From Structure to Function: New Insights into Hepatitis C Virus RNA Replication (2005)

With an estimated number of about 180 million affected people worldwide and a limited therapy option, infection with the hepatitis C virus (HCV) 2The abbreviations used are: HCV, hepatitis C virus; nt, nucleotide(s); NTR, non-translated region; IRES, internal ribosome entry site; CRE, cis-acting RNA element; NS, non-structural; TLR-3, Toll-like receptor-3; dsRNA, double-stranded RNA; RIG-I, retinoic acid-inducible gene I; IFN, interferon; IRF-3, IFN regulatory factor-3; RC, replicase complex; LCS, low complexity sequence; RdRp, RNA-dependent RNA polymerase; VAP-A, vesicle-associated membrane protein-associated protein A. 2The abbreviations used are: HCV, hepatitis C virus; nt, nucleotide(s); NTR, non-translated region; IRES, internal ribosome entry site; CRE, cis-acting RNA element; NS, non-structural; TLR-3, Toll-like receptor-3; dsRNA, double-stranded RNA; RIG-I, retinoic acid-inducible gene I; IFN, interferon; IRF-3, IFN regulatory factor-3; RC, replicase complex; LCS, low complexity sequence; RdRp, RNA-dependent RNA polymerase; VAP-A, vesicle-associated membrane protein-associated protein A. is an important medical problem. Initial limitations in propagating HCV in cell culture have been overcome step-by-step in the past few years and culminated in the recent development of a system allowing efficient propagation of infectious HCV in tissue culture. Nevertheless, structural and biochemical studies of viral proteins as well as molecular analysis of viral RNA replication are still major challenges. The recent resolution of the three-dimensional structures of some HCV proteins or domains along with elegant reverse genetic and cell biological studies provided first insights into how HCV amplifies its RNA, exploits the cellular machinery, and eventually overcomes innate immune responses.Organization of the Viral GenomeHCV is a positive strand RNA virus that has been classified as the genus Hepacivirus in the Flaviviridae family. The HCV genome is an uncapped, linear molecule with a length of ∼9600 nucleotides (nt; Fig. 1A). It carries a long open reading frame that is flanked at the 5′- and 3′-ends by short highly structured non-translated regions (NTRs). The 5′-NTR has a length of about 340 nt and contains an internal ribosome entry site (IRES) required for translation of the HCV genome (1Bartenschlager R. Frese M. Pietschmann T. Adv. Virus Res. 2004; 63: 71-180Crossref PubMed Scopus (243) Google Scholar). This RNA element binds the 40 S ribosomal subunit in the absence of other translation initiation factors in a way that the initiation codon is placed in the immediate vicinity of the P site (2Pisarev A.V. Shirokikh N.E. Hellen U.T. C. R. Biol. 2005; 328: 589-605Crossref PubMed Scopus (97) Google Scholar). Part of the IRES (domain II) overlaps with RNA signals essential for viral replication (Fig. 1A) arguing for a possible role of domain II in regulating a translation-RNA replication switch. The 3′-NTR has a tripartite structure composed of an ∼40-nt-long variable region downstream of the HCV coding sequence, a poly(U/UC) tract of heterogeneous length, and a highly conserved 98-nt-long sequence designated X-tail (Fig. 1A). Genetic studies have shown that a poly(U/UC) tract of at least ∼25 nt as well as the complete X-tail are required for RNA replication in cell culture and for infectivity of the viral genome in vivo. An additional cis-acting RNA element (CRE) has been identified in the 3′-terminal coding region of NS5B (Fig. 1A). This CRE (designated 5BSL3.2) (3You S. Stump D.D. Branch A.D. Rice C.M. J. Virol. 2004; 78: 1352-1366Crossref PubMed Scopus (187) Google Scholar) forms a long distance RNA-RNA interaction with SL2 in the X-tail (4Friebe P. Boudet J. Simorre J.P. Bartenschlager R. J. Virol. 2005; 79: 380-392Crossref PubMed Scopus (296) Google Scholar), which is indispensable for RNA replication.Expression of the viral proteins from the monocistronic genome is primarily achieved by production of a polyprotein that is proteolytically cleaved into the structural proteins (core, envelope proteins E1 and E2), the hydrophobic peptide p7, and the non-structural (NS) proteins NS2, NS3, NS4A, NS4B, NS5A, and NS5B (Fig. 1A) (1Bartenschlager R. Frese M. Pietschmann T. Adv. Virus Res. 2004; 63: 71-180Crossref PubMed Scopus (243) Google Scholar, 5Penin F. Dubuisson J. Rey F.A. Moradpour D. Pawlotsky J.M. Hepatology. 2004; 39: 5-19Crossref PubMed Scopus (508) Google Scholar). Processing of the core to p7 region is mediated by host cell signalases, and in the case of the core protein, in addition by signal peptide peptidase. All remaining cleavages are carried out by two viral proteases: the NS2/3 protease mediating cleavage between NS2 and NS3 and the NS3 serine-type protease that is responsible for processing at all other sites in the NS polyprotein region. Alternative forms of the core protein generated by internal initiation of translation of an alternative reading frame or by ribosomal frameshifting have been reported (6Branch A.D. Stump D.D. Gutierrez J.A. Eng F. Walewski J.L. Semin. Liver Dis. 2005; 25: 105-117Crossref PubMed Scopus (108) Google Scholar). These proteins designated ARF-P or F-proteins (for "alternative reading frame" or "frameshift") are dispensable for RNA replication, at least in cell culture, and will therefore not be discussed in this review.Components of the HCV Replication ComplexOur current understanding of the HCV life cycle and the molecular composition of viral particles is still mainly hypothetical. However, some details begin to emerge due to the availability of efficient in vitro systems, most notably the HCV replicon system (7Lohmann V. Körner F. Koch J.O. Herian U. Theilmann L. Bartenschlager R. Science. 1999; 285: 110-113Crossref PubMed Scopus (2480) Google Scholar, 8Blight K.J. Kolykhalov A.A. Rice C.M. Science. 2000; 290: 1972-1974Crossref PubMed Scopus (1271) Google Scholar), HCV pseudoparticles (9Bartosch B. Dubuisson J. Cosset F.L. J. Exp. Med. 2003; 197: 633-642Crossref PubMed Scopus (942) Google Scholar, 10Hsu M. Zhang J. Flint M. Logvinoff C. Cheng-Mayer C. Rice C.M. McKeating J.A. Proc. Natl. Acad. Sci. U. S. A. 2003; 100: 7271-7276Crossref PubMed Scopus (687) Google Scholar), and, very recently, the first system for efficient production of infectious HCV in cell culture (11Zhong J. Gastaminza P. Cheng G. Kapadia S. Kato T. Burton D.R. Wieland S.F. Uprichard S.L. Wakita T. Chisari F.V. Proc. Natl. Acad. Sci. U. S. A. 2005; 102: 9294-9299Crossref PubMed Scopus (1507) Google Scholar, 12Lindenbach B.D. Evans M.J. Syder A.J. Wölk B. Tellinghuisen T.L. Liu C.C. Maruyama T. Hynes R.O. Burton D.R. McKeating J.A. Rice C.M. Science. 2005; 309: 623-626Crossref PubMed Scopus (1943) Google Scholar, 13Wakita T. Pietschmann T. Kato T. Date T. Miyamoto M. Zhao Z. Murthy K. Habermann A. Krausslich H.G. Mizokami M. Bartenschlager R. Liang T.J. Nat. Med. 2005; 11: 791-796Crossref PubMed Scopus (2400) Google Scholar). Since the minimum components required for HCV RNA translation and replication are the NTRs and the NS3 to NS5B coding region, in the following we will only refer to these viral elements.The Non-translated Regions—Apart from the genetic studies of the NTRs described above, detailed structural analyses have been performed only with parts of the 5′-NTR, in particular the IRES and fragments thereof (2Pisarev A.V. Shirokikh N.E. Hellen U.T. C. R. Biol. 2005; 328: 589-605Crossref PubMed Scopus (97) Google Scholar). By using cryo-electron microscopy Spahn et al. (14Spahn C.M. Kieft J.S. Grassucci R.A. Penczek P.A. Zhou K. Doudna J.A. Frank J. Science. 2001; 291: 1959-1962Crossref PubMed Scopus (440) Google Scholar) established a ∼20 Å resolution map of the IRES bound to the 40 S ribosomal subunit. This study revealed an important role of domain II in inducing conformational changes in the 40 S subunit that appears to be essential for assembly of the 80 S ribosome. Very recently, cryo-electron microscopy reconstruction was also used to determine the structure of human translation factor eIF3 complexed to the HCV IRES and to model an HCV IRES-eIF3–40S ribosomal subunit complex (15Siridechadilok B. Fraser C.S. Hall R.J. Doudna J.A. Nogales E. Science. 2005; 310: 1513-1515Crossref PubMed Scopus (226) Google Scholar). This model provides an explanation how eIF3 prevents premature joining of 40 and 60 S ribosomal subunits.The NS3 Serine-type Protease and Its Cofactor NS4A—NS3 is a bifunctional molecule that carries in the N-terminal ∼180 amino acids a serine-type protease. This enzyme has a typical chymotrypsin-like fold and is composed of two β-barrel domains displaying on their interface the classical active site residues (His, Asp, Ser) that are a hallmark of serine-type proteases (Fig. 1B) (1Bartenschlager R. Frese M. Pietschmann T. Adv. Virus Res. 2004; 63: 71-180Crossref PubMed Scopus (243) Google Scholar, 5Penin F. Dubuisson J. Rey F.A. Moradpour D. Pawlotsky J.M. Hepatology. 2004; 39: 5-19Crossref PubMed Scopus (508) Google Scholar, 16Kim J.L. Morgenstern K.A. Lin C. Fox T. Dwyer M.D. Landro J.A. Chambers S.P. Markland W. Lepre C.A. OMalley E.T. Harbeson S.L. Rice C.M. Murcko M.A. Caron P.R. Thomson J.A. Cell. 1996; 87: 343-355Abstract Full Text Full Text PDF PubMed Scopus (669) Google Scholar, 17Love R.A. Parge H.E. Wickersham J.A. Hostomsky Z. Habuka N. Moomaw E.W. Adachi T. Hostomska Z. Cell. 1996; 87: 331-342Abstract Full Text Full Text PDF PubMed Scopus (495) Google Scholar). Although NS3 possesses intrinsic proteolytic activity, polyprotein cleavage is dramatically enhanced by the NS4A cofactor. This short polypeptide of 54 amino acid residues serves multiple purposes. First, it anchors the protease to intracellular membranes via an N-terminal transmembrane segment present in NS4A; second, it contributes one β-strand to the N-terminal protease domain and thereby allows its complete folding (Fig. 1B); third, it stabilizes the protease against proteolytic degradation; fourth, it activates protease activity by changing the geometry of the catalytic triad. The three-dimensional structure of the holoenzyme revealed in addition a tetrahedrally coordinated zinc ion required for proper folding of the C-terminal NS3 protease domain (Fig. 1B). The enzyme has an unusually shallow substrate-binding pocket and therefore requires rather long interaction surfaces with the substrate (usually decapeptides). This made the design of efficient NS3-specific compounds with a sufficient therapeutic window challenging but on the other side may explain why the enzyme can recognize several cellular substrates. In fact, it was found that NS3 can cleave two components of the dsRNA signaling pathway. One is the Toll-like receptor-3 (TLR-3) adaptor TRIF (also called TICAM-1) (18Li K. Foy E. Ferreon J.C. Nakamura M. Ferreon A.C. Ikeda M. Ray S.C. Gale Jr., M. Lemon S.M. Proc. Natl. Acad. Sci. U. S. A. 2005; 102: 2992-2997Crossref PubMed Scopus (912) Google Scholar), the other is Cardif (also called IPS-1, MAVS, or VISA) (19Meylan E. Curran J. Hofmann K. Moradpour D. Binder M. Bartenschlager R. Tschopp J. Nature. 2005; 437: 1167-1172Crossref PubMed Scopus (1932) Google Scholar). Both adaptor molecules relay their signal from the dsRNA sensor (TLR-3 or retinoic acid-inducible gene I (RIG-I)) to the kinase complex that is responsible for the phosphorylation of IFN regulatory factor-3 (IRF-3). Phosphorylated IRF-3, in turn, induces transcription of IFN-β and other antiviral genes. In this respect, the NS314A protease is not only required for polyprotein processing but also for counteracting cellular antiviral defense pathways.The NS3 Helicase—The C-terminal ∼400 amino acids of NS3 form a superfamily 2 DE×H/D-box RNA helicase that is capable of unwinding RNA-RNA duplexes in an ATP-dependent manner (20Tai C.L. Chi W.K. Chen D.S. Hwang L.H. J. Virol. 1996; 70: 8477-8484Crossref PubMed Google Scholar). The protein binds to homopolymeric RNAs with a preference for poly(U). Moreover, some specificity of helicase binding to the terminal stem-loop in the X-tail was observed (21Banerjee R. Dasgupta A. J. Virol. 2001; 75: 1708-1721Crossref PubMed Scopus (69) Google Scholar) arguing that a preferred binding to the 3′-NTR also occurs in vivo. Earlier studies often came to the conclusion that NS3 protease and helicase function are largely independent. This view is difficult to envisage given the tight interaction of both domains observed in the crystal structure of full-length NS3 (Fig. 1B) (5Penin F. Dubuisson J. Rey F.A. Moradpour D. Pawlotsky J.M. Hepatology. 2004; 39: 5-19Crossref PubMed Scopus (508) Google Scholar) and by the finding that an isolated NS3 helicase fragment showed a slower kinetic of duplex RNA unwinding as compared with the full-length NS3 protein (22Frick D.N. Rypma R.S. Lam A.M. Gu B. J. Biol. Chem. 2004; 279: 1269-1280Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar). Moreover, NS4A appears to act as an RNA loading factor that greatly enhances productive RNA binding of a full-length NS3/4A complex (23Pang P.S. Jankowsky E. Planet P.J. Pyle A.M. EMBO J. 2002; 21: 1168-1176Crossref PubMed Scopus (203) Google Scholar) arguing for a cross-talk between protease and helicase domains.Mutational and biochemical studies suggest that NS3 forms multimers and, in particular, dimers. Although monomeric NS3 was found to bind RNA with high affinity, it was convincingly shown that RNA unwinding requires an NS3 dimer (24Serebrov V. Pyle A.M. Nature. 2004; 430: 476-480Crossref PubMed Scopus (120) Google Scholar). The molecular mechanism underlying RNA unwinding is not yet clear. However, recent kinetic analyses have shown that the enzyme undergoes highly coordinated cycles of fast dsRNA unwinding with high processivity for about 20 nt (23Pang P.S. Jankowsky E. Planet P.J. Pyle A.M. EMBO J. 2002; 21: 1168-1176Crossref PubMed Scopus (203) Google Scholar, 24Serebrov V. Pyle A.M. Nature. 2004; 430: 476-480Crossref PubMed Scopus (120) Google Scholar, 25Levin M.K. Gurjar M. Patel S.S. Nat. Struct. Mol. Biol. 2005; 12: 429-435Crossref PubMed Scopus (120) Google Scholar). Thereafter, the enzyme "pauses" and may fall off the template or start a new cycle of duplex unwinding.The crystal structure of the HCV helicase revealed a Y-shaped molecule composed of 3 nearly equally sized subdomains (Fig. 1B) (26Kim J.L. Morgenstern K.A. Griffith J.P. Dwyer M.D. Thomson J.A. Murcko M.A. Lin C. Caron P.R. Structure. 1998; 6: 89-100Abstract Full Text Full Text PDF PubMed Scopus (581) Google Scholar, 27Yao N. Hesson T. Cable M. Hong Z. Kwong A.D. Le H.V. Weber P.C. Nat. Struct. Biol. 1997; 4: 463-467Crossref PubMed Scopus (420) Google Scholar). The cleft between domains I and II forms the nucleotide-binding site, whereas the interfaces between the three domains are predominantly involved in nucleic acid recognition and binding. The helicase domain is connected to the serine-protease domain via a flexible linker that may allow a rotation of both domains against each other and in this way a fine regulation of their respective enzymatic activities (Fig. 1B) (22Frick D.N. Rypma R.S. Lam A.M. Gu B. J. Biol. Chem. 2004; 279: 1269-1280Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar, 28Yao N.H. Reichert P. Taremi S.S. Prosise W.W. Weber P.C. Struct. Fold. Des. 1999; 7: 1353-1363Abstract Full Text Full Text PDF Scopus (366) Google Scholar). It will therefore be interesting to determine whether inhibitors of the protease also affect NS3 helicase activity.The role of the NS3 helicase in the HCV life cycle remains to be unraveled. The enzyme may be involved in initiation of RNA replication by unwinding stable stem-loop structures at the termini of positive and negative strand RNA. NS3 helicase may also contribute to the processivity of the replicase complex (RC) by removing stable RNA secondary structures in the template strand and by displacing bound proteins that may otherwise interfere with RNA synthesis. Finally, the helicase may be required for dissociation of the replicative form into positive and negative strand HCV RNA.NS4B: Inducer of a Membrane Scaffold for the Viral RC?—The NS4B is a highly hydrophobic protein predicted to contain four transmembrane domains, while its N-terminal region may contribute to targeting of NS4B to intracellular membranes (29Lundin M. Monne M. Widell A. Von Heijne G. Persson M.A. J. Virol. 2003; 77: 5428-5438Crossref PubMed Scopus (170) Google Scholar). Overexpression of NS4B in cell culture is sufficient to induce membrane alterations arguing that the main function of this protein is the formation of membranous structures serving as the scaffold of the HCV RC (30Egger D. Wölk B. Gosert R. Bianchi L. Blum H.E. Moradpour D. Bienz K. J. Virol. 2002; 76: 5974-5984Crossref PubMed Scopus (689) Google Scholar). However, the structure of NS4B-induced membrane alterations appears to be morphologically distinct from the membranous web suggesting that one or several viral and cellular components contribute to the formation of the viral RC. A nucleotide-binding motif of the sequence GX4GK was identified in NS4B, and it was shown that a GFP-NS4B fusion protein can bind GTP upon expression in cell culture (31Einav S. Elazar M. Danieli T. Glenn J.S. J. Virol. 2004; 78: 11288-11295Crossref PubMed Scopus (106) Google Scholar). Moreover, recombinant NS4B appears to possess GTPase activity. However, the results described by Einav et al. (31Einav S. Elazar M. Danieli T. Glenn J.S. J. 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Biol. 1998; PubMed Scopus Google Scholar). is only conserved between can in be with only of RNA replication in cell culture, and the of rather N. Pietschmann T. Bartenschlager R. J. Virol. 2005; 79: PubMed Scopus Google Scholar, D. Evans M.J. Gosert R. Z. Blum H.E. S.P. B.D. Rice C.M. J. Virol. 2004; 78: PubMed Scopus Google Scholar). In fact, be generated by using in which for have been into domain of the crystal structure of domain I was at Å resolution (Fig. 1B) T.L. J. Rice C.M. Nature. 2005; PubMed Scopus Google Scholar). It is composed of a N-terminal and a predominantly C-terminal In a zinc ion is coordinated by a motif of conserved which are essential for RNA replication T.L. J. Rice C.M. J. Biol. Chem. 2004; 279: Full Text Full Text PDF PubMed Scopus Google Scholar, T.L. J. Rice C.M. Nature. 2005; PubMed Scopus Google Scholar). In an 2 residues the C-terminal was Since this is rather for a role can be However, mutational analysis showed that it is not essential for HCV RNA replication T.L. J. Rice C.M. J. Biol. Chem. 2004; 279: Full Text Full Text PDF PubMed Scopus Google Scholar). It remains to be whether the also forms in and whether it a role in some of the viral life I forms via the N-terminal of the molecules in a or (Fig. 1B). The molecular involved in dimer formation is highly conserved that also in vivo. domain I a a and a The has been to with the groups by the N-terminal α-helix (Fig. 1B) T.L. J. Rice C.M. Nature. 2005; PubMed Scopus Google Scholar). The in the side of the is from the membrane and with RNA T.L. J. Rice C.M. Nature. 2005; PubMed Scopus Google Scholar). It was found that binds to the of HCV positive and negative strand RNA with a preference for the poly(U/UC) tract in the 3′-NTR of positive strand RNA L. Hwang J. Chen J. Biol. Chem. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar). into an This may as a system viral RNA between for RNA replication, and In of HCV RNA by binding to it from and the of intracellular dsRNA as the of domains II and on structure and function of domain I is not However, one can that these domains domain I by of the or by of host cell and this be by phosphorylation is as a and a form and with phosphorylation mediated by an as yet cellular at and to a residues (1Bartenschlager R. Frese M. Pietschmann T. Adv. Virus Res. 2004; 63: 71-180Crossref PubMed Scopus (243) Google Scholar). phosphorylation on from the C-terminal region of I to the of NS5A, while residues required for in I T. S. K. J. Virol. PubMed Google Scholar). The major sites of to be or and have been only for and B. D.R. C.M. P. S.L. R. 2000; PubMed Scopus Google Scholar, Rice C.M. J. Biol. 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This binding may the enzyme to the of positive strand RNA for which the and SL2 RNA-RNA interaction may be required (Fig. crystal structure of the NS5B catalytic domain revealed a structural fold with other with and subdomains (Fig. 1B) S. L. A. M. R. Rey F.A. Proc. Natl. Acad. Sci. U. S. A. 1999; PubMed Scopus Google Scholar, C.A. Cable E. Hong Z. Weber P.C. Nat. Struct. Biol. 1999; 6: PubMed Scopus Google Scholar). One structural of the enzyme is the active site, which is due to multiple between the and subdomains a in which a RNA molecule is to the active the active site via of the RNA template and initiation of RNA are to be by a highly flexible (Fig. 1B) in the domain and the active site C.A. Cable E. Hong Z. Weber P.C. Nat. Struct. Biol. 1999; 6: PubMed Scopus Google Scholar, W. E. Hong Z. J. Virol. 2000; PubMed Scopus Google Scholar). This a that prevents the of the template from the active site and that initiation of RNA from the of the interesting of NS5B is a low site at the interface of the and and on the