As obligatory intracellular parasites, viruses depend on their host for all steps of their reproduction, starting from uptake by the cell to the final encapsidation of progeny virions and exit from the cell, as well as their spread within the host. Thus, host factors can be expected to participate at most-if not all-levels of virus reproduction. The present review aims at providing an updated view of the host factors presently believed to participate in replication/transcription of RNA viruses. However, it does not deal with viruses that resort to reverse transcription, nor does it discuss the many protein-modifying enzymes such as phosphorylating enzymes whose indirect participation in viral genome amplification is undeniable. The reader may wish to turn to various other reviews dealing with certain aspects of genome amplification of RNA viruses for complementary information (Ahlquist et al., 2003; Buck, 1996; De and Banerjee, 1997; Lai, 1998). Determining what host factors are required for viral protein synthesis has been rather straightforward since viruses rely entirely on the host protein synthesizing machinery to produce their own proteins (Ehrenfeld, 1996), although in certain cases they recruit additional cell proteins not normally involved in translation regulation. On the other hand, searching for host factors involved in transcription and replication of RNA viruses has proven to be much trickier. Originally, the prevailing seemingly simple view of virus genome replication was modeled on the replication of RNA phages such as Qβ (Klovins and van Duin, 1999; Schuppli et al., 2000). Yet it soon became apparent that the situation is far more complex for eukaryotic RNA viruses than for RNA phages. Multiplication of the genome of most RNA viruses takes place in the cytoplasm. However, influenza virus (Orthomyxoviridae) (Wang et al., 1997) and Borna disease virus (Paramyxoviridae) (Pyper et al., 1998) replicate in the nucleus. An interesting consequence of this nuclear localization is that transcription in these viruses can be accompanied by splicing, a process requiring the host's splicing machinery (Lamb and Horvath, 1991; Tomonaga et al., 2002). In addition, an increasing number of RNA viruses require the nucleus in certain steps of their life cycle (Hiscox, 2003). Arenaviruses cannot complete their replication cycle in cells enucleated soon after infection (Borden et al., 1998). On the other hand, certain (+) as well as (-) strand RNA viruses grow in enucleate cells, virus yield being related to the length of the virus growth cycle (Follett et al., 1975). Several viruses target some of their proteins to the nucleus (Hiscox, 2003; Urcuqui-Inchima et al., 2001), whereas others such as hepatitis C virus (HCV; Flaviviridae) code for proteins that contain nuclear localization signals but do not seem to enter the nucleus (Song et al., 2000). Finally, infection by members of the Picornaviridae, such as poliovirus and coxsackievirus, and by vesicular stomatitis virus (VSV; Rhabdoviridae) (Belov et al., 2000; Gustin and Sarnow, 2001) triggers relocation of certain nuclear proteins to the cytoplasm, suggesting that these proteins probably participate in the life cycle of the virus (Hiscox, 2003). For viruses that produce subgenomic (sg) RNAs, a distinction must be made between two mechanisms, replication of the entire genome and transcription, which usually entails amplification of only certain regions of the genome to yield the sg mRNAs. Since sgRNAs are generally 3′ coterminal, an internally located open reading frame (ORF) in the genomic (g) RNA can become 5′ proximal in the sgRNA, a more favorable situation for the eukaryotic translation apparatus. To date, most of the information available concerning the role of host factors in viral RNA amplification deals with replication, while information concerning host factors and transcription is less abundant except for (-) strand RNA viruses and for viruses of the Coronaviridae, Arteriviridae, and Closteroviridae families (Miller and Koev, 2000). All RNA viruses contain within their genome the information for the synthesis of an RNA-dependent RNA polymerase that shall be referred to as the RdRp or polymerase. The viral polymerase and other viral proteins as well as host factors participate in RNA transcription and replication. Yet, how the switch occurs between transcription and replication remains largely enigmatic. During replication, the RNA strand complementary to the genome strand is produced in far lower amounts than the newly synthesized genome strands. How this imbalance is regulated and what factors may be involved in this bias is also far from clear. Nevertheless, some results have appeared suggesting that certain host factors participate in synthesis of one but not of the other strand. The sequence of events that leads to virus amplification depends on whether the viral RNA entering the cell is of (+) or of (-) polarity. The incoming genome of many (+) strand RNA viruses (Fig. 1) serves as mRNA for virus protein synthesis including the RdRp, and is then replicated yielding the complementary (-) RNA strand. In many virus groups, the (-) strand serves as a template to transcribe the sgRNAs that will serve as mRNAs (Miller and Koev, 2000). The (-) strand is also replicated, producing nascent full-length (+) strands; these are used as mRNA for protein synthesis, as a template for further (-) strand synthesis, and ultimately as a genome to be encapsidated, yielding progeny virus particles. Exceptions to this general scheme exist. Red clover necrotic mosaic tombusvirus (Sit et al., 1998) and citrus tristeza closterovirus (Gowda et al., 2001) generate (-) strand sgRNAs that might function as templates for sg mRNA synthesis. Production of sgRNAs in viruses of the Coronaviridae and Arteriviridae families (both of the order Nidovirales) involves a mechanism similar to splicing known as discontinuous sgRNA synthesis: the transcripts are both 3′ and 5′ coterminal (Fig. 2). In this strategy, synthesis of a sgRNA proceeds on a template. The initiated sgRNA, together with the polymerase, then switches from its position to another complementary region called transcription-regulating sequence (TRS) on the template to which it can base-pair and resume synthesis. The step at which the nascent RNA chain is transferred from one region of the template to another remains controversial-it could occur during (+) or (-) strand synthesis. The recent demonstration of the presence of (-) sg strands favors the latter possibility (Pasternak et al., 2001; Sawicki et al., 2001). TRSs present in the 3′ end of the leader and at the 5′ end of the sgRNA body regions in the gRNA could allow the nascent RNA chain to be transferred to the leader TRS by TRS-TRS (sense-antisense) base-pairing, or conversely could allow the RNA chain in the leader to be transferred to the sgRNA. The scheme for (-) strand RNA viruses is different from that of (+) strand RNA viruses because the incoming RNA cannot serve as a template for protein synthesis. Consequently, all viruses with a (-) strand RNA genome encapsidate their polymerase complex, including host factors. The genome tightly bound to the nucleocapsid protein as a ribouncleoprotein (RNP) with its associated polymerase (De and Banerjee, 1997) is either replicated into complementary (+) strands, or transcribed to produce sg mRNAs. The mechanism of transcription depends on whether the virus contains a nonsegmented or a segmented genome. In nonsegmented (i.e., monopartite) (-) RNA viruses (order: Mononegavirales), such as the Paramyxoviridae and Rhabdoviridae, the 3′ and the 5′ termini of the (-) sense gRNA are known as the 3′ leader promoter and 5′ trailer region, respectively (Fig. 3). The 3′ region of the complementary (+) sense RNA or antigenome, known as the trailer, directs synthesis of the gRNA. In transcription, synthesis of complementary (+) sgRNAs begins at the 3′ end (3′ leader) of the incoming (-) strand genome producing a short leader RNA, followed by monocistronic capped and poly(A)-tailed mRNAs by sequential transcription. The 5′ trailer region of the genome and the intercistronic regions separating the ORFs are not transcribed (Kolakofsky et al., 2004). Transcription of segmented (-) strand RNA viruses such as the Orthomyxoviridae, Arenaviridae, Bunyaviridae, and Tenuiviruses requires a primer to initiate synthesis of the mRNAs. This is achieved by cap-snatching in which the replicase complex, or a protein thereof, binds to the 5′ region of cell mRNAs, cleaves off the cap together with generally 7-15 nucleotides from the 5′ end of the cell mRNA, and uses this fragment as a primer to initiate synthesis of the viral mRNAs (Bouloy et al., 1978; Nguyen and Haenni, 2003). Hence, the viral mRNAs are capped and have cell-derived nucleotides at their 5′ end; they also contain a poly(A) tail at their 3′ end. Replication, on the other hand, is not primer-dependent, and the RNAs complementary to the genome are devoid of cap and of poly(A) tail. © 2005 Elsevier Inc. All rights reserved.
