zassenhaus Characterization of a novel NTP-dependent 3′ exoribonuclease from yeast mitochondria SAAS Bull. Biochem. Biotechnol. 4 1991 1 5
42. A Dmochowska P Golik P.P Stepien The novel nuclear gene DSS-1 of Saccharomyces cerevisiae is necessary for mitocbondrial biogenesis Curr Genet. 28 1995 108 112
43. A Dziembowski M Malewiez M Minczuk P Golik A Dmochowska P.P Stepien The yeast nuclear gene DSS1, which codes for a putative RNase II, is necessary for the function of the mitochondria) degradosome in processing and turnover of RNA Mol. Gen. Genet. 260 1998 108 114
44. B Turcq K.F Dobinson N Serizawa A.M Lambowitz A protein required for RNA processing and splicing in Neurospora mitochondria is related to gene products involved in cell cycle protein phosphatase functions 6th ed. Proc. Natl. Acad. Sci. USA 89 1992 1676 1680
45. G Garriga H Bertrand A.M Lambowitz RNA splicing in Neurospora mitochondria: nuclear mutants defective in both splicing and 3′ end synthesis of the large rRNA Cell 36 1984 623 634
46. H Bertrand P Bridge R.A Collins G Garriga A.M Lambowitz RNA splicing in Neurospora mitochondria. Characterization of new nuclear mutants with defects in splicing the mitochondrial large rRNA Cell 29 1982 517 526
47. K.F Dobinson M Henderson R.L Kelley R.A Collins A.M Lambowitz Mutations in nuclear gene cyt-4 of Neurospora crassa result in pleiotropic defects in processing and splicing of mitochondria) RNAs Genetics 123 1989 97 108
48. M.J Moser W.R Holley A Chatterjee I.S Mian The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains Nucleic Acids Res. 25 1997 5110 5118
49. E.V Koonin M.P Deutscher RNase T shares conserved sequence motifs with DNA proofreading exonucleases Nucleic Acids Res. 21 1993 2521 2522
50. T.A Steitz J.A Steitz A general two-metal-ion mechanism for catalytic RNA 6th ed. Proc. Natl. Acad. Sci. USA 90 1993 6498 6502
51. R.K Ghosh M.P Deutscher Purification of potential 3′ processing nucleases using synthetic tRNA precursors Nucleic Acids Res. 5 1978 3831 3842
52. H Cudny R Zaniewski M.P Deutscher Escherichia coli RNase D. Purification and structural characterization of a putative processing nuclease J. Biol. Chem. 256 1981 5627 5632
53. H Cudny R Zaniewski M.P Deutscher Escherichia coli RNase D. Catalytic properties and substrate specificity J. Biol. Chem. 256 1981 5633 5637
54. R.K Ghosh M.P Deutscher Identification of an Escherichia coli nuclease acting on structurally altered transfer RNA molecules J. Biol. Chem. 253 1978 997 1000
55. H Cudny M.P Deutscher Apparent involvement of ribonuclease D in the 3′ processing of tRNA precursors 6th ed. Proc. Natl. Acad. Sci. USA 77 1980 837 841
56. J.R Zhang M.P Deutscher Escherichia coli RNase D: sequencing of the rnd structural gene and purification of the overexpressed protein Nucleic Acids Res. 16 1988 6265 6278
57. R.T Blouin R Zaniewski M.P Deutscher Ribonuclease D is not essential for the normal growth of Escherichia coli or bacteriophage T4 or for the biosynthesis of a T4 suppressor tRNA J. Biol. Chem. 258 1983 1423 1426
58. N.B Reuven M.P Deutscher Multiple exoribonucleases are required for the 3′ processing of Escherichia coli tRNA precursors in vivo FASEB J. 7 1993 143 148
59. R Zaniewski M.P Deutscher Genetic mapping of mutation in Escherichia coli leading to a temperature-sensitive RNase D Mol. Gen. Genet. 185 1982 142 147
60. J.R Zhang M.P Deutscher Analysis of the upstream region of the Escherichia coli rnd gene encoding RNase D. Evidence for translational regulation of a putative tRNA processing enzyme J. Biol. Chem. 264 1989 18228 18233
61. J.R Zhang M.P Deutscher A uridine-rich sequence required for translation of prokaryotic mRNA 6th ed. Proc. Natl. Acad. Sci. USA 89 1992 2605 2609
62. C.G Korner E Wahle Poly(A) tail shortening by a mammalian poly(A)-specific 3′ exoribonuclease J. Biol. Chem. 272 1997 10448 10456
63. C.G Korner M Wormington M Muckenthaler S Schneider E Dehlin E Wahle The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes EMBO J. 17 1998 5427 5437
64. M.W Briggs K.T Burkard J.S Butler Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3′ end formation J. Biol. Chem. 273 1998 13255 13263
65. C Allmang J Kufel G Chanfreau P Mitchell E Petfalski D Tollervey Functions of the exosome in rRNA, snoRNA, and snRNA synthesis EMBO J. 18 1999 5399 5410
66. C Allmang E Petfalski A Podtelejnikov M Mann D Tollervey P Mitchell The yeast exosome and human PM-Scl are related complexes of 3′→5′ exonucleases Genes Dev. 13 1999 2148 2158
67. M Bluthner F.A Bautz Cloning and characterization of the cDNA coding for a polymyositis-scleroderma overlap syndrome-related nucleolar 100-kD protein J. Exp. Med. 176 1992 973 980
68. Q Ge M.B Frank C O'Brien I.N Targoff Cloning of a complementary DNA coding for the 100-kD antigenic protein of the PM-Scl autoantigen J. Clin. Invest. 90 1992 559 570
69. M.P Deutscher C.W Marlor R Zaniewski Ribonuclease T: new exoribonuclease possibly involved in end-turnover of tRNA 6th ed. Proc. Natl. Acad. Sci. USA 81 1984 4290 4293
70. M.P Deutscher Ribonucleases, tRNA nucleotidyltransferase, and the 3′ processing of tRNA Prog. Nucleic Acid Res. Mol. Biol. 39 1990 209 240
71. M.P Deutscher C.W Marlor R Zaniewski RNase T is responsible for the end-turnover of tRNA in Escherichia coli 6th ed. Proc. Natl. Acad. Sci. USA 82 1985 6427 6430
72. K.P Padmanabha M.P Deutscher RNase T affects Escherichia coli growth and recovery from metabolic stress J. Bacteriol. 173 1991 1376 1381
73. M.P Deutscher C.W Marlor Purification and characterization of Escherichia coli RNase T J. Biol. Chem. 260 1985 7067 7071
74. Z Li L Zhan M.P Deutscher The role of individual cysteine residues in the activity of Escherichia coli RNase T J. Biol. Chem. 271 1996 1127 1132
75. S Huang M.P Deutscher Sequence and transcriptional analysis of the Escherichia coli rut gene encoding RNase T J. Biol. Chem. 267 1992 25609 25613
76. Z Li L Zhan M.P Deutscher Escherichia coli RNase T functions in vivo as a dimer dependent on cysteine 168 J. Biol. Chem. 271 1996 1133 1137
77. M Viswanathan K.W Dower S.T Lovett Identification of a potent DNase activity associated with RNase T of Escherichia coli J. Biol. Chem. 273 1998 35126 35131
78. M Viswanathan A Lanjuin S.T Lovett Identification of RNase T as a high-copy suppressor of the UV sensitivity associated with single-strand DNA exonuclease deficiency in Escherichia coli Genetics 151 1999 929 934
79. Y Zuo M.P Deutscher The DNase activity of RNase T and its application to DNA cloning Nucleic Acids Res. 27 1999 4077 4082
80. L.M Case X.N Chen M.P Deutscher Localization of the Escherichia coli rat gene encoding RNase T by using a combination of physical and genetic mapping J. Bacteriol. 171 1989 5736 5737
81. N.B Reuven E.V Koonin K.E Rudd M.P Deutscher The gene for the longest known Escherichia coli protein is a member of helicase superfamily II J. Bacteriol. 177 1995 5393 5400
82. R Boeck S.Z Tarun Jr. M Rieger J.A Deardorff S Muller-Auer A.B Sachs The yeast Pant protein is required for poly(A)-binding protein-stimulated poly(A)-nuclease activity J. Biol. Chem. 271 1996 432 438
83. C.E Brown S.Z Tarun Jr. R Boeck A.B Sachs PANS encodes a subunit of the Pablp-dependent poly(A) nuclease in Saccharomyces cerevisiae Mol. Cell Biol. 16 1996 5744 5753
84. S.K Niyogi A.K Datta A novel oligoribonuclease of Escherichia coli . I. Isolation and properties J. Biol. Chem. 250 1975 7307 7312
85. A.K Datta S.K Niyogi A novel oligoribonuclease of Escherichia coli . II. Mechanism of action J. Biol. Chem. 250 1975 7313 7319
86. D Yu M.P Deutscher Oligoribonuclease is distinct from the other known exoribonueleases of Escherichia coli J. Bacteriol. 177 1995 4137 4139
87. X Zhang L Zhu M.P Deutscher Oligoribonuclease is encoded by a highly conserved gene in the 3′–5′ exonuclease superfamily J. Bacteriol. 180 1998 2779 2781
88. U.Z Littauer H Soreq Polynucleotide phosphorylase 6th ed. P.O Boyer The Enzymes Vol. XV 1982 Academic Press New York 518 553 part B
89. E.V Koonin A conserved ancient domain joins the growing superfamily of 3′–5′ exonucleases Curr. Biol. 7 1997 R604 606
90. P.K Asha R.T Blouin R Zaniewski M.P Deutscher Ribonuclease BN: identification and partial characterization of a new tRNA processing enzyme 6th ed. Proc. Natl. Acad. Sci. USA 80 1983 3301 3304
91. J.G Seidman F.J Schmidt K Foss W.H McClain A mutant of Escherichia coli defective in removing 3′ terminal nucleotides from some transfer RNA precursor molecules Cell 5 1975 389 400
92. A.N Maisurian E.A Buyanovskaya Isolation of an Escherichia coli strain restricting bacteriophage suppressor Mol. Gen. Genet. 120 1973 227 229
93. P.K Asha M.P Deutscher Escherichia coli CAN lacks a tRNA-processing nuclease J. Bacteriol. 156 1983 419 420
94. C Callahan D Neri-Cortes M.P Deutscher Purification and characterization of the tRNA processing enzyme RNase BN J. Biol. Chem. 275 2000 1030 1034
95. C Callahan M.P Deutscher Identification and characterization of the Escherichia coli rbn gene encoding the tRNA processing enzyme RNase BN J. Bacteriol. 178 1996 7329 7332
96. N.B Reuven Z Zhou M.P Deutscher Functional overlap of tRNA nucleotidyltransferase, poly(A) polymerase I, and polynucleotide phosphorylase J. Biol. Chem. 272 1997 33255 33259
97. G.A Coburn G.A Mackie Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes J. Mol. Biol. 279 1998 1061 1074
98. C Portier Quaternary structure of Escherichia coli polynucleotide phosphorylase: new evidence for a trimeric structure FEBS Lett. 50 1975 79 81
99. P Regnier M Grunberg-Manago C Portier 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 1987 63 68
100. C Portier Quaternary structure of polynucleotide phosphorylase from Escherichia coli : evidence of a complex between two types of polypeptide chains Eur. J. Biochem. 55 1975 573 582
101. B Py C.F Higgins H.M Krisch A.J Carpousis A DEAD-box RNA helicase in the Escherichia coli RNA degradosome Nature 381 1996 169 172
102. A Miczak V.R Kaberdin C.L Wei S Lin-Chao Proteins associated with RNase E in a multicomponent ribonucleolytic complex 6th ed. Proc. Natl. Acad. Sci. USA 93 1996 3865 3869
103. A.J Carpousis G Van Houwe C Ehretsmann H.M Krisch Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation Cell 76 1994 889 900
104. R.S McLaren S.F Newbury G.S Dance H.C Causton C.F Higgins mRNA degradation by processine 3−5′ exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo J. Mol. Biol. 221 1991 81 95
105. F Xu S.N Cohen RNA degradation in Escherichia coli regulated by 3′ adenylation and 5′ phosphorylation Nature 374 1995 180 183
106. I Lisitsky G Schuster Preferential degradation of polyadenylated and polyuridinylated RNAs by the bacterial exoribonuclease polynucleotide phosphorylase Eur. J. Biochem. 261 1999 468 474
107. K.E Rudd Linkage map of Escherichia coli K-12, edition 10: the physical map Microbiol. Mol. Biol. Rev. 62 1998 985 1019
108. S Evans P.P Dennis Promoter activity and transcript mapping in the regulatory region for genes encoding ribosomal protein S15 and polynucleotide phosphorylase of Escherichia coli Gene 40 1985 15 22
109. C Portier L Dondon M Grunberg-Manago P Regnier 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 1987 2165 2170
110. M Robert-Le Meur C Portier E. coli polynucleotide phosphorylase expression is autoregulated through an RNase III-dependent mechanism EMBO J. 11 1992 2633 2641
111. M Robert-Le Meur C Portier Polynucleotide phosphorylase of Escherichia coli induces the degradation of its RNase III processed messenger by preventing its translation Nucleic Acids Res. 22 1994 397 403
112. J Garcia-Mena A Das A Sanchez-Trujillo C Portier C Montanez A novel mutation in the KH domain of polynueleotide phosphorylase affects autoregulation and mRNA decay in Escherichia coli Mol. Microbiol. 33 1999 235 248
113. L.M McMurry S.B Levy Tn5 insertion in the polynueleotide phosphorylase (pnp) gene in Escherichia coli increases susceptibility to antibiotics J. Bacteriol. 169 1987 1321 1324
114. A Luttinger J Hahn D Dubnau Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis Mol. Microbiol. 19 1996 343 356
115. P.G Jones R.A VanBogelen F.C Neidhardt Induction of proteins in response to low temperature in Escherichia coli J. Bacteriol. 169 1987 2092 2095
116. D.J Clarke B.C Dowds The gene coding for polynueleotide phosphorylase in Photorhabdus sp. strain K122 is induced at low temperatures J. Bacteriol. 176 1994 3775 3784
117. R.L Goverde J.H Huis in't Veld J.G Kusters F.R Mooi The psychrotrophic bacterium Yersinia enterocolitica requires expression of pap, the gene for polynueleotide phosphorylase, for growth at low temperature (5°C) Mol. Microbiol. 28 1998 555 569
118. Z Zhou M.P Deutscher An essential function for the phosphate-dependent exoribonucleases RNase PH and polynueleotide phosphorylase J. Bacteriol. 179 1997 4391 4395
119. S.G Chaney P.D Boyer Incorporation of water oxygens into intracellular nucleotides and RNA. II. Predominantly hydrolytic RNA turnover in Escherichia coli J. Mol. Biel. 64 1972 581 591
120. G.H Jones M.J Bibb Guanosine pentaphosphate synthetase from Streptomyces antibioticus is also a polynueleotide phosphorylase J. Bacteriol. 178 1996 4281 4288
121. R Hayes J Kudla G Schuster L Gabay P Maliga W Gruissem Chloroplast mRNA 3′-end processing by a high molecular weight protein complex is regulated by nuclear encoded RNA binding proteins EMBO J. 15 1996 1132 1141
122. I Lisitsky A Kotler G Schuster The mechanism of preferential degradation of polyadenylated RNA in the chloroplast. The exoribonuclease 100RNP/polynueleotide phosphorylase displays high binding affinity for poly(A) sequence J. Biol. Chem. 272 1997 17648 17653
123. Q.S Li J.D Gupta A.G Hunt Polynucleotide phosphorylase is a component of a novel plant poly(A) polymerase J. Biol. Chem. 273 1998 17539 17543
124. H Cudny M.P Deutscher 3′ processing of tRNA precursors in ribonuclease-deficient Escherichia coli . Development and characterization of an in vitro processing system and evidence for a phosphate requirement J. Biol. Chem. 263 1988 1518 1523
125. M.P Deutscher G.T Marshall H Cudny RNase PH: an Escherichia coli phosphatedependent nuclease distinct from polynueleotide phosphorylase 6th ed. Proc. Natl. Acad. Sci. USA 85 1988 4710 4714
126. K.A Ost M.P Deutscher Escherichia coli orfE (upstream of pyrE) encodes RNase PH J. Bacteriol. 173 1991 5589 5591
127. K.F Jensen J.T Andersen P Poulsen Overexpression and rapid purification of the orjE/rph gene product, RNase PH of Escherichia coli J. Biol. Chem. 267 1992 17147 17152
128. K.O Kelly M.P Deutscher Characterization of Escherichia coli RNase PH J. Biol. Chem. 267 1992 17153 17158
129. P Poulsen K.F Jensen P Valentin-Hansen P Carlsson L.G Lundberg Nucleotide sequence of the Escherichia coli pyrE gene and of the DNA in front of the protein-coding region Eur. J. Biochem. 135 1983 223 229
130. K.A Ost M.P Deutscher RNase PH catalyzes a synthetic reaction, the addition of nucleotides to the 3′ end of RNA Biochimie 72 1990 813 818
131. Z Li M.P Deutscher The role of individual exoribonucleases in processing at the 3′ end of Escherichia coli tRNA precursors J. Biol. Chem. 269 1994 6064 6071
132. P Poulsen F Bonekamp K.F Jensen Structure of the Escherichia coli pyrE operon and control of pyrE expression by a UTP modulated intercistronic attentuation EMBO J. 3 1984 1783 1790
133. K.F Jensen The Escherichia coli K-12 “wild types” W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels J. Bacteriol. 175 1993 3401 3407
134. P Poulsen J.T Andersen K.F Jensen Molecular and mutational analysis of three genes preceding pyrE on the Escherichia coli chromosome Mol. Microbiol. 3 1989 393 404
135. K.O Kelly N.B Reuven Z Li M.P Deutscher RNase PH is essential for tRNA processing and viability in RNase-deficient Escherichia coli cells J. Biol. Chem. 267 1992 16015 16018
136. M.G Craven D.J Henner D Alessi A.T Schauer K.A Ost M.P Deutscher D.I Friedman Identification of the rph (RNase PH) gene of Bacillus subtilis : evidence for suppression of cold-sensitive mutations in Escherichia coli J. Bacteriol. 174 1992 4727 4735
137. L Benard K Carroll R.C Valle R.B Wickner Ski6p is a homolog of RNA-processing enzymes that affects translation of non-poly(A) mRNAs and 60S ribosomal subunit biogenesis Mol. Cell Biol. 18 1998 2688 2696
138. J.S Jacobs A.R Anderson R.P Parker The 3′ to 5′ degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3′ to 5′ exonucleases of the exosome complex EMBO J. 17 1998 1497 1506
139. N.I Zanchin D.S Goldfarb The exosome subunit Rrp43p is required for the efficient maturation of 5.8S, 18S and 25S rRNA Nucleic Acids Res. 27 1999 1283 1288
140. J.A Solinger D Pascolini W.D Heyer Active-site mutations in the Xrn1p exoribonuclease of Saccharomyces cerevisiae reveal a specific role in meiosis Mol. Cell Biol. 19 1999 5930 5942
141. G Caponigro R Parker Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae Microbiol. Rev. 60 1996 233 249
142. A Stevens An exoribonuclease from Saccharomyces cerevisiae : effect of modifications of 5′ end groups on the hydrolysis of substrates to 5′ mononucleotides Biochem. Biophys. Res. Commun. 81 1978 656 661
143. A Stevens Evidence for a 5′ leads to 3′ direction of hydrolysis by a 5' mononucleotide-producing exoribonuclease from Saccharomyces cerevisiae Biochem. Biophys. Res. Commun. 86 1979 1126 1132
144. A Stevens Purification and characterization of a Saccharomyces cerevisiae exoribonuclease which yields 5′-mononucleotides by a 5′ to 3′ mode of hydrolysis J. Biol. Chem. 255 1980 3080 3085
145. A Stevens M.K Maupin A 5′-3′ exoribonuclease of Saccharomyces cerevisiae : size and novel substrate specificity Arch. Biochem. Biophys. 252 1987 339 347
146. F.W Larimer A Stevens Disruption of the gene XRN1, coding for a 5′→3′ exoribonuclease, restricts yeast cell growth Gene 95 1990 85 90
147. F.W Larimer C.L Hsu M.K Maupin A Stevens Characterization of the XRN1 gene encoding a 5′→3′ exoribonuclease: sequence data and analysis of disparate protein and mRNA levels of gene-disrupted yeast cells Gene 120 1992 51 57
148. W.D Heyer A.W Johnson U Reinhart R.D Kolodner Regulation and intracellular localization of Saccharomyces cerevisiae strand exchange protein 1 (Sep1/XrnI/Keml), a multifunctional exonuclease Mol. Cell Biol. 15 1995 2728 2736
149. J Kim P.O Ljungdahl G.R Fink kem mutations affect nuclear fusion in Saccharomyces cerevisiae Genetics 126 1990 799 812
150. C.L Hsu A Stevens Yeast cells lacking 5′→3′ exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure Mol. Cell Biol. 13 1993 4826 4835
151. D Muhlrad C.J Decker R Parker Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5′→3′ digestion of the transcript Genes Dev. 8 1994 855 866
152. C.J Decker R Parker A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation Genes Dev. 7 1993 1632 1643
153. Y Henry H Wood J.P Morrissey E Petfalski S Kearsey D Tollervey The 5′ end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site EMBO J. 13 1994 2452 2463
154. E Petfalski T Dandekar Y Henry D Tollervey Processing of the precursors to small nucleolar RNAs and rRNAs requires common components Mol. Cell Biol. 18 1998 1181 1189
155. A Stevens C.L Hsu K.R Isham F.W Larimer Fragments of the internal transcribed spacer 1 of pre-rRNA accumulate in Saccharomyces cerevisiae lacking 5′-3′ exoribonuclease I J. Bacteriol. 173 1991 7024 7028
156. A Stevens mRNA-decapping enzyme from Saccharomyces cerevisiae : purification and unique specificity for long RNA chains Mol. Cell Biol. 8 1988 2005 2010
157. M Kenna A Stevens M McCammon M.G Douglas An essential yeast gene with homology to the exonuclease-encoding XRN1/KEM 1 gene also encodes a protein with exoribonuclease activity Mol. Cell Biol. 13 1993 341 350
158. G Di Segni B.L McConaughy R.A Shapiro T.L Aldrich B.D Hall TAPI, a yeast gene that activates the expression of a tRNA gene with a defective internal promoter Mol. Cell Biol. 13 1993 3424 3433
159. D.C Amberg A.L Goldstein C.N Cole Isolation and characterization of RATI: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA Genes Dev. 6 1992 1173 1189
160. T.L Poole A Stevens Comparison of features of the RNase activity of 5′-exonuclease1 and 5′-exonuclease-2 of Saccharomyces cerevisiae 6th ed. Nucleic Acids Symp. Ser. 33 1995 79 81
161. A Stevens T.L Poole 5′-exonuclease-2 of Saccharomyces cerevisiae . Purification and features of ribonuclease activity with comparison to 5′-exonuclease-1 J. Biol. Chem. 270 1995 16063 16069
162. T.L Poole A Stevens Structural modifications of RNA influence the 5′ exoribonucleolytie hydrolysis by XRN1 and HKEI of Saccharomyces cerevisiae Biochem. Biophys. Res. Commun. 235 1997 799 805
163. A.W Johnson Ratlp and Xrnlp are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively Mol. Cell Biol. 17 1997 6122 6130
164. + gene of Schizosaccharomyces pombe : an essential gene that has homology to the DST2 and RATI genes of Saccharomyces cerevisiae Mol. Gen. Genet. 243 1994 1 8
165. + gene: structural and functional conservation Nucleic Acids Res. 23 1995 357 361
166. M Zhang L Yu Y Xin P Hu Q Fu C Yu S Zhao Cloning and mapping of the XRN2 gene to human chromosome 20p11.1-p11.2 Genomics 59 1999 252 254
167. P Mitchell E Petfalski D Tollervey The 3′ end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism Genes Dev. 10 1996 502 513
168. D.C Eichler S.J Eales Purification and properties of a novel nucleolar exoribonuclease capable of degrading both single-stranded and double-stranded RNA Biochemistry 24 1985 686 691
169. H Kumagai M Nakamura N Ozaki K Igarashi S Hirose Purification and mode of action of a microsomal exoribonuclease from rat liver Biochim. Biophys. Acta 827 1985 431 438
170. C.N Kwan A cytoplasmic exoribonuclease from HeLa cells Biochim. Biophys. Acta 479 1977 322 331
171. J Aström A Aström A Virtanen Properties of a HeLa cell 3′ exonuclease specific for degrading poly(A) tails of mammalian mRNA J. Biol. Chem. 267 1992 18154 18159
172. N Caruccio J Ross Purification of a human polyribosome-associated 3′ to 5′ exoribonuclease J. Biol. Chem. 269 1994 31814 31821
173. A Papadimitriou H.J Gross Pre-tRNA 3′-processing in Saccharomyces cerevisiae . Purification and characterization of exo- and endoribonucleases Eur. J. Biochem. 242 1996 747 759
174. G.O Gbenle Simultaneous isolation of cytoplasmic endoribonuclease and exoribonuclease of Trypanosoma brucei Mol. Biochem. Parasitol. 15 1985 37 47
175. A Cuba Purification and mode of action of exoribonuclease from bovine brain J. Biol. Chem. 252 1977 6416 6420
176. K.G Murthy P Park J.L Manley A nuclear micrococcal-sensitive, ATP-dependent exoribonuclease degrades uncapped but not capped RNA substrates Nucleic Acids Res. 19 1991 2685 2692
177. B.L Booth Jr. B.F Pugh Identification and characterization of a nuclease specific for the 3′ end of the U6 small nuclear RNA J. Biol. Chem. 272 1997 984 991
178. M Coutts G Brawerman A 5′ exoribonuclease from cytoplasmic extracts of mouse sarcoma 180 ascites cells Biochim. Biophys. Acta 1173 1993 57 62
179. S Somoskeoy M.N Rao L.I Slobin Purification and characterization of a 5′ to 3′ exoribonuclease from rabbit reticulocytes that degrades capped and uncapped RNAs Eur. J. Biochem. 237 1996 171 179
180. S Kurosawa A.M Shimabuku H Ishizawa K Sen Oligonucleotidase activity of phosphodiesterase from the fruit body of Flammulina velutipes Agric. Biol. Chem. 54 1990 587 592
181. A.D Scadden C.W Smith A ribonuclease specific for inosine-containing RNA: a potential role in antiviral defence? EMBO J. 16 1997 2140 2149
182. E Blum B Py A.J Carpousis C.F Higgins Polyphosphate kinase is a component of the Escherichia coli RNA degradosome Mol. Microbiol. 26 1997 387 398
183. D.A Bessarab V.R Kaberdin C.L Wei G.G Lion S Lin-Chao RNA components of Escherichia coli degradosome: evidence for rRNA decay 6th ed. Proc. Natl. Acad. Sci. USA 95 1998 3157 3161
184. N.F Vanzo Y.S Li B Py E Blum C.F Higgins L.C Raynal H.M Krisch A.J Carpousis Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome Genes Dev. 12 1998 2770 2781
185. V.R Kaberdin A Miczak J.S Jakobsen S Lin-Chao K.J McDowall A von Gabain The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly 6th ed. Proc. Natl. Acad. Sci. USA 95 1998 11637 11642
186. G.A Coburn X Miao D.J Briant G.A Mackie Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEADbox RNA helicase Genes Dev. 13 1999 2594 2603
187. T.K Misra D Apirion RNase E, an RNA processing enzyme from Escherichia coli J. Biol. Chem. 254 1979 11154 11159
188. Z Li S Pandit M.P Deutscher RNase G (CafA protein) and RNase E are both required for the 5′ maturation of 16S ribosomal RNA EMBO J. 18 1999 2878 2885
189. J Kudla R Hayes W Gruissem Polyadenylation accelerates degradation of chloroplast mRNA EMBO J. 15 1996 7137 7146
190. R Hayes J Kudla W Gruissem Degrading chloroplast mRNA: the role of polyadenylation Trends Biochem. Sci. 24 1999 199 202
191. J Das Gupta Q Li A.B Thompson A.G Hunt Characterization of a novel plant poly(A) polymerise Plant Sci. 110 1995 215 226
192. Q.S Li J.D Gupta A.G Hunt A plant poly(A) polymerase requires a novel RNAbinding protein for activity J. Biol. Chem. 271 1996 19831 19835
193. J Min R.M Heuertz H.P Zassenhaus Isolation and characterization of an NTPdependent 3′-exoribonuclease from mitochondria of Saccharomyces cerevisiae J. Biol. Chem. 268 1993 7350 7357
194. S.P Margossian H Li H.P Zassenhaus R.A Butow The DExH box protein Suv3p is a component of a yeast mitochondrial 3′-to-5′ exoribonuclease that suppresses group I intron toxicity Cell 84 1996 199 209