Viral polymerases

Advances in Experimental Medicine and Biology

Volumn 726, Issue , 2012, Pages 267-304

  Choi, Kyung H ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED DNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; DOUBLE STRANDED DNA; DOUBLE STRANDED RNA; MINUS SENSE SINGLE STRANDED RNA; MOLECULAR MOTOR; PLUS SENSE SINGLE STRANDED RNA; PRIMER RNA; PROTEIN VPG; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED RNA POLYMERASE; SINGLE STRANDED DNA; SINGLE STRANDED RNA; UNCLASSIFIED DRUG; VIRAL POLYMERASE; VIRUS ENZYME; VIRUS PROTEIN; VIRUS RNA;

ARTICLE; BACTERIOPHAGE; BACTERIOPHAGE T7; CALICIVIRUS; DNA SYNTHESIS; ENZYME ACTIVITY; ENZYME MECHANISM; ENZYME STRUCTURE; EUKARYOTE; FLAVIVIRUS; GENE SYNTHESIS; HEPATITIS B VIRUS; NONHUMAN; NUCLEOTIDE TRANSPORT; NUCLEOTIDYL TRANSFER REACTION; PICORNAVIRUS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN METABOLISM; PROTEIN PROTEIN INTERACTION; PROTEIN URIDYLATION; RETROVIRUS; RNA DEGRADATION; RNA SYNTHESIS; RNA TRANSLATION; SEQUENCE MOTIF; VIRUS CLASSIFICATION; VIRUS GENOME; VIRUS REPLICATION; VIRUS TRANSCRIPTION;

DNA-DIRECTED DNA POLYMERASE; DNA-DIRECTED RNA POLYMERASES; MODELS, MOLECULAR; MOLECULAR MOTOR PROTEINS; PROTEIN CONFORMATION; PROTEIN FOLDING; VIRAL PROTEINS; VIRUSES;

EID: 84858190920     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4614-0980-9_12     Document Type: Article

References (93)

1. Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM (2005) Direct observation of base-pair stepping by RNA polymerase. Nature 438:460-465 (Pubitemid 41742012)
2. Abbondanzieri EA, Bokinsky G, Rausch JW, Zhang JX, Le Grice SF, Zhuang X (2008) Dynamic binding orientations direct activity of HIV reverse transcriptase. Nature 453:184-189 (Pubitemid 351667984)
3. Ackermann M, Padmanabhan R (2001) De novo synthesis of RNA by the dengue virus RNA-dependent RNA polymerase exhibits temperature dependence at the initiation but not elongation phase. J Biol Chem 276: 39926-39937
4. Ago H, Adachi T, Yoshida A, Yamamoto M, Habuka N, Yatsunami K, Miyano M (1999) Crystal structure of the RNAdependent RNA polymerase of hepatitis C virus. Structure 7:1417-1426 (Pubitemid 29529882)
5. Baltimore D (1971) Expression of animal virus genomes. Bacteriol Rev 35:235-241
6. Basu VP, Song M, Gao L, Rigby ST, Hanson MN, Bambara RA (2008) Strand transfer events during HIV-1 reverse transcription. Virus Res 134:19-38
7. Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2007) Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. EMBO J 26:3494-3505 (Pubitemid 47123545)
8. Bishop DH, Gay ME, Matsuoko Y (1983) Nonviral heterogeneous sequences are present at the 5' ends of one species of snowshoe hare bunyavirus S complementary RNA. Nucleic Acids Res 11:6409-6418
9. Blanco L, Salas M (1996) Relating structure to function in phi29 DNA polymerase. J Biol Chem 271:8509-8512 (Pubitemid 26123264)
10. Boivin S, Cusack S, Ruigrok RW, Hart DJ (2010) Infl uenza A virus polymerase: structural insights into replication and host adaptation mechanisms. J Biol Chem 285(37):28411-28417
11. Bressanelli S, Tomei L, Roussel A, Incitti I, Vitale RL, Mathieu M, De Francesco R, Rey FA (1999) Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proc Natl Acad Sci USA 96:13034-13039
12. Broyles SS (2003) Vaccinia virus transcription. J Gen Virol 84:2293-2303 (Pubitemid 37063117)
13. Cheetham GM, Steitz TA (1999) Structure of a transcribing T7 RNA polymerase initiation complex. Science 286: 2305-2309 (Pubitemid 30016883)
14. Choi KH, Groarke JM, Young DC, Kuhn RJ, Smith JL, Pevear DC, Rossmann MG (2004) The structure of the RNAdependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation. Proc Natl Acad Sci USA 101:4425-4430 (Pubitemid 38437428)
15. Choi KH, Gallei A, Becher P, Rossmann MG (2006) The structure of bovine viral diarrhea virus RNA-dependent RNA polymerase and its amino-terminal domain. Structure 14:1107-1113 (Pubitemid 44037427)
16. Choi KH, Rossmann MG (2009) RNA-dependent RNA polymerases from Flaviviridae. Curr Opin Struct Biol 19(6):746-751
17. Delarue M, Poch O, Tordo N, Moras D, Argos P (1990) An attempt to unify the structure of polymerases. Protein Eng 3:461-467 (Pubitemid 20290022)
18. DeStefano JJ, Mallaber LM, Fay PJ, Bambara RA (1994) Quantitative analysis of RNA cleavage during RNA-directed DNA synthesis by human immunodefi ciency and avian myeloblastosis virus reverse transcriptases. Nucleic Acids Res 22:3793-3800 (Pubitemid 24299863)
19. Drake JW (1991) A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci USA 88:7160-7164 (Pubitemid 21915109)
20. Dufour E, Rodriguez I, Lazaro JM, de Vega M, Salas M (2003) A conserved insertion in protein-primed DNA polymerases is involved in primer terminus stabilisation. J Mol Biol 331:781-794 (Pubitemid 36945437)
21. Durniak KJ, Bailey S, Steitz TA (2008) The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation. Science 322:553-557
22. Egloff MP, Decroly E, Malet H, Selisko B, Benarroch D, Ferron F, Canard B (2007) Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5. J Mol Biol 372:723-736 (Pubitemid 47313487)
23. Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N (2004) Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA. J Biol Chem 279:47212-47221 (Pubitemid 39518378)
24. Ferrer-Orta C, Arias A, Agudo R, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N (2006) The structure of a protein primer-polymerase complex in the initiation of genome replication. EMBO J 25:880-888 (Pubitemid 43292448)
25. Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N (2007) Sequential structures provide insights into the fi delity of RNA replication. Proc Natl Acad Sci USA 104:9463-9468 (Pubitemid 47185802)
26. Furfine ES, Reardon JE (1991) Reverse transcriptase.RNase H from the human immunodefi ciency virus. Relationship of the DNA polymerase and RNA hydrolysis activities. J Biol Chem 266: 406-412 (Pubitemid 21906136)
27. Gao G, Orlova M, Georgiadis MM, Hendrickson WA, Goff SP (1997) Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection. Proc Natl Acad Sci USA 94:407-411 (Pubitemid 27053645)
28. Golomb M, Chamberlin M (1974) Characterization of T7-specifi c ribonucleic acid polymerase. IV. Resolution of the major in vitro transcripts by gel electrophoresis. J Biol Chem 249(9):2858-2863
29. Gu M, Lima CD (2005) Processing the message: structural insights into capping and decapping mRNA. Curr Opin Struct Biol 15:99-106 (Pubitemid 40249516)
30. Guajardo R, Sousa R (1997) A model for the mechanism of polymerase translocation. J Mol Biol 265:8-19 (Pubitemid 27110561)
31. Hansen JL, Long AM, Schultz SC (1997) Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5:1109-1122 (Pubitemid 27393094)
32. Hogg M, Wallace SS, Doublie S (2004) Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site. EMBO J 23:1483-1493 (Pubitemid 38579509)
33. Hong Z, Cameron CE, Walker MP, Castro C, Yao N, Lau JY, Zhong W (2001) A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase. Virology 285:6-11 (Pubitemid 32589002)
34. Huang H, Chopra R, Verdine GL, Harrison SC (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282:1669-1675 (Pubitemid 28549275)
35. Ibarra B, Chemla YR, Plyasunov S, Smith SB, Lazaro JM, Salas M, Bustamante C (2009) Proofreading dynamics of a processive DNA polymerase. EMBO J 28:2794-2802
36. Jacobo-Molina A, Ding J, Nanni RG, Clark AD Jr, Lu X, Tantillo C, Williams RL, Kamer G, Ferris AL, Clark P et al (1993) Crystal structure of human immunodefi ciency virus type 1 reverse transcriptase complexed with doublestranded DNA at 3.0 A resolution shows bent DNA. Proc Natl Acad Sci USA 90:6320-6324 (Pubitemid 23191507)
37. Jeruzalmi D, Steitz TA (1998) Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J 17:4101-4113 (Pubitemid 28333994)
38. Julias JG, McWilliams MJ, Sarafi anos SG, Arnold E, Hughes SH (2002) Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specifi city of RNase H cleavage in vivo. Proc Natl Acad Sci USA 99:9515-9520 (Pubitemid 34764645)
39. Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2006) The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition. EMBO J 25: 1335-1343
40. Kao CC, Del Vecchio AM, Zhong W (1999) De novo initiation of RNA synthesis by a recombinant fl aviviridae RNAdependent RNA polymerase. Virology 253:1-7 (Pubitemid 29391552)
41. Kasamatsu H, Nakanishi A (1998) How do animal DNA viruses get to the nucleus? Annu Rev Microbiol 52:627-686 (Pubitemid 28481204)
42. Kim S, Lee J, Ryu WS (2009) Four conserved cysteine residues of the hepatitis B virus polymerase are critical for RNA pregenome encapsidation. J Virol 83:8032-8040
43. Kohlstaedt LA, Steitz TA (1992) Reverse transcriptase of human immunodefi ciency virus can use either human tRNA(3Lys) or Escherichia coli tRNA(2Gln) as a primer in an in vitro primer-utilization assay. Proc Natl Acad Sci USA 89:9652-9656
44. Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA (1992) Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256:1783-1790
45. Krug MS, Berger SL (1989) Ribonuclease H activities associated with viral reverse transcriptases are endonucleases. Proc Natl Acad Sci USA 86:3539-3543 (Pubitemid 19141817)
46. Lai VC, Kao CC, Ferrari E, Park J, Uss AS, Wright-Minogue J, Hong Z, Lau JY (1999) Mutational analysis of bovine viral diarrhea virus RNA-dependent RNA polymerase. J Virol 73:10129-10136
47. Lazaro JM, Blanco L, Salas M (1995) Purifi cation of bacteriophage phi 29 DNA polymerase. Methods Enzymol 262:42-49
48. Lelke M, Brunotte L, Busch C, Gunther S (2010) An N-terminal region of Lassa virus L protein plays a critical role in transcription but not replication of the virus genome. J Virol 84:1934-1944
49. Lesburg CA, Cable MB, Ferrari E, Hong Z, Mannarino AF, Weber PC (1999) Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site. Nat Struct Biol 6:937-943 (Pubitemid 29463307)
50. Luo G, Hamatake RK, Mathis DM, Racela J, Rigat KL, Lemm J, Colonno RJ (2000) De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virus. J Virol 74:851-863 (Pubitemid 30036222)
51. Malet H, Egloff MP, Selisko B, Butcher RE, Wright PJ, Roberts M, Gruez A, Sulzenbacher G, Vonrhein C, Bricogne G, Mackenzie JM, Khromykh AA, Davidson AD, Canard B (2007) Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5. J Biol Chem 282:10678-10689 (Pubitemid 47093413)
52. Masters BS, Stohl LL, Clayton DA (1987) Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell 51:89-99
53. Meijer WJ, Horcajadas JA, Salas M (2001) Phi29 family of phages. Microbiol Mol Biol Rev 65:261-287, second page, table of contents
54. Mendez J, Blanco L, Salas M (1997) Protein-primed DNA replication: a transition between two modes of priming by a unique DNA polymerase. EMBO J 16:2519-2527 (Pubitemid 27258647)
55. Mesters JR, Tan J, Hilgenfeld R (2006) Viral enzymes. Curr Opin Struct Biol 16:776-786 (Pubitemid 44827732)
56. Morin B, Coutard B, Lelke M, Ferron F, Kerber R, Jamal S, Frangeul A, Baronti C, Charrel R, de Lamballerie X, Vonrhein C, Lescar J, Bricogne G, Gunther S, Canard B (2010) The N-terminal domain of the arenavirus L protein is an RNA endonuclease essential in mRNA transcription. PLoS Pathog 6:e1001038
57. Murray KE, Barton DJ (2003) Poliovirus CRE-dependent VPg uridylylation is required for positive-strand RNA synthesis but not for negative-strand RNA synthesis. J Virol 77:4739-4750 (Pubitemid 36402824)
58. Nassal M (2008) Hepatitis B viruses: reverse transcription a different way. Virus Res 134:235-249
59. Ng KK, Cherney MM, Vazquez AL, Machin A, Alonso JM, Parra F, James MN (2002) Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase. J Biol Chem 277:1381-1387 (Pubitemid 34968894)
60. Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA (1985) Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature 313:762-766 (Pubitemid 15130824)
61. Orlowski J, Bujnicki JM (2008) Structural and evolutionary classifi cation of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res 36:3552-3569 (Pubitemid 351917520)
62. Paul AV, Peters J, Mugavero J, Yin J, van Boom JH, Wimmer E (2003a) Biochemical and genetic studies of the VPg uridylylation reaction catalyzed by the RNA polymerase of poliovirus. J Virol 77:891-904 (Pubitemid 36055511)
63. Paul AV, Yin J, Mugavero J, Rieder E, Liu Y, Wimmer E (2003b) A "slide-back" mechanism for the initiation of protein-primed RNA synthesis by the RNA polymerase of poliovirus. J Biol Chem 278:43951-43960 (Pubitemid 37377134)
64. Plotch SJ, Bouloy M, Ulmanen I, Krug RM (1981) A unique cap(m7G pppXm)-dependent infl uenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell 23:847-858 (Pubitemid 11156997)
65. Poch O, Sauvaget I, Delarue M, Tordo N (1989) Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J 8:3867-3874 (Pubitemid 20016069)
66. Polyak SJ, Zheng S, Harnish DG (1995) 5′ termini of Pichinde arenavirus S RNAs and mRNAs contain nontemplated nucleotides. J Virol 69:3211-3215
67. Radziwill G, Tucker W, Schaller H (1990) Mutational analysis of the hepatitis B virus P gene product: domain structure and RNase H activity. J Virol 64:613-620 (Pubitemid 20032673)
68. Ranjith-Kumar CT, Kim YC, Gutshall L, Silverman C, Khandekar S, Sarisky RT, Kao CC (2002) Mechanism of de novo initiation by the hepatitis C virus RNA-dependent RNA polymerase: role of divalent metals. J Virol 76:12513-12525 (Pubitemid 35386937)
69. Rausch JW, Lener D, Miller JT, Julias JG, Hughes SH, Le Grice SF (2002) Altering the RNase H primer grip of human immunodefi ciency virus reverse transcriptase modifi es cleavage specifi city. Biochemistry 41:4856-4865 (Pubitemid 34298652)
70. Reguera J, Weber F, Cusack S (2010) Bunyaviridae RNA polymerases (L-protein) have an N-terminal, infl uenza-like endonuclease domain, essential for viral cap-dependent transcription. PLoS Pathog 6:e1001101
71. Rodgers DW, Gamblin SJ, Harris BA, Ray S, Culp JS, Hellmig B, Woolf DJ, Debouck C, Harrison SC (1995) The structure of unliganded reverse transcriptase from the human immunodefi ciency virus type 1. Proc Natl Acad Sci USA 92:1222-1226
72. Rodriguez I, Lazaro JM, Blanco L, Kamtekar S, Berman AJ, Wang J, Steitz TA, Salas M, de Vega M (2005) A specifi c subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity. Proc Natl Acad Sci USA 102:6407-6412 (Pubitemid 40617456)
73. Rodriguez-Wells V, Plotch SJ, DeStefano JJ (2001) Primer-dependent synthesis by poliovirus RNA-dependent RNA polymerase (3D(pol)). Nucleic Acids Res 29:2715-2724 (Pubitemid 32685034)
74. Rothwell PJ, Waksman G (2005) Structure and mechanism of DNA polymerases. Adv Protein Chem 71:401-440 (Pubitemid 41446935)
75. Sarafi anos SG, Das K, Tantillo C, Clark AD Jr, Ding J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E (2001) Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. EMBO J 20: 1449-1461 (Pubitemid 32233984)
76. Sarafi anos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E (2009) Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. J Mol Biol 385: 693-713
77. Sohn JA, Litwin S, Seeger C (2009) Mechanism for CCC DNA synthesis in hepadnaviruses. PLoS One 4:e8093
78. Sousa R, Chung YJ, Rose JP, Wang BC (1993) Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution. Nature 364:593-599 (Pubitemid 23274714)
79. Steitz TA (1998) A mechanism for all polymerases. Nature 391:231-232
80. Tahirov TH, Temiakov D, Anikin M, Patlan V, McAllister WT, Vassylyev DG, Yokoyama S (2002) Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. Nature 420:43-50 (Pubitemid 35291434)
81. Temiakov D, Mentesana PE, Ma K, Mustaev A, Borukhov S, McAllister WT (2000) The specifi city loop of T7 RNA polymerase interacts fi rst with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance. Proc Natl Acad Sci USA 97:14109-14114 (Pubitemid 32016538)
82. Thompson AA, Peersen OB (2004) Structural basis for proteolysis-dependent activation of the poliovirus RNAdependent RNA polymerase. EMBO J 23:3462-3471 (Pubitemid 39265536)
83. Truniger V, Lazaro JM, Salas M, Blanco L (1996) A DNA binding motif coordinating synthesis and degradation in proofreading DNA polymerases. EMBO J 15:3430-3441 (Pubitemid 26231950)
84. Truniger V, Blanco L, Salas M (1999) Role of the "YxGG/A" motif of Phi29 DNA polymerase in protein-primed replication. J Mol Biol 286:57-69 (Pubitemid 29078395)
85. Uchil PD, Satchidanandam V (2003) Architecture of the fl aviviral replication complex. Protease, nuclease, and detergents reveal encasement within double-layered membrane compartments. J Biol Chem 278:24388-24398 (Pubitemid 37548590)
86. van Dijk AA, Makeyev EV, Bamford DH (2004) Initiation of viral RNA-dependent RNA polymerization. J Gen Virol 85:1077-1093 (Pubitemid 38659772)
87. Wang HY, Elston T, Mogilner A, Oster G (1998) Force generation in RNA polymerase. Biophys J 74:1186-1202 (Pubitemid 28108530)
88. Weigel C, Seitz H (2006) Bacteriophage replication modules. FEMS Microbiol Rev 30:321-381
89. Wendeler M, Miller JT, Le Grice SFJ (2009) Human immunodefi ciency virus reverse transcriptase. Cameron, Craig E.; Gotte, Matthias; Raney, Kevin D. (Eds.) In: Viral genome replication, Springer Science + Business Media, New York, pp 403-427
90. Yap TL, Xu T, Chen YL, Malet H, Egloff MP, Canard B, Vasudevan SG, Lescar J (2007) Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution. J Virol 81: 4753-4765 (Pubitemid 46668672)
91. Yin YW, Steitz TA (2002) Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 298:1387-1395 (Pubitemid 35346133)
92. Yin YW, Steitz TA (2004) The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell 116:393-404 (Pubitemid 38366316)
93. Zamyatkin DF, Parra F, Alonso JM, Harki DA, Peterson BR, Grochulski P, Ng KK (2008) Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase. J Biol Chem 283:7705-7712