Diverse roles of host RNA-binding proteins in RNA virus replication

RNA Biology

Volumn 8, Issue 2, 2011, Pages

  Li, Zhenghe ^a   Nagy, Peter D ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

Hepatitis C virus; Host factor; Poliovirus; Positive strand; Replication; RNA virus; RNA binding; Tomato bushy stunt virus; West nile virus

Indexed keywords

AUTOANTIGEN; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; LUPUS AUTOANTIGEN; POLYADENYLIC ACID BINDING PROTEIN; POLYPYRIMIDINE TRACT BINDING PROTEIN; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; VIRUS RNA; RNA DIRECTED RNA POLYMERASE;

3' UNTRANSLATED REGION; ALFALFA MOSAIC VIRUS; GENE CONTROL; HOST; INTERACTIONS WITH RNA; INTERNAL RIBOSOME ENTRY SITE; MOSAIC VIRUS; NONHUMAN; PROTEIN ANALYSIS; PROTEIN FUNCTION; REVIEW; RNA DEGRADATION; RNA STABILITY; RNA SYNTHESIS; RNA TRANSLATION; RNA VIRUS; SIGNAL TRANSDUCTION; TOMATO BUSHY STUNT VIRUS; TURNIP MOSAIC VIRUS; VIRUS ASSEMBLY; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS REPLICATION; WEST NILE FLAVIVIRUS; ANIMAL; CHEMISTRY; GENETICS; HUMAN; METABOLISM; PHYSIOLOGY;

HEPATITIS C VIRUS; POLIOVIRUS; RNA VIRUSES; TOMATO BUSHY STUNT VIRUS; WEST NILE VIRUS;

ANIMALS; HUMANS; RNA REPLICASE; RNA VIRUSES; RNA, VIRAL; RNA-BINDING PROTEINS; VIRUS REPLICATION;

EID: 79954510568     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.8.2.15391     Document Type: Review

References (152)

1. Barton DJ, Morasco BJ, Flanegan JB. Translating ribosomes inhibit poliovirus negative-strand RNA synthesis. J Virol 1999; 73:10104-12.
2. Kolakofsky D, Weissmann C. Q[beta] replicase as repressor of Q[beta] RNA-directed protein synthesis. Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis 1971; 246:596-9.
3. Dreher TW. Functions of the 3′-untranslated regions of positive strand RNA viral genomes. Annu Rev Phytopathol 1999; 37:151-74. (Pubitemid 29523932)
4. Ranjith-Kumar CT, Zhang X, Kao CC. Enhancer-like activity of a Brome mosaic virus RNA promoter. J Virol 2003; 77:1830-9. (Pubitemid 36109995)
5. Panavas T, Nagy PD. The RNA replication enhancer element of tombusviruses contains two interchangeable hairpins that are functional during plus-strand synthesis. J Virol 2003; 77:258-69. (Pubitemid 36004966)
6. Ray D, Na H, White KA. Structural properties of a multifunctional T-shaped RNA domain that mediate efficient Tomato bushy stunt virus RNA replication. J Virol 2004; 78:10490-500. (Pubitemid 39258374)
7. Panavas T, Nagy PD. Mechanism of stimulation of plus-strand synthesis by an RNA replication enhancer in a tombusvirus. J Virol 2005; 79:9777-85. (Pubitemid 41022320)
8. Ray D, White KA. An internally located RNA hairpin enhances replication of Tomato bushy stunt virus RNAs. J Virol 2003; 77:245-57. (Pubitemid 36004965)
9. Garneau NL, Sokoloski KJ, Opyrchal M, Neff CP, Wilusz CJ, Wilusz J. The 3 ′ untranslated region of Sindbis virus represses deadenylation of viral transcripts in mosquito and mammalian cells. J Virol 2008; 82:880-92.
10. Quadt R, Ishikawa M, Janda M, Ahlquist P. Formation of brome mosaic virus RNA-dependent RNA polymerase in yeast requires coexpression of viral proteins and viral RNA. Proc Natl Acad Sci U S A 1995; 92:4892-96.
11. Panaviene Z, Panavas T, Nagy PD. Role of an internal and two 3′-terminal RNA elements in assembly of tombusvirus replicase. J Virol 2005; 79:10608-18. (Pubitemid 41098600)
12. Ahola T, den Boon JA, Ahlquist P. Helicase and capping enzyme active site mutations in brome mosaic virus protein 1a cause defects in template recruitment, negative-strand RNA synthesis, and viral RNA capping. J Virol 2000; 74:8803-11.
13. Andino R, Rieckhof GE, Achacoso PL, Baltimore D. Poliovirus RNA-synthesis utilizes an RNP complex formed around the 5′-end of viral RNA. EMBO J 1993; 12:3587-98. (Pubitemid 23256445)
14. Filomatori CV, Lodeiro MF, Alvarez DE, Samsa MM, Pietrasanta L, Gamarnik AV. A 5′ RNA element promotes dengue virus RNA synthesis on a circular genome. Genes & Dev 2006; 20:2238-49.
15. Monkewich S, Lin H-X, Fabian MR, Xu W, Na H, Ray D, et al. The p92 polymerase coding region contains an internal RNA element required at an early step in tombusvirus genome replication. J Virol 2005; 79:4848-58. (Pubitemid 40464235)
16. Pogany J, White KA, Nagy PD. Specific binding of tombusvirus replication protein p33 to an internal replication element in the viral RNA is essential for replication. J Virol 2005; 79:4859-69. (Pubitemid 40464236)
17. Van Wynsberghe PM, Ahlquist P. 5′ cis elements direct nodavirus RNA1 recruitment to mitochondrial sites of replication complex formation. J Virol 2009; 83:2976-88.
18. Wang X, Lee W-M, Watanabe T, Schwartz M, Janda M, Ahlquist P. Brome mosaic virus 1a nucleoside triphosphatase/helicase domain plays crucial roles in recruiting RNA replication templates. J Virol 2005; 79:13747-58. (Pubitemid 41508186)
19. Glisovic T, Bachorik JL, Yong J, Dreyfuss G. RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 2008; 582:1977-86.
20. Boguszewska-Chachulska AM, Haenni A. RNA Viruses redirect host factors to better amplify their genome. In: Karl M, Aaron JS, eds. Adv Virus Res. Academic Press, 2005:29-61.
21. Lai MM. Cellular factors in the transcription and replication of viral RNA genomes: a parallel to DNA-dependent RNA transcription. Virology 1998; 244:1-12. (Pubitemid 28384119)
22. Ortín J, Parra F. Structure and function of RNA replication. Annu Rev Microbiol 2006; 60:305-26. (Pubitemid 44627951)
23. Ahlquist P, Noueiry AO, Lee W-M, Kushner DB, Dye BT. Host factors in positive-strand RNA virus genome replication. J Virol 2003; 77:8181-6. (Pubitemid 36871445)
24. Shi ST, Lai MMC. Viral and cellular proteins involved in coronavirus replication. Curr Top Microbiol Immunol 2005; 287:95-131. (Pubitemid 39371916)
25. Li HP, Zhang X, Duncan R, Comai L, Lai MM. Heterogeneous nuclear ribonucleoprotein A1 binds to the transcription-regulatory region of mouse hepatitis virus RNA. Proc Natl Acad Sci U S A 1997; 94:9544-9.
26. Nanda SK, Leibowitz JL. Mitochondrial aconitase binds to the 3′ untranslated region of the mouse hepatitis virus genome. J Virol 2001; 75:3352-62. (Pubitemid 32225898)
27. Spagnolo JF, Hogue BG. Host protein interactions with the 3′ end of bovine coronavirus RNA and the requirement of the poly(A) tail for coronavirus defective genome replication. J Virol 2000; 74:5053-65. (Pubitemid 30313844)
28. Li W, Li Y, Kedersha N, Anderson P, Emara M, Swiderek KM, et al. Cell proteins TIA-1 and TIAR interact with the 3′ stem-loop of the West Nile virus complementary minus-strand RNA and facilitate virus replication. J Virol 2002; 76:11989-2000. (Pubitemid 35304299)
29. Aizaki H, Choi K, Liu M, Li Y-j, Lai MM. Polypyrimidine-tract-binding protein is a component of the HCV RNA replication complex and necessary for RNA synthesis. J Biomed Sci 2006; 13:469-80.
30. Huang T-S, Wei T, Laliberte J-F, Wang A. A host RNA helicase-like protein, AtRH8, interacts with the potyviral genome-linked protein, VPg, associates with the virus accumulation complex, and is essential for infection. Plant Physiol 2010; 152:255-66.
31. Nishikiori M, Dohi K, Mori M, Meshi T, Naito S, Ishikawa M. Membrane-bound Tomato mosaic virus replication proteins participate in RNA synthesis and are associated with host proteins in a pattern distinct from those that are not membrane bound. J Virol 2006; 80:8459-68. (Pubitemid 44384858)
32. Thivierge K, Cotton S, Dufresne PJ, Mathieu I, Beauchemin C, Ide C, et al. Eukaryotic elongation factor 1A interacts with Turnip mosaic virus RNA-dependent RNA polymerase and VPg-Pro in virus-induced vesicles. Virology 2008; 377:216-25.
33. You S, Rice CM. 3′ RNA elements in Hepatitis C virus replication: kissing partners and long poly(U). J Virol 2008; 82:184-95. (Pubitemid 350309135)
34. Serva S, Nagy PD. Proteomics analysis of the tombusvirus replicase: Hsp70 molecular chaperone is associated with the replicase and enhances viral RNA replication. J Virol 2006; 80:2162-9. (Pubitemid 43271523)
35. Wang RYL, Nagy PD. Tomato bushy stunt virus coopts the RNA-binding function of a host metabolic enzyme for viral genomic RNA synthesis. Cell Host & Microbe 2008; 3:178-87. (Pubitemid 351325761)
36. Emara MM, Brinton MA. Interaction of TIA-1/TIAR with West Nile and dengue virus products in infected cells interferes with stress granule formation and processing body assembly. Proc Natl Acad Sci U S A 2007; 104:9041-6. (Pubitemid 47175433)
37. Zhu J, Gopinath K, Murali A, Yi G, Hayward SD, Zhu H, et al. RNA-binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci U S A 2007; 104:3129-34. (Pubitemid 46364125)
38. Li Z, Pogany J, Panavas T, Xu K, Esposito AM, Kinzy TG, et al. Translation elongation factor 1A is a component of the tombusvirus replicase complex and affects the stability of the p33 replication co-factor. Virology 2009; 385:245-60.
39. Thivierge K, Cotton S, Dufresne PJ, Mathieu I, Beauchemin C, Ide C, et al. Eukaryotic elongation factor 1A interacts with Turnip mosaic virus RNA-dependent RNA polymerase and VPg-Pro in virusinduced vesicles. Virology 2008; 377:216-25.
40. Nishikiori M, Dohi K, Mori M, Meshi T, Naito S, Ishikawa M. Membrane-bound tomato mosaic virus replication proteins participate in RNA synthesis and are associated with host proteins in a pattern distinct from those that are not membrane bound. J Virol 2006; 80:8459-68. (Pubitemid 44384858)
41. Cherry S, Doukas T, Armknecht S, Whelan S, Wang H, Sarnow P, et al. Genome-wide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition. Genes Dev 2005; 19:445-52. (Pubitemid 40256276)
42. Fernandez-Garcia MD, Mazzon M, Jacobs M, Amara A. Pathogenesis of flavivirus infections: using and abusing the host cell. Cell Host & Microbe 2009; 5:318-28.
43. Krishnan MN, Ng A, Sukumaran B, Gilfoy FD, Uchil PD, Sultana H, et al. RNA interference screen for human genes associated with West Nile virus infection. Nature 2008; 455:242-5.
44. Randall G, Panis M, Cooper JD, Tellinghuisen TL, Sukhodolets KE, Pfeffer S, et al. Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A 2007; 104:12884-9. (Pubitemid 47255249)
45. Kushner DB, Lindenbach BD, Grdzelishvili VZ, Noueiry AO, Paul SM, Ahlquist P. Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus. Proc Natl Acad Sci U S A 2003; 100:15764-9. (Pubitemid 38021064)
46. Panavas T, Serviene E, Brasher J, Nagy PD. Yeast genome-wide screen reveals dissimilar sets of host genes affecting replication of RNA viruses. Proc Natl Acad Sci U S A 2005; 102:7326-31. (Pubitemid 40696378)
47. Jiang Y, Serviene E, Gal J, Panavas T, Nagy PD. Identification of essential host factors affecting tombusvirus RNA replication based on the yeast Tet promoters Hughes Collection. J Virol 2006; 80:7394-404. (Pubitemid 44092562)
48. Jiang Y, Li Z, Nagy PD. Nucleolin/Nsr1p binds to the 3′ noncoding region of the tombusvirus RNA and inhibits replication. Virology 2010; 396:10-20.
49. Nagy PD, Pogany J. Global genomics and proteomics approaches to identify host factors as targets to induce resistance against tomato bushy stunt virus. Adv Virus Res 2010; 76:123-77.
50. Van Wynsberghe PM, Chen HR, Ahlquist P. Nodavirus RNA replication protein A induces membrane association of genomic RNA. J Virol 2007; 81:4633-44. (Pubitemid 46668661)
51. Iwakawa HO, Mine A, Hyodo K, An M, Kaido M, Mise K, et al. Template recognition mechanisms by replicase proteins differ between bipartite positive-strand genomic RNAs of a plant virus. J Virol 2011; 85:497-509.
52. Andino R, Rieckhof GE, Trono D, Baltimore D. Substitutions in the protease (3Cpro) gene of poliovirus can suppress a mutation in the 5′ noncoding region. J Virol 1990; 64:607-12. (Pubitemid 20032672)
53. Panavas T, Hawkins CM, Panaviene Z, Nagy PD. The role of the p33 : p33/p92 interaction domain in RNA replication and intracellular localization of p33 and p92 proteins of Cucumber necrosis tombusvirus. Virology 2005; 338:81-95. (Pubitemid 40835929)
54. Pogany J, Stork J, Li Z, Nagy PD, In vitro assembly of the Tomato bushy stunt virus replicase requires the host Heat shock protein 70. Proc Natl Acad Sci U S A 2008; 105:19956-61.
55. Li Z. Pogany J, Tupman S, Esposito AM, Kinzy TG and Nagy PD. Translation elongation factor 1A facilitates the assembly of the tombusvirus replicase and stimulates minus-strand synthsis. PLoS Pathog 2010; 6(11): e1001175. doi:10.1371
56. Mas A, Alves-Rodrigues I, Noueiry A, Ahlquist P, Diez J. Host deadenylation-dependent mRNA decapping factors are required for a key step in brome mosaic virus RNA replication. J Virol 2006; 80:246-51.
57. Diez J, Ishikawa M, Kaido M, Ahlquist P. Identification and characterization of a host protein required for efficient template selection in viral RNA replication. Proc Natl Acad Sci U S A 2000; 97:3913-8. (Pubitemid 30226061)
58. Oster SK, Wu B, White KA. Uncoupled expression of p33 and p92 permits amplification of Tomato bushy stunt virus RNAs. J Virol 1998; 72:5845-51. (Pubitemid 28283371)
59. Vlot AC, Laros SM, Bol JF. Coordinate replication of Alfalfa mosaic virus RNAs 1 and 2 involves cis- and trans-acting functions of the encoded helicase-like and polymerase-like domains. J Virol 2003; 77:10790-8. (Pubitemid 37204272)
60. Yi GG, Kao C. cis- and trans-acting functions of Brome mosaic virus protein 1a in genomic RNA1 replication. J Virol 2008; 82:3045-53.
61. Okamoto K, Nagano H, Iwakawa H, Mizumoto H, Takeda A, Kaido M, et al. cis-preferential requirement of a-1 frameshift product p88 for the replication of Red clover necrotic mosaic virus RNA1. Virology 2008; 375:205-12.
62. Novak JE, Kirkegaard K. Coupling between genome translation and replication in an RNA virus. Genes & Dev 1994; 8:1726-37. (Pubitemid 24236250)
63. Weiland JJ, Dreher TW. Cis-preferential replication of the Turnip yellow mosaic virus RNA genome. Proc Natl Acad Sci U S A 1993; 90:6095-9. (Pubitemid 23191461)
64. Wang J, Yeh H-H, Falk BW. cis preferential replication of Lettuce infectious yellows virus (LIYV) RNA 1: The initial step in the asynchronous replication of the LIYV genomic RNAs. Virology 2009; 386:217-23.
65. Gamarnik AV, Andino R. Interactions of viral protein 3CD and poly(rC) binding protein with the 5 ′ untranslated region of the poliovirus genome. J Virol 2000; 74:2219-26. (Pubitemid 30091476)
66. Blyn LB, Swiderek KM, Richards O, Stahl DC, Semler BL, Ehrenfeld E. Poly(rC) binding protein 2 binds to stem-loop IV of the poliovirus RNA 5′ noncoding region: identification by automated liquid chromatography tandem mass spectrometry. Proc Natl Acad Sci U S A 1996; 93:11115-20.
67. Blyn LB, Towner JS, Semler BL, Ehrenfeld E. Requirement of poly(rC) binding protein 2 for translation of poliovirus RNA. J Virol 1997; 71:6243-6. (Pubitemid 27304973)
68. Gamarnik AV, Andino R. Two functional complexes formed by KH domain containing proteins with the 5′ noncoding region of poliovirus RNA. RNA 1997; 3:882-92.
69. Andino R, Rieckhof GE, Baltimore D. A functional ribonucleoprotein complex forms around the 5′ end of poliovirus RNA. Cell 1990; 63:369-80.
70. Parsley TB, Towner JS, Blyn LB, Ehrenfeld E, Semler BL. Poly (rC) binding protein 2 forms a ternary complex with the 5′-terminal sequences of poliovirus RNA and the viral 3CD proteinase. RNA 1997; 3:1124-34.
71. Noueiry AO, Diez J, Falk SP, Chen JB, Ahlquist P. Yeast Lsm1p-7p/Pat1p deadenylation-dependent mRNA-decapping factors are required for brome mosaic virus genomic RNA translation. Mol Cell Biol 2003; 23:4094-106. (Pubitemid 36666415)
72. Scheller N, Mina LB, Galão RP, Chari A, Giménez- Barcons M, Noueiry A, et al. Translation and replication of hepatitis C virus genomic RNA depends on ancient cellular proteins that control mRNA fates. Proc Natl Acad Sci U S A 2009; 106:13517-22.
73. Miranda G, Schuppli D, Barrera I, Hausherr C, Sogo JM, Weber H. Recognition of bacteriophage Q[beta] plus strand RNA as a template by Q[beta] replicase: role of RNA interactions mediated by ribosomal proteins S1 and host factor. J Mol Biol 1997; 267:1089-103. (Pubitemid 27192624)
74. Brown D, Gold L. RNA replication by Q beta replicase: a working model. Proc Natl Acad Sci U S A 1996; 93:11558-62. (Pubitemid 26347160)
75. Fujisaki K, Ishikawa M. Identification of an Arabidopsis thaliana protein that binds to tomato mosaic virus genomic RNA and inhibits its multiplication. Virology 2008; 380:402-11.
76. Gamarnik AV, Andino R. Switch from translation to RNA replication in a positive-stranded RNA virus. Genes & Dev 1998; 12:2293-304. (Pubitemid 28371350)
77. Ichihashi N, Matsuura T, Kita H, Hosoda K, Sunami T, Tsukada K, et al. Importance of translation-replication balance for efficient replication by the self-encoded replicase. ChemBioChem 2008; 9:3023-8.
78. Weber H, Weissman.C, Billeter MA, Kahane S, Hindley J, Porter A. Molecular basis for repressor activity of Q beta replicase. Nat New Biol 1972; 237:166-170.
79. Kolakofs.D, Weissman.C. Possible mechanism for transition of viral RNA from polysome to replication complex. Nat New Biol 1971; 231:42-46.
80. Stupina VA, Meskauskas A, McCormack JC, Yingling YG, Shapiro BA, Dinman JD, et al. The 3′ proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits. RNA 2008; 14:2379-93.
81. Zuo X, Wang J, Yu P, Eyler D, Xu H, Starich MR, et al. Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3′ UTR of turnip crinkle virus. Proc Natl Acad Sci U S A 2010; 107:1385-90.
82. Perera R, Daijogo S, Walter BL, Nguyen JH, Semler BL. Cellular protein modification by poliovirus: the two faces of poly(rC)-binding protein. J Virol 2007; 81:8919-32. (Pubitemid 47311436)
83. Sean P, Nguyen JH, Semler BL. The linker domain of poly(rC) binding protein 2 is a major determinant in poliovirus cap-independent translation. Virology 2008; 378:243-53.
84. Belsham GJ, Sonenberg N. Picornavirus RNA translation: roles for cellular proteins. Trends Microbiol 2000; 8:330-5. (Pubitemid 30421067)
85. Back SH, Kim YK, Kim WJ, Cho S, Oh HR, Kim J-E, et al. Translation of polioviral mRNA is inhibited by cleavage of polypyrimidine tract-binding proteins executed by polioviral 3Cpro. J Virol 2002; 76:2529-42. (Pubitemid 34150721)
86. Bonderoff JM, LaRey JL, Lloyd RE. Cleavage of poly(A)-binding protein by poliovirus 3C proteinase inhibits viral internal ribosome entry site-mediated translation. J Virol 2008; 82:9389-99.
87. Galao RP, Chari A, Alves-Rodrigues I, Lobao D, Mas A, Kambach C, et al. Lsm1-7 complexes bind to specific sites in viral RNA genomes and regulate their translation and replication. RNA 2010; 16:817-27.
88. Garneau NL, Wilusz J, Wilusz CJ. The highways and byways of mRNA decay. Nat Rev Mol Cell Biol 2007; 8:113-26. (Pubitemid 46432531)
89. Parker R, Song H. The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 2004; 11:121-7. (Pubitemid 38146514)
90. Jangra RK, Yi M, Lemon SM. DDX6 (Rck/p54) is required for efficient hepatitis C virus replication but not for internal ribosome entry site-directed translation. J Virol 2010; 84:6810-24.
91. Isken O, Grassmann CW, Sarisky RT, Kann M, Zhang S, Grosse F, et al. Members of the NF90/NFAR protein group are involved in the life cycle of a positive-strand RNA virus. EMBO J 2003; 22:5655-65. (Pubitemid 37408806)
92. Isken O, Baroth M, Grassmann CW, Weinlich S, Ostareck DH, Ostareck-Lederer A, et al. Nuclear factors are involved in hepatitis C virus RNA replication. RNA 2007; 13:1675-92. (Pubitemid 47481676)
93. Isken O, Grassmann CW, Yu HY, Behrens SE. Complex signals in the genomic 3′ nontranslated region of bovine viral diarrhea virus coordinate translation and replication of the viral RNA. RNA 2004; 10:1637-52. (Pubitemid 39288197)
94. Vlot AC, Neeleman L, Linthorst HJM, Bol JF. Role of the 3′-untranslated regions of Alfalfa mosaic virus RNAs in the formation of a transiently expressed replicase in plants and in the assembly of virions. J Virol 2001; 75:6440-9. (Pubitemid 32578163)
95. Panaviene Z, Panavas T, Serva S, Nagy PD. Purification of the cucumber necrosis virus replicase from yeast cells: role of coexpressed viral RNA in stimulation of replicase activity. J Virol 2004; 78:8254-63. (Pubitemid 38944309)
96. Blumenthal T, Landers TA, Weber K. Bacteriophage Q replicase contains the protein biosynthesis elongation factors EF Tu and EF Ts. Proc Natl Acad Sci U S A 1972; 69:1313-17.
97. Wahba AJ, Miller MJ, Niveleau A, Landers TA, Carmichael GG, Weber K, et al. Subunit I of Q Replicase and 30S Ribosomal Protein Sl of Escherichia coli. J Biol Chem 1974; 249:3314-16..
98. Blumenthal T, Carmichael GG. RNA replication: function and structure of Qbeta-replicase. Annu Rev Biochem 1979; 48:525-48.
99. Takeshita D, Tomita K. Assembly of Q viral RNA polymerase with host translational elongation factors EF-Tu and -Ts. Proc Natl Acad Sci U S A 2010; 107:15733-8.
100. Kidmose RT, Vasiliev NN, Chetverin AB, Andersen GR, Knudsen CR. Structure of the Q replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins. Proc Natl Acad Sci U S A 2010; 107:10884-9.
101. Schuppli D, Miranda G, Tsui H-CT, Winkler ME, Sogo JM, Weber H. Altered 3′-terminal RNA structure in phage Q adapted to host factor-less Escherichia coli. Proc Natl Acad Sci U S A 1997; 94:10239-42. (Pubitemid 27407025)
102. Kim CS, Seol SK, Song O-K, Park JH, Jang SK. An RNA-binding protein, hnRNP A1, and a scaffold protein, septin 6, facilitate hepatitis C virus replication. J Virol 2007; 81:3852-65. (Pubitemid 46586882)
103. Brunner JE, Nguyen JH, Roehl HH, Ho TV, Swiderek KM, Semler BL. Functional interaction of heterogeneous nuclear ribonucleoprotein C with poliovirus RNA synthesis initiation complexes. J Virol 2005; 79:3254-66. (Pubitemid 40327915)
104. Ertel KJ, Brunner JE, Semler BL. Mechanistic consequences of hnRNP C binding to both RNA termini of poliovirus negative-strand RNA intermediates. J Virol 2010; 84:4229-42.
105. Davis WG, Blackwell JL, Shi P-Y, Brinton MA. Interaction between the cellular protein eEF1A and the 3′-terminal stem-loop of West Nile virus genomic RNA facilitates viral minus-strand RNA synthesis. J Virol 2007; 81:10172-87. (Pubitemid 350067720)
106. Blackwell J, Brinton M. Translation elongation factor-1 alpha interacts with the 3′ stem-loop region of West Nile virus genomic RNA. J Virol 1997; 71:6433-44. (Pubitemid 27355297)
107. Zeenko VV, Ryabova LA, Spirin AS, Rothnie HM, Hess D, Browning KS, et al. Eukaryotic elongation factor 1A interacts with the upstream pseudoknot domain in the 3′ untranslated region of Tobacco mosaic virus RNA. J Virol 2002; 76:5678-91. (Pubitemid 34517918)
108. Yamaji Y, Kobayashi T, Hamada K, Sakurai K, Yoshii A, Suzuki M, et al. In vivo interaction between Tobacco mosaic virus RNA-dependent RNA polymerase and host translation elongation factor 1A. Virology 2006; 347:100-8.
109. Li Z, Barajas D, Panavas T, Herbst DA, Nagy PD. Cdc34p ubiquitin-conjugating enzyme is a component of the tombusvirus replicase complex and ubiquitinates p33 replication protein. J Virol 2008; 82:6911-26. (Pubitemid 351977712)
110. Kao CC, Singh P, Ecker DJ. De novo initiation of viral RNA-dependent RNA synthesis. Virology 2001; 287:251-60. (Pubitemid 32804011)
111. Brown D, Gold L. Template recognition by an RNA-Dependent RNA-polymerase: identification and characterization of two RNA binding sites on Qbeta. replicase. Biochemistry 1995; 34:14765-74.
112. Klovins J, Berzins V, van Duin J. A long-range interaction in Qbeta RNA that bridges the thousand nucleotides between the M-site and the 3′ end is required for replication. RNA 1998; 4:948-57. (Pubitemid 28359765)
113. Klovins J, van Duin J. A long-range pseudoknot in Q RNA is essential for replication. J Mol Biol 1999; 294:875-84. (Pubitemid 30000381)
114. Wu BD, Pogany J, Na H, Nicholson BL, Nagy PD, White KA. A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes. Plos Pathog 2009; 5(3): e1000323. doi:10.1371.
115. Villordo SM, Alvarez DE, Gamarnik AV. A balance between circular and linear forms of the dengue virus genome is crucial for viral replication. RNA 2010; 16:2325-35.
116. Lodeiro MF, Filomatori CV, Gamarnik AV. Structural and functional studies of the promoter element for dengue virus RNA replication. J Virol 2009; 83:993-1008.
117. Filomatori CV, Lodeiro MF, Alvarez DE, Samsa MM, Pietrasanta L, Gamarnik AV. A 5′ RNA element promotes dengue virus RNA synthesis on a circular genome. Genes Dev 2006; 20:2238-49.
118. Friebe P, Boudet J, Simorre J-P, Bartenschlager R. Kissing-loop interaction in the 3′ end of the hepatitis C virus genome essential for RNA replication. J Virol 2005; 79:380-92. (Pubitemid 39648391)
119. Barton DJ, O'Donnell BJ, Flanegan JB. 5′ cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J 2001; 20:1439-48. (Pubitemid 32233983)
120. Herold J, Andino R. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol Cell 2001; 7:581-91. (Pubitemid 32706350)
121. Huang P, Lai MM. Heterogeneous nuclear ribonucleoprotein A1 binds to the 3′-untranslated region and mediates potential 5′-3′-end cross talks of mouse hepatitis virus RNA. J Virol 2001; 75:5009-17. (Pubitemid 32448521)
122. Matsuda D, Yoshinari S, Dreher TW. eEF1A binding to aminoacylated viral RNA represses minus strand synthesis by TYMV RNA-dependent RNA polymerase. Virology 2004; 321:47-56. (Pubitemid 38368102)
123. Pogany J, Fabian MR, White KA, Nagy PD. A replication silencer element in a plus-strand RNA virus. EMBO J 2003; 22:5602-11. (Pubitemid 37279969)
124. Roehl H, Semler B. Poliovirus infection enhances the formation of two ribonucleoprotein complexes at the 3′ end of viral negative-strand RNA. J Virol 1995; 69:2954-61.
125. Chambers TJ, Hahn CS, Galler R, Rice CM. Flavivirus genome organization, expression, and replication. Annu Rev Microbiol 1990; 44:649-88.
126. Li W, Li Y, Kedersha N, Anderson P, Emara M, Swiderek KM, et al. Cell proteins TIA-1 and TIAR interact with the 3′ stem-loop of the West Nile virus complementary minus-strand RNA and facilitate virus replication. J Virol 2002; 76:11989-2000. (Pubitemid 35304299)
127. Emara MM, Liu H, Davis WG, Brinton MA. Mutation of mapped TIA-1/TIAR binding sites in the 3′ terminal stem-loop of West Nile virus minus-strand RNA in an infectious clone negatively affects genomic RNA amplification. J Virol 2008; 82:10657-70. (Pubitemid 352691195)
128. Vogt DA, Andino R. An RNA element at the 5 ′-end of the poliovirus genome functions as a general promoter for RNA synthesis. Plos Pathog 2010; 6(6): e1000936. doi:10.1371.
129. den Boon JA, Ahlquist P. Organelle-Like Membrane compartmentalization of positive-strand RNA virus replication factories. Annu Rev Microbiol 2010; 64:241-56.
130. Miller WA, Koev G. Synthesis of subgenomic RNAs by positive-strand RNA viruses. Virology 2000; 273:1-8. (Pubitemid 30602002)
131. White KA. The Premature Termination Model: A possible third mechanism for subgenomic mRNA transcription in (+)-strand RNA viruses. Virology 2002; 304:147-54. (Pubitemid 36069157)
132. Sit TL, Vaewhongs AA, Lommel SA. RNA-mediated trans-activation of transcription from a viral RNA. Science 1998; 281:829-32. (Pubitemid 28376044)
133. Shi S, Lai MMC. Viral and cellular proteins involved in coronavirus replication. In: Enjuanes L, ed. Coronavirus replication and reverse genetics. Berlin Heidelberg: Springer, 2005:95-131.
134. Li H-P, Zhang X, Duncan R, Comai L, Lai MM. Heterogeneous nuclear ribonucleoprotein A1 binds to the transcription-regulatory region of mouse hepatitis virus RNA. Proc Natl Acad Sci U S A 1997; 94:9544-9.
135. Zhang X, Lai MM. Interactions between the cytoplasmic proteins and the intergenic (promoter) sequence of mouse hepatitis virus RNA: correlation with the amounts of subgenomic mRNA transcribed. J Virol 1995; 69:1637-44.
136. Shi ST, Huang P, Li HP, Lai MM. Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus. EMBO J 2000; 19:4701-11.
137. Zhang X, Li HP, Xue W, Lai MM. Formation of a ribonucleoprotein complex of mouse hepatitis virus involving heterogeneous nuclear ribonucleoprotein A1 and transcription-regulatory elements of viral RNA. Virology 1999; 264:115-24. (Pubitemid 29531892)
138. Wang Y, Zhang X. The nucleocapsid protein of coronavirus mouse hepatitis virus interacts with the cellular heterogeneous nuclear ribonucleoprotein A1 in vitro and in vivo. Virology 1999; 265:96-109. (Pubitemid 30012389)
139. Li HP, Huang P, Park S, Lai MM. Polypyrimidine tract-binding protein binds to the leader RNA of mouse hepatitis virus and serves as a regulator of viral transcription. J Virol 1999; 73:772-7. (Pubitemid 28565425)
140. Huang P, Lai MM. Polypyrimidine tract-binding protein binds to the complementary strand of the mouse hepatitis virus 3′ untranslated region, thereby altering RNA conformation. J Virol 1999; 73:9110-6. (Pubitemid 29487064)
141. Burnham AJ, Gong L, Hardy RW. Heterogeneous nuclear ribonuclear protein K interacts with Sindbis virus nonstructural proteins and viral subgenomic mRNA. Virology 2007; 367:212-21. (Pubitemid 47418923)
142. Silva PA, Pereira CF, Dalebout TJ, Spaan WJ, Bredenbeek PJ. An RNA pseudoknot is required for production of yellow fever virus subgenomic RNA by the host nuclease XRN1. J Virol 2010; 84:11395-406.
143. Funk A, Truong K, Nagasaki T, Torres S, Floden N, Balmori Melian E, et al. RNA structures required for production of subgenomic flavivirus RNA. J Virol 2010; 84:11407-17.
144. Cheng CP, Serviene E, Nagy PD. Suppression of viral RNA recombination by a host exoribonuclease. J Virol 2006; 80:2631-40. (Pubitemid 43346359)
145. Sokoloski KJ, Dickson AM, Chaskey EL, Garneau NL, Wilusz CJ, Wilusz J. Sindbis virus usurps the cellular HuR protein to stabilize its transcripts and promote productive infections in mammalian and mosquito cells. Cell Host & Microbe 2010; 8:196-207.
146. Nanda SK, Leibowitz JL. Mitochondrial aconitase binds to the 3′ untranslated region of the mouse hepatitis virus genome. J Virol 2001; 75:3352-62. (Pubitemid 32225898)
147. Murray KE, Roberts AW, Barton DJ. Poly(rC) binding proteins mediate poliovirus mRNA stability. RNA 2001; 7:1126-41. (Pubitemid 32726911)
148. Spangberg K, Wiklund L, Schwartz S. Binding of the La autoantigen to the hepatitis C virus 3 ′ untranslated region protects the RNA from rapid degradation in vitro. J Gen Virol 2001; 82:113-20. (Pubitemid 32045801)
149. Spångberg K, Wiklund L, Schwartz S. HuR, a protein implicated in oncogene and growth factor mRNA decay, binds to the 3′ ends of hepatitis C virus RNA of both polarities. Virology 2000; 274:378-90.
150. Korf M, Jarczak D, Beger C, Manns MP, Kruger M. Inhibition of hepatitis C virus translation and subgenomic replication by siRNAs directed against highly conserved HCV sequence and cellular HCV cofactors. J Hepatol 2005; 43:225-34. (Pubitemid 40956874)
151. Harris D, Zhang Z, Chaubey B, Pandey VN. Identification of cellular factors associated with the 3′-nontranslated region of the hepatitis C virus genome. Mol Cell Proteomics 2006; 5:1006-18. (Pubitemid 43985926)
152. Joshi RL, Ravel JM, Haenni AL. Interaction of turnip yellow mosaic virus Val-RNA with eukaryotic elongation- factor EF-1[alpha]. Search for a function. EMBO J 1986; 5:1143-8.