| [1] | Eigen M, Schuster P (1979) The hypercycle. A principle of natural self-organization. Heidelberg: Springer-Verlag. 92 p.
|
| [2] | Crowder S, Kirkegaard K (2005) Trans-dominant inhibition of RNA viral replication can slow growth of drug-resistant viruses. Nat Genet 37: 701–709. pmid:15965477 doi: 10.1038/ng1583
|
| [3] | Li JP, Baltimore D (1988) Isolation of poliovirus 2C mutants defective in viral RNA synthesis. J Virol 62: 4016–4021. pmid:2845120
|
| [4] | Tanner EJ, Liu HM, Oberste MS, Pallansch M, Collett MS, et al. (2014) Dominant drug targets suppress the emergence of antiviral resistance. Elife 3. doi: 10.7554/elife.03830
|
| [5] | Vignuzzi M, Stone JK, Arnold JJ, Cameron CE, Andino R (2006) Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 439: 344–348. pmid:16327776 doi: 10.1038/nature04388
|
| [6] | Huang AS, Baltimore D (1970) Defective viral particles and viral disease processes. Nature 226: 325–327. pmid:5439728 doi: 10.1038/226325a0
|
| [7] | van der Most RG, Luytjes W, Rutjes S, Spaan WJ (1995) Translation but not the encoded sequence is essential for the efficient propagation of the defective interfering RNAs of the coronavirus mouse hepatitis virus. J Virol 69: 3744–3751. pmid:7745722
|
| [8] | Molenkamp R, Greve S, Spaan WJ, Snijder EJ (2000) Efficient homologous RNA recombination and requirement for an open reading frame during replication of equine arteritis virus defective interfering RNAs. J Virol 74: 9062–9070. pmid:10982351 doi: 10.1128/jvi.74.19.9062-9070.2000
|
| [9] | Su YP, Fan YH, Brian DA (2014) Dependence of coronavirus RNA replication on an NH2-terminal partial nonstructural protein 1 in cis. J Virol 88: 8868–8882. doi: 10.1128/JVI.00738-14. pmid:24872586
|
| [10] | Yi G, Kao C (2008) cis- and trans-acting functions of brome mosaic virus protein 1a in genomic RNA1 replication. J Virol 82: 3045–3053. pmid:18160434 doi: 10.1128/jvi.02390-07
|
| [11] | Novak JE, Kirkegaard K (1994) Coupling between genome translation and replication in an RNA virus. Genes Dev 8: 1726–1737. pmid:7958852 doi: 10.1101/gad.8.14.1726
|
| [12] | Collis PS, O'Donnell BJ, Barton DJ, Rogers JA, Flanegan JB (1992) Replication of poliovirus RNA and subgenomic RNA transcripts in transfected cells. J Virol 66: 6480–6488. pmid:1328676
|
| [13] | Grassmann CW, Isken O, Tautz N, Behrens SE (2001) Genetic analysis of the pestivirus nonstructural coding region: defects in the NS5A unit can be complemented in trans. J Virol 75: 7791–7802. pmid:11483722 doi: 10.1128/jvi.75.17.7791-7802.2001
|
| [14] | Khromykh AA, Sedlak PL, Westaway EG (2000) cis- and trans-acting elements in flavivirus RNA replication. J Virol 74: 3253–3263. pmid:10708442 doi: 10.1128/jvi.74.7.3253-3263.2000
|
| [15] | Paul AV, Rieder E, Kim DW, van Boom JH, Wimmer E (2000) Identification of an RNA hairpin in poliovirus RNA that serves as the primary template in the in vitro uridylylation of VPg. J Virol 74: 10359–10370. pmid:11044080 doi: 10.1128/jvi.74.22.10359-10370.2000
|
| [16] | Goodfellow I, Chaudhry Y, Richardson A, Meredith J, Almond JW, et al. (2000) Identification of a cis-acting replication element within the poliovirus coding region. J Virol 74: 4590–4600. pmid:10775595 doi: 10.1128/jvi.74.10.4590-4600.2000
|
| [17] | Friebe P, Boudet J, Simorre JP, Bartenschlager R (2005) Kissing-loop interaction in the 3' end of the hepatitis C virus genome essential for RNA replication. J Virol 79: 380–392. pmid:15596831 doi: 10.1128/jvi.79.1.380-392.2005
|
| [18] | Lee H, Shin H, Wimmer E, Paul AV (2004) cis-acting RNA signals in the NS5B C-terminal coding sequence of the hepatitis C virus genome. J Virol 78: 10865–10877. pmid:15452207 doi: 10.1128/jvi.78.20.10865-10877.2004
|
| [19] | You S, Stump DD, Branch AD, Rice CM (2004) A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. J Virol 78: 1352–1366. pmid:14722290 doi: 10.1128/jvi.78.3.1352-1366.2004
|
| [20] | Liao CL, Lai MM (1995) A cis-acting viral protein is not required for the replication of a coronavirus defective-interfering RNA. Virology 209: 428–436. pmid:7778278 doi: 10.1006/viro.1995.1275
|
| [21] | Lin J, Guo J, Finer J, Dorrance AE, Redinbaugh MG, et al. (2014) The bean pod mottle virus RNA2-encoded 58-kilodalton protein P58 is required in cis for RNA2 accumulation. J Virol 88: 3213–3222. doi: 10.1128/JVI.03301-13. pmid:24390330
|
| [22] | Lindenbach BD, Murray CL, Thiel HJ, Rice CM (2013) Flaviviridae. In: Knipe DM, Howley PM, editors. Fields Virology. Sixth ed. Philadelphia: Lippincott Williams & Wilkins. pp. 712–746.
|
| [23] | Bartenschlager R, Lohmann V, Penin F (2013) The molecular and structural basis of advanced antiviral therapy for hepatitis C virus infection. Nat Rev Microbiol 11: 482–496. doi: 10.1038/nrmicro3046. pmid:23748342
|
| [24] | Lindenbach BD, Rice CM (2013) The ins and outs of hepatitis C virus entry and assembly. Nat Rev Microbiol 11: 688–700. doi: 10.1038/nrmicro3098. pmid:24018384
|
| [25] | Lohmann V, Korner F, Koch JO, Herian U, Theilmann L, et al. (1999) Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line. Science 285: 110–113. pmid:10390360 doi: 10.1126/science.285.5424.110
|
| [26] | Bartenschlager R, Frese M, Pietschmann T (2004) Novel insights into hepatitis C virus replication and persistence. Adv Virus Res 63: 71–180. pmid:15530561 doi: 10.1016/s0065-3527(04)63002-8
|
| [27] | Ranjith-Kumar CT, Kao CC (2006) Biochemical Activities of the HCV NS5B RNA-Dependent RNA Polymerase. In: Tan SL, editor. Hepatitis C Viruses: Genomes and Molecular Biology. Norfolk (UK).
|
| [28] | Steinkühler C (2004) Hepacivirin. In: Barrett AJ, Rawlings ND, Woessner JF, editors. Handbook of proteolytic enzymes. 2nd ed. London: Elsevier. pp. 1773–1779.
|
| [29] | Li XD, Sun L, Seth RB, Pineda G, Chen ZJ (2005) Hepatitis C virus protease NS3/4A cleaves mitochondrial antiviral signaling protein off the mitochondria to evade innate immunity. Proc Natl Acad Sci U S A 102: 17717–17722. pmid:16301520 doi: 10.1073/pnas.0508531102
|
| [30] | Meylan E, Curran J, Hofmann K, Moradpour D, Binder M, et al. (2005) Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus. Nature 437: 1167–1172. pmid:16177806 doi: 10.1038/nature04193
|
| [31] | Li K, Foy E, Ferreon JC, Nakamura M, Ferreon AC, et al. (2005) Immune evasion by hepatitis C virus NS3/4A protease-mediated cleavage of the Toll-like receptor 3 adaptor protein TRIF. Proc Natl Acad Sci U S A 102: 2992–2997. pmid:15710891 doi: 10.1073/pnas.0408824102
|
| [32] | Kang X, Chen X, He Y, Guo D, Guo L, et al. (2013) DDB1 is a cellular substrate of NS3/4A protease and required for hepatitis C virus replication. Virology 435: 385–394. doi: 10.1016/j.virol.2012.10.025. pmid:23137809
|
| [33] | Morikawa K, Gouttenoire J, Hernandez C, Dao Thi VL, Tran HT, et al. (2014) Quantitative proteomics identifies the membrane-associated peroxidase GPx8 as a cellular substrate of the hepatitis C virus NS3-4A protease. Hepatology 59: 423–433. doi: 10.1002/hep.26671. pmid:23929719
|
| [34] | Kolykhalov AA, Mihalik K, Feinstone SM, Rice CM (2000) Hepatitis C virus-encoded enzymatic activities and conserved RNA elements in the 3' nontranslated region are essential for virus replication in vivo. J Virol 74: 2046–2051. pmid:10644379 doi: 10.1128/jvi.74.4.2046-2051.2000
|
| [35] | Lam AM, Frick DN (2006) Hepatitis C virus subgenomic replicon requires an active NS3 RNA helicase. J Virol 80: 404–411. pmid:16352565 doi: 10.1128/jvi.80.1.404-411.2006
|
| [36] | Pyle AM (2008) Translocation and unwinding mechanisms of RNA and DNA helicases. Annu Rev Biophys 37: 317–336. doi: 10.1146/annurev.biophys.37.032807.125908. pmid:18573084
|
| [37] | Beran RK, Lindenbach BD, Pyle AM (2009) The NS4A protein of hepatitis C virus promotes RNA-coupled ATP hydrolysis by the NS3 helicase. J Virol 83: 3268–3275. doi: 10.1128/JVI.01849-08. pmid:19153239
|
| [38] | Tanji Y, Hijikata M, Satoh S, Kaneko T, Shimotohno K (1995) Hepatitis C virus-encoded nonstructural protein NS4A has versatile functions in viral protein processing. J Virol 69: 1575–1581. pmid:7853491
|
| [39] | Gouttenoire J, Penin F, Moradpour D (2010) Hepatitis C virus nonstructural protein 4B: a journey into unexplored territory. Rev Med Virol 20: 117–129. doi: 10.1002/rmv.640. pmid:20069613
|
| [40] | Paul D, Romero-Brey I, Gouttenoire J, Stoitsova S, Krijnse-Locker J, et al. (2011) NS4B Self-Interaction through Conserved C-Terminal Elements Is Required for the Establishment of Functional Hepatitis C Virus Replication Complexes. J Virol 85: 6963–6976. doi: 10.1128/JVI.00502-11. pmid:21543474
|
| [41] | Ross-Thriepland D, Harris M (2014) Hepatitis C virus NS5A: enigmatic but still promiscuous 10 years on! J Gen Virol. doi: 10.1099/jgv.0.000009
|
| [42] | Verdegem D, Badillo A, Wieruszeski JM, Landrieu I, Leroy A, et al. (2011) Domain 3 of NS5A protein from the hepatitis C virus has intrinsic alpha-helical propensity and is a substrate of cyclophilin A. J Biol Chem 286: 20441–20454. doi: 10.1074/jbc.M110.182436. pmid:21489988
|
| [43] | Grise H, Frausto S, Logan T, Tang H (2012) A conserved tandem cyclophilin-binding site in hepatitis C virus nonstructural protein 5A regulates Alisporivir susceptibility. J Virol 86: 4811–4822. doi: 10.1128/JVI.06641-11. pmid:22345441
|
| [44] | Hanoulle X, Badillo A, Wieruszeski JM, Verdegem D, Landrieu I, et al. (2009) Hepatitis C virus NS5A protein is a substrate for the peptidyl-prolyl cis/trans isomerase activity of cyclophilins A and B. J Biol Chem 284: 13589–13601. doi: 10.1074/jbc.M809244200. pmid:19297321
|
| [45] | Fernandes F, Ansari IU, Striker R (2010) Cyclosporine inhibits a direct interaction between cyclophilins and hepatitis C NS5A. PLoS One 5: e9815. doi: 10.1371/journal.pone.0009815. pmid:20352119
|
| [46] | Foster TL, Gallay P, Stonehouse NJ, Harris M (2011) Cyclophilin A Interacts with Domain II of Hepatitis C Virus NS5A and Stimulates RNA Binding in an Isomerase-Dependent Manner. J Virol 85: 7460–7464. doi: 10.1128/JVI.00393-11. pmid:21593166
|
| [47] | Reiss S, Rebhan I, Backes P, Romero-Brey I, Erfle H, et al. (2011) Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe 9: 32–45. doi: 10.1016/j.chom.2010.12.002. pmid:21238945
|
| [48] | Evans MJ, Rice CM, Goff SP (2004) Phosphorylation of hepatitis C virus nonstructural protein 5A modulates its protein interactions and viral RNA replication. Proc Natl Acad Sci U S A 101: 13038–13043. pmid:15326295 doi: 10.1073/pnas.0405152101
|
| [49] | Hamamoto I, Nishimura Y, Okamoto T, Aizaki H, Liu M, et al. (2005) Human VAP-B is involved in hepatitis C virus replication through interaction with NS5A and NS5B. J Virol 79: 13473–13482. pmid:16227268 doi: 10.1128/jvi.79.21.13473-13482.2005
|
| [50] | Tu H, Gao L, Shi ST, Taylor DR, Yang T, et al. (1999) Hepatitis C virus RNA polymerase and NS5A complex with a SNARE-like protein. Virology 263: 30–41. pmid:10544080 doi: 10.1006/viro.1999.9893
|
| [51] | Brass V, Gouttenoire J, Wahl A, Pal Z, Blum HE, et al. (2010) Hepatitis C Virus RNA Replication Requires a Conserved Structural Motif within the Transmembrane Domain of the NS5B RNA-Dependent RNA Polymerase. J Virol 84: 11580–11584. doi: 10.1128/JVI.01519-10. pmid:20739529
|
| [52] | Moradpour D, Brass V, Bieck E, Friebe P, Gosert R, et al. (2004) Membrane association of the RNA-dependent RNA polymerase is essential for hepatitis C virus RNA replication. J Virol 78: 13278–13284. pmid:15542678 doi: 10.1128/jvi.78.23.13278-13284.2004
|
| [53] | Adair R, Patel AH, Corless L, Griffin S, Rowlands DJ, et al. (2009) Expression of hepatitis C virus (HCV) structural proteins in trans facilitates encapsidation and transmission of HCV subgenomic RNA. J Gen Virol 90: 833–842. doi: 10.1099/vir.2008.006049-0. pmid:19223490
|
| [54] | Ishii K, Murakami K, Hmwe SS, Zhang B, Li J, et al. (2008) Trans-encapsidation of hepatitis C virus subgenomic replicon RNA with viral structure proteins. Biochem Biophys Res Commun 371: 446–450. doi: 10.1016/j.bbrc.2008.04.110. pmid:18445476
|
| [55] | Pacini L, Graziani R, Bartholomew L, De Francesco R, Paonessa G (2009) Naturally occurring hepatitis C virus subgenomic deletion mutants replicate efficiently in Huh-7 cells and are trans-packaged in vitro to generate infectious defective particles. J Virol 83: 9079–9093. doi: 10.1128/JVI.00308-09. pmid:19587042
|
| [56] | Steinmann E, Brohm C, Kallis S, Bartenschlager R, Pietschmann T (2008) Efficient trans-encapsidation of hepatitis C virus RNAs into infectious virus-like particles. J Virol 82: 7034–7046. doi: 10.1128/JVI.00118-08. pmid:18480457
|
| [57] | Appel N, Herian U, Bartenschlager R (2005) Efficient rescue of hepatitis C virus RNA replication by trans-complementation with nonstructural protein 5A. J Virol 79: 896–909. pmid:15613318 doi: 10.1128/jvi.79.2.896-909.2005
|
| [58] | Jones DM, Patel AH, Targett-Adams P, McLauchlan J (2009) The hepatitis C virus NS4B protein can trans-complement viral RNA replication and modulates production of infectious virus. J Virol 83: 2163–2177. doi: 10.1128/JVI.01885-08. pmid:19073716
|
| [59] | Fridell RA, Qiu D, Valera L, Wang C, Rose RE, et al. (2011) Distinct functions of NS5A in hepatitis C virus RNA replication uncovered by studies with the NS5A inhibitor BMS-790052. J Virol 85: 7312–7320. doi: 10.1128/JVI.00253-11. pmid:21593143
|
| [60] | Fridell RA, Valera L, Qiu D, Kirk MJ, Wang C, et al. (2013) Intragenic complementation of hepatitis C virus NS5A RNA replication-defective alleles. J Virol 87: 2320–2329. doi: 10.1128/JVI.02861-12. pmid:23236071
|
| [61] | Tong X, Malcolm BA (2006) Trans-complementation of HCV replication by non-structural protein 5A. Virus Res 115: 122–130. pmid:16146661 doi: 10.1016/j.virusres.2005.07.012
|
| [62] | Herod MR, Schregel V, Hinds C, Liu M, McLauchlan J, et al. (2014) Genetic complementation of hepatitis C virus nonstructural protein functions associated with replication exhibits requirements that differ from those for virion assembly. J Virol 88: 2748–2762. doi: 10.1128/JVI.03588-13. pmid:24352463
|
| [63] | Krieger N, Lohmann V, Bartenschlager R (2001) Enhancement of hepatitis C virus RNA replication by cell culture-adaptive mutations. J Virol 75: 4614–4624. pmid:11312331 doi: 10.1128/jvi.75.10.4614-4624.2001
|
| [64] | Lohmann V (2009) HCV replicons: overview and basic protocols. Methods Mol Biol 510: 145–163. doi: 10.1007/978-1-59745-394-3_11. pmid:19009259
|
| [65] | Phan T, Kohlway A, Dimberu P, Pyle AM, Lindenbach BD (2011) The acidic domain of hepatitis C virus NS4A contributes to RNA replication and virus particle assembly. J Virol 85: 1193–1204. doi: 10.1128/JVI.01889-10. pmid:21047963
|
| [66] | Kato T, Date T, Miyamoto M, Furusaka A, Tokushige K, et al. (2003) Efficient replication of the genotype 2a hepatitis C virus subgenomic replicon. Gastroenterology 125: 1808–1817. pmid:14724833 doi: 10.1053/j.gastro.2003.09.023
|
| [67] | Lesburg CA, Cable MB, Ferrari E, Hong Z, Mannarino AF, et al. (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. pmid:10504728
|
| [68] | Kim YC, Russell WK, Ranjith-Kumar CT, Thomson M, Russell DH, et al. (2005) Functional analysis of RNA binding by the hepatitis C virus RNA-dependent RNA polymerase. J Biol Chem 280: 38011–38019. pmid:16166071 doi: 10.1074/jbc.m508145200
|
| [69] | Mosley RT, Edwards TE, Murakami E, Lam AM, Grice RL, et al. (2012) Structure of hepatitis C virus polymerase in complex with primer-template RNA. J Virol 86: 6503–6511. doi: 10.1128/JVI.00386-12. pmid:22496223
|
| [70] | Grakoui A, McCourt DW, Wychowski C, Feinstone SM, Rice CM (1993) Characterization of the hepatitis C virus-encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites. J Virol 67: 2832–2843. pmid:8386278 doi: 10.1073/pnas.90.22.10583
|
| [71] | Tomei L, Failla C, Santolini E, De Francesco R, La Monica N (1993) NS3 is a serine protease required for processing of hepatitis C virus polyprotein. Journal of virology 67: 4017–4026. pmid:7685406
|
| [72] | Kim JL, Morgenstern KA, Griffith JP, Dwyer MD, Thomson JA, et al. (1998) Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. Structure 6: 89–100. pmid:9493270 doi: 10.1016/s0969-2126(98)00010-0
|
| [73] | Lin C, Kim JL (1999) Structure-based mutagenesis study of hepatitis C virus NS3 helicase. J Virol 73: 8798–8807. pmid:10482634
|
| [74] | Appleby TC, Anderson R, Fedorova O, Pyle AM, Wang R, et al. (2011) Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV. J Mol Biol 405: 1139–1153. doi: 10.1016/j.jmb.2010.11.034. pmid:21145896
|
| [75] | Preugschat F, Danger DP, Carter LH 3rd, Davis RG, Porter DJ (2000) Kinetic analysis of the effects of mutagenesis of W501 and V432 of the hepatitis C virus NS3 helicase domain on ATPase and strand-separating activity. Biochemistry 39: 5174–5183. pmid:10819985 doi: 10.1021/bi9923860
|
| [76] | Gu M, Rice CM (2010) Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism. Proc Natl Acad Sci U S A 107: 521–528. doi: 10.1073/pnas.0913380107. pmid:20080715
|
| [77] | Kim JW, Seo MY, Shelat A, Kim CS, Kwon TW, et al. (2003) Structurally conserved amino Acid W501 is required for RNA helicase activity but is not essential for DNA helicase activity of hepatitis C virus NS3 protein. J Virol 77: 571–582. pmid:12477861 doi: 10.1128/jvi.77.1.571-582.2003
|
| [78] | Kohlway A, Pirakitikulr N, Ding SC, Yang F, Luo D, et al. (2014) The linker region of NS3 plays a critical role in the replication and infectivity of hepatitis C virus. J Virol 88: 10970–10974. doi: 10.1128/JVI.00745-14. pmid:24965468
|
| [79] | Lindenbach BD, Prágai BM, Montserret R, Beran RK, Pyle AM, et al. (2007) The C terminus of hepatitis C virus NS4A encodes an electrostatic switch that regulates NS5A hyperphosphorylation and viral replication. J Virol 81: 8905–8918. pmid:17581983 doi: 10.1128/jvi.00937-07
|
| [80] | Kohlway A, Pirakitikulr N, Barrera FN, Potapova O, Engelman DM, et al. (2014) Hepatitis C Virus RNA Replication and Virus Particle Assembly Require Specific Dimerization of the NS4A Protein Transmembrane Domain. Journal of Virology 88: 628–642. doi: 10.1128/JVI.02052-13. pmid:24173222
|
| [81] | Appel N, Pietschmann T, Bartenschlager R (2005) Mutational analysis of hepatitis C virus nonstructural protein 5A: potential role of differential phosphorylation in RNA replication and identification of a genetically flexible domain. J Virol 79: 3187–3194. pmid:15709040 doi: 10.1128/jvi.79.5.3187-3194.2005
|
| [82] | Blight KJ, Kolykhalov AA, Rice CM (2000) Efficient initiation of HCV RNA replication in cell culture. Science 290: 1972–1974. pmid:11110665 doi: 10.1126/science.290.5498.1972
|
| [83] | Evans MJ, Rice CM, Goff SP (2004) Genetic interactions between hepatitis C virus replicons. J Virol 78: 12085–12089. pmid:15479852 doi: 10.1128/jvi.78.21.12085-12089.2004
|
| [84] | Petrakova O, Volkova E, Gorchakov R, Paessler S, Kinney RM, et al. (2005) Noncytopathic replication of Venezuelan equine encephalitis virus and eastern equine encephalitis virus replicons in Mammalian cells. J Virol 79: 7597–7608. pmid:15919912 doi: 10.1128/jvi.79.12.7597-7608.2005
|
| [85] | Agapov EV, Frolov I, Lindenbach BD, Pr？gai BM, Schlesinger S, et al. (1998) Noncytopathic Sindbis virus RNA vectors for heterologous gene expression. Proc Natl Acad Sci USA 95: 12989–12994. pmid:9789028 doi: 10.1073/pnas.95.22.12989
|
| [86] | Khromykh AA, Sedlak PL, Guyatt KJ, Hall RA, Westaway EG (1999) Efficient trans-complementation of the flavivirus kunjin NS5 protein but not of the NS1 protein requires its coexpression with other components of the viral replicase. J Virol 73: 10272–10280. pmid:10559344
|
| [87] | Lindenbach BD, Rice CM (1997) trans-Complementation of yellow fever virus NS1 reveals a role in early RNA replication. J Virol 71: 9608–9617. pmid:9371625
|
| [88] | Lindenbach BD, Rice CM (1999) Genetic interaction of flavivirus nonstructural proteins NS1 and NS4A as a determinant of replicase function. J Virol 73: 4611–4621. pmid:10233920
|
| [89] | Yi M, Ma Y, Yates J, Lemon SM (2009) Trans-complementation of an NS2 defect in a late step in hepatitis C virus (HCV) particle assembly and maturation. PLoS Pathog 5: e1000403. doi: 10.1371/journal.ppat.1000403. pmid:19412343
|
| [90] | Gao M (2013) Antiviral activity and resistance of HCV NS5A replication complex inhibitors. Curr Opin Virol. doi: 10.1016/j.coviro.2013.06.014
|
| [91] | Gao M, Nettles RE, Belema M, Snyder LB, Nguyen VN, et al. (2010) Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect. Nature 465: 96–100. doi: 10.1038/nature08960. pmid:20410884
|
| [92] | Berger C, Romero-Brey I, Radujkovic D, Terreux R, Zayas M, et al. (2014) Daclatasvir-Like Inhibitors of NS5A Block Early Biogenesis of Hepatitis C Virus-Induced Membranous Replication Factories, Independent of RNA Replication. Gastroenterology 147: 1094–1105 e1025. doi: 10.1053/j.gastro.2014.07.019. pmid:25046163
|
| [93] | National Center for Biotechnology Information PubChem BioAssay Database; CID = 25154714, Source = Bristol Meyers Squibb Co.
|
| [94] | Bachmair A, Finley D, Varshavasky A (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Science 234: 179–186. pmid:3018930 doi: 10.1126/science.3018930
|
| [95] | Baker RT, Tobias JW, Varshavsky A (1992) Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family. J Biol Chem 267: 23364–23375. pmid:1429680
|
| [96] | Phan T, Beran RK, Peters C, Lorenz IC, Lindenbach BD (2009) Hepatitis C virus NS2 protein contributes to virus particle assembly via opposing epistatic interactions with the E1-E2 glycoprotein and NS3-NS4A enzyme complexes. J Virol 83: 8379–8395. doi: 10.1128/JVI.00891-09. pmid:19515772
|
| [97] | Pietschmann T, Lohmann V, Kaul A, Krieger N, Rinck G, et al. (2002) Persistent and transient replication of full-length hepatitis C virus genomes in cell culture. J Virol 76: 4008–4021. pmid:11907240 doi: 10.1128/jvi.76.8.4008-4021.2002
|
| [98] | Chen J, Noueiry A, Ahlquist P (2003) An alternate pathway for recruiting template RNA to the brome mosaic virus RNA replication complex. J Virol 77: 2568–2577. pmid:12551995 doi: 10.1128/jvi.77.4.2568-2577.2003
|
| [99] | Derbyshire KM, Grindley ND (1996) Cis preference of the IS903 transposase is mediated by a combination of transposase instability and inefficient translation. Mol Microbiol 21: 1261–1272. pmid:8898394 doi: 10.1111/j.1365-2958.1996.tb02587.x
|
| [100] | Duval-Valentin G, Chandler M (2011) Cotranslational control of DNA transposition: a window of opportunity. Mol Cell 44: 989–996. doi: 10.1016/j.molcel.2011.09.027. pmid:22195971
|
| [101] | Burt DW, Brammar WJ (1982) The cis-specificity of the Q-gene product of bacteriophage lambda. Mol Gen Genet 185: 468–472. pmid:6212756 doi: 10.1007/bf00334142
|
| [102] | Francke B, Ray DS (1972) Cis-limited action of the gene-A product of bacteriophage phiX174 and the essential bacterial site (E. coli-electron microscopy-cis-acting protein-specifically-nicked RF). Proc Natl Acad Sci U S A 69: 475–479. pmid:4551145
|
| [103] | Kulpa DA, Moran JV (2006) Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 13: 655–660. pmid:16783376 doi: 10.1038/nsmb1107
|
| [104] | Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, et al. (2001) Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 21: 1429–1439. pmid:11158327 doi: 10.1128/mcb.21.4.1429-1439.2001
|
| [105] | Spagnolo JF, Rossignol E, Bullitt E, Kirkegaard K (2010) Enzymatic and nonenzymatic functions of viral RNA-dependent RNA polymerases within oligomeric arrays. RNA 16: 382–393. doi: 10.1261/rna.1955410. pmid:20051491
|
| [106] | Pata JD, Schultz SC, Kirkegaard K (1995) Functional oligomerization of poliovirus RNA-dependent RNA polymerase. Rna 1: 466–477. pmid:7489508
|
| [107] | Hobson SD, Rosenblum ES, Richards OC, Richmond K, Kirkegaard K, et al. (2001) Oligomeric structures of poliovirus polymerase are important for function. EMBO J 20: 1153–1163. pmid:11230138 doi: 10.1093/emboj/20.5.1153
|
| [108] | Wang QM, Hockman MA, Staschke K, Johnson RB, Case KA, et al. (2002) Oligomerization and cooperative RNA synthesis activity of hepatitis C virus RNA-dependent RNA polymerase. J Virol 76: 3865–3872. pmid:11907226 doi: 10.1128/jvi.76.8.3865-3872.2002
|
| [109] | Asabe SI, Tanji Y, Satoh S, Kaneko T, Kimura K, et al. (1997) The N-terminal region of hepatitis C virus-encoded NS5A is important for NS4A-dependent phosphorylation. J Virol 71: 790–796. pmid:8985418
|
| [110] | Kaneko T, Tanji Y, Satoh S, Hijikata M, Asabe S, et al. (1994) Production of two phosphoproteins from the NS5A region of the hepatitis C viral genome. Biochem Biophys Res Commun 205: 320–326. pmid:7999043 doi: 10.1006/bbrc.1994.2667
|
| [111] | Koch JO, Bartenschlager R (1999) Modulation of hepatitis C virus NS5A hyperphosphorylation by nonstructural proteins NS3, NS4A, and NS4B. J Virol 73: 7138–7146. pmid:10438800
|
| [112] | Neddermann P, Clementi A, De Francesco R (1999) Hyperphosphorylation of the hepatitis C virus NS5A protein requires an active NS3 protease, NS4A, NS4B, and NS5A encoded on the same polyprotein. J Virol 73: 9984–9991. pmid:10559312
|
| [113] | Bernardin F, Stramer SL, Rehermann B, Page-Shafer K, Cooper S, et al. (2007) High levels of subgenomic HCV plasma RNA in immunosilent infections. Virology 365: 446–456. pmid:17493654 doi: 10.1016/j.virol.2007.04.003
|
| [114] | Noppornpanth S, Smits SL, Lien TX, Poovorawan Y, Osterhaus AD, et al. (2007) Characterization of hepatitis C virus deletion mutants circulating in chronically infected patients. J Virol 81: 12496–12503. pmid:17728237 doi: 10.1128/jvi.01059-07
|
| [115] | Sugiyama K, Suzuki K, Nakazawa T, Funami K, Hishiki T, et al. (2009) Genetic analysis of hepatitis C virus with defective genome and its infectivity in vitro. J Virol 83: 6922–6928. doi: 10.1128/JVI.02674-08. pmid:19369330
|
| [116] | Delang L, Neyts J, Vliegen I, Abrignani S, Neddermann P, et al. (2013) Hepatitis C virus-specific directly acting antiviral drugs. Curr Top Microbiol Immunol 369: 289–320. doi: 10.1007/978-3-642-27340-7_12. pmid:23463206
|
| [117] | Sulkowski MS, Gardiner DF, Rodriguez-Torres M, Reddy KR, Hassanein T, et al. (2014) Daclatasvir plus sofosbuvir for previously treated or untreated chronic HCV infection. N Engl J Med 370: 211–221. doi: 10.1056/NEJMoa1306218. pmid:24428467
|
| [118] | Grassmann CW, Isken O, Behrens SE (1999) Assignment of the multifunctional NS3 protein of bovine viral diarrhea virus during RNA replication: an in vivo and in vitro study. J Virol 73: 9196–9205. pmid:10516027
|
| [119] | Tai CL, Pan WC, Liaw SH, Yang UC, Hwang LH, et al. (2001) Structure-based mutational analysis of the hepatitis C virus NS3 helicase. J Virol 75: 8289–8297. pmid:11483774 doi: 10.1128/jvi.75.17.8289-8297.2001
|
| [120] | Wang X, Lee WM, Watanabe T, Schwartz M, Janda M, et al. (2005) Brome mosaic virus 1a nucleoside triphosphatase/helicase domain plays crucial roles in recruiting RNA replication templates. J Virol 79: 13747–13758. pmid:16227294 doi: 10.1128/jvi.79.21.13747-13758.2005
|
| [121] | Bartenschlager R, Ahlborn-Laake L, Mous J, Jacobsen H (1993) Nonstructural protein 3 of the hepatitis C virus encodes a serine-type proteinase required for cleavage at the NS3/4 and NS4/5 junctions. J Virol 67: 3835–3844. pmid:8389908
|
| [122] | Yao N, Reichert P, Taremi SS, Prosise WW, Weber PC (1999) Molecular views of viral polyprotein processing revealed by the crystal structure of the hepatitis C virus bifunctional protease-helicase. Structure 7: 1353–1363. pmid:10574797 doi: 10.1016/s0969-2126(00)80025-8
|
| [123] | Dumas E, Masante C, Astier-Gin T, Lapaillerie D, Ventura M (2007) The hepatitis C virus minigenome: a new cellular model for studying viral replication. J Virol Methods 142: 59–66. pmid:17320981 doi: 10.1016/j.jviromet.2007.01.005
|
| [124] | King RW, Zecher M, Jeffries MW, Carroll DR, Parisi JM, et al. (2002) A cell-based model of HCV-negative-strand RNA replication utilizing a chimeric hepatitis C virus/reporter RNA template. Antivir Chem Chemother 13: 353–362. pmid:12718407 doi: 10.1177/095632020201300603
|
| [125] | Yang J, Lei YF, An QX, Yin W, Lu X, et al. (2010) Properties of hepatitis C virus minigenome containing mutated 5'UTR region and luciferase transgene. Acta Virol 54: 105–112. pmid:20545439 doi: 10.4149/av_2010_02_105
|
| [126] | Zhang J, Yamada O, Sakamoto T, Yoshida H, Araki H, et al. (2005) Exploiting cis-acting replication elements to direct hepatitis C virus-dependent transgene expression. J Virol 79: 5923–5932. pmid:15857978 doi: 10.1128/jvi.79.10.5923-5932.2005
|
| [127] | Zhang J, Yamada O, Yoshida H, Sakamoto T, Araki H, et al. (2007) Helper virus-independent trans-replication of hepatitis C virus-derived minigenome. Biochem Biophys Res Commun 352: 170–176. pmid:17112469 doi: 10.1016/j.bbrc.2006.10.188
|
| [128] | DeMarini DJ, Johnston VK, Konduri M, Gutshall LL, Sarisky RT (2003) Intracellular hepatitis C virus RNA-dependent RNA polymerase activity. J Virol Methods 113: 65–68. pmid:14500128 doi: 10.1016/s0166-0934(03)00226-x
|
| [129] | Ranjith-Kumar CT, Wen Y, Baxter N, Bhardwaj K, Cheng Kao C (2011) A cell-based assay for RNA synthesis by the HCV polymerase reveals new insights on mechanism of polymerase inhibitors and modulation by NS5A. PLoS One 6: e22575. doi: 10.1371/journal.pone.0022575. pmid:21799903
|
| [130] | Lindenbach BD, Evans MJ, Syder AJ, Wolk B, Tellinghuisen TL, et al. (2005) Complete replication of hepatitis C virus in cell culture. Science 309: 623–626. pmid:15947137 doi: 10.1126/science.1114016
|
| [131] | Fuerst TR, Niles EG, Studier FW, Moss B (1986) Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase. Proc Natl Acad Sci U S A 83: 8122–8126. pmid:3095828 doi: 10.1073/pnas.83.21.8122
|
| [132] | Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9: 671–675. pmid:22930834 doi: 10.1038/nmeth.2089
|
| [133] | Beran RK, Pyle AM (2008) Hepatitis C viral NS3-4A protease activity is enhanced by the NS3 helicase. J Biol Chem 283: 29929–29937. doi: 10.1074/jbc.M804065200. pmid:18723512
|
| [134] | Harlow E, Lane DP (1988) Antibodies: a laboratory manual. In: Harlow E, Lane DP, editors. Antibodies: a laboratory manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory.
|
| [135] | Lindberg V (2000) Uncertainties and Error Propagation: Part I of a manual on Uncertainties, Graphing, and the Vernier Caliper.
|
