Host Factors in Positive-Strand RNA Virus Genome Replication

All viruses are gene poor relative to their hosts: even the largest viral genomes only encode hundreds of genes, while those of host cells typically encode tens of thousands of genes. Thus, most steps in virus infection involve interactions between relatively few different types of viral components and much more complex pools of host factors. This sea of host factors represents both the essential milieu to which viruses must adapt for survival and a tremendous, manipulatable resource for gene-poor viruses. Accordingly, host factors play important roles in most steps of viral infection, and identifying such host factors and their contributions has long been recognized as an important frontier. The continuing emergence of close integration between viral and host functions in infection suggests moving beyond separate views of virus and host to a more holistic view of the virus-infected cell as a unified entity that constitutes the functional unit of infection. One area in which the importance of host factors is increasingly emerging is the replication of positive-strand RNA viruses. Positive-strand RNA viruses encompass over one-third of all virus genera and include numerous pathogens, such as the severe acute respiratory syndrome coronavirus SARS, hepatitis C virus (HCV), and many of the viruses on the U.S. Health and Human Services Department Select List of potential bioterrorism agents. Host factors participate in most, if not all, steps of positive-strand RNA virus infection, including entry, viral gene expression, virion assembly, and release. Moreover, host factors are targeted by positive-strand RNA viruses to modulate host gene expression and defenses. This review focuses on host factors involved in positivestrand RNA virus genome replication. The evidence for such host factor involvement has come from varied genetic and biochemical approaches (15). These include, among others, studies based on the varying permissiveness of some cell types and extracts for RNA replication (2, 3, 4, 19); identification of many host proteins that interact with viral genomic RNAs or replication proteins and, in some cases, have been functionally linked to replication (5, 18, 27, 35, 37, 40); and mutational screens in genetic model systems, such as Arabidopsis thaliana (17, 39) and the yeast Saccharomyces cerevisiae (8, 11, 16, 23, 38). Recent data show that host factors play important roles in assembling the viral RNA replication complex, selecting and recruiting viral RNA replication templates, activating the complex for RNA synthesis, and other steps. Each of these virushost interactions may contribute to the host specificity, tissue specificity, or pathology of infections. Each such virus-host interaction also represents a potential target for virus control or for optimization to improve beneficial uses of viruses and their components. Positive-strand RNA viruses can be divided into a number of superfamilies defined by distinguishable RNA replication genes and features (41). Nevertheless, the RNA replication mechanisms of these viruses share sufficient similarities to make it reasonable to discuss their replication as a class and to attempt to draw general lessons by comparing examples from different superfamilies. As discussed further below, a few of the common features shared by positive-strand RNA viruses are the need to coordinate use of the infecting viral genomic RNA as a template for translation and replication, assembly of replication complexes on intracellular membranes, and production of 10- to 100-fold excesses of positive- over negativestrand RNA. A simplified general scheme for RNA replication by positive-strand RNA viruses is shown in Fig. 1. Below we discuss the involvement of host factors in the various stages of this RNA replication process, using examples from a number of viruses. We regret that space limitations do not allow us to cite all of the work being done in this exciting area.