Genetic Analysis of the Carboxy-Terminal Region of the Hepatitis C Virus Core Protein

Hepatitis C virus (HCV) is a liver-tropic pathogen with severe health consequences for infected individuals. Chronic HCV infection can progress to cirrhosis and hepatocellular carcinoma and is a leading indicator for liver transplantation. The HCV core protein is an essential component of the infectious virus particle, but many aspects of its role remain undefined. The C-terminal region of the core protein acts as a signal sequence for the E1 glycoprotein and undergoes dual processing events during infectious virus assembly. The exact C terminus of the mature, virion-associated core protein is not known. Here, we performed genetic analyses to map the essential determinants of the HCV core C-terminal region, as well as to define the minimal length of the protein that can function for infectious virus production in trans.Hepatitis C virus (HCV) is a major contributor to the development of human liver diseases, infecting approximately 2% of the population, or 130 million people, worldwide (2). Up to 80% of HCV infections progress to chronic hepatitis and can lead to cirrhosis and hepatocellular carcinoma (38). No vaccine exists to prevent HCV infection, and current treatments are frequently inadequate.HCV is an enveloped virus of the genus Hepacivirus in the family Flaviviridae (30). The single-stranded, positive-sense RNA genome encodes a polyprotein of about 3,000 amino acids, which is processed by viral and host proteases into three structural proteins (the core protein, E1, and E2) and seven presumed nonstructural proteins (p7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B). The core protein is thought to encapsidate the RNA genome within the virion, forming a complex that is surrounded by a host cell-derived lipid bilayer displaying the envelope glycoproteins, E1 and E2. Although not thought to be components of the virion, p7 and NS2 have recently been implicated in the production of infectious virus (5, 12, 29, 33, 39). The remaining nonstructural proteins, NS3 to NS5B, are essential for genome replication and have additional emerging roles in virus assembly. NS3 possesses RNA helicase/NTPase activities and together with its cofactor, NS4A, forms the major viral protease. NS5B is the RNA-dependent RNA polymerase (reviewed in references 16 and 27).The core protein is the first protein produced during translation of the incoming viral genome. A signal sequence in its C-terminal region targets the nascent E1 glycoprotein to the endoplasmic reticulum (ER) membrane and is the substrate for processing by two host proteases. Cleavage by signal peptidase (SP) following core amino acid 191 (31) is thought to precede processing by signal peptide peptidase (SPP) (20, 26), an integral membrane aspartyl protease that cleaves within transmembrane segments (37). The C terminus of the mature, infectious-virion-associated core protein has not been determined, but it is speculated to lie between amino acids 173 and 182 (24, 31). SPP processing has been shown to mobilize the core from the ER membrane and enable it to traffic to lipid droplets (20). These triglyceride-rich storage organelles have recently been shown to be the sites of HCV particle assembly (21). Consistent with this finding, impaired SPP activity leads to decreased HCV infectious titers (34). Dual processing of the core proteins is a common feature of the Flaviviridae family. GB virus B, a hepacivirus, and classical swine fever virus, a related pestivirus, encode core proteins that undergo SP and SPP processing during maturation (8, 35). In the genus Flavivirus, the capsid protein undergoes regulated cleavage by the viral NS2B-3 protease and SP; this stepwise processing has been shown to be essential for proper encapsidation of genomes into infectious particles (3).The development of an infectious cell culture system for HCV has been a major breakthrough in the field (7). Many details of virus morphogenesis and infectivity, however, are still unknown. In this study, we examined the role of the C-terminal portion of the HCV core protein and identified individual amino acids that are essential for infectious virus assembly and core protein stability. Findings from alanine-scanning and transcomplementation studies suggest that at least 177 residues of the core protein are needed to produce infectious particles.