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The cellular protein GBF1, an activator of Arf GTPases (ArfGEF: Arf guanine nucleotide exchange factor), is recruited to the replication organelles of enteroviruses through interaction with the viral protein 3A, and its ArfGEF activity is required for viral replication, however how GBF1-dependent Arf activation supports the infection remains enigmatic. Here, we investigated the development of resistance of poliovirus, a prototype enterovirus, to increasing concentrations of brefeldin A (BFA), an inhibitor of GBF1. High level of resistance required a gradual accumulation of multiple mutations in the viral protein 2C. The 2C mutations conferred BFA resistance even in the context of a 3A mutant previously shown to be defective in the recruitment of GBF1 to replication organelles, and in cells depleted of GBF1, suggesting a GBF1-independent replication mechanism. Still, activated Arfs accumulated on the replication organelles of this mutant even in the presence of BFA, its replication was inhibited by a pan-ArfGEF inhibitor LM11, and the BFA-resistant phenotype was compromised in Arf1-knockout cells. Importantly, the mutations strongly increased the interaction of 2C with the activated form of Arf1. Analysis of other enteroviruses revealed a particularly strong interaction of 2C of human rhinovirus 1A with activated Arf1. Accordingly, the replication of this virus was significantly less sensitive to BFA than that of poliovirus. Thus, our data demonstrate that enterovirus 2Cs may behave like Arf1 effector proteins and that GBF1 but not Arf activation can be dispensable for enterovirus replication. These findings have important implications for the development of host-targeted anti-viral therapeutics. Author summary: As ultimate intracellular parasites, viruses rely on cellular proteins for every step of their life cycle. This provides a possibility of controlling viral replication by targeting the cellular factors. Such therapeutics are expected to be more difficult to develop resistance to since cellular proteins do not change. Yet, enteroviruses, a large group of small positive RNA viruses that are associated with multiple human pathologies, rapidly develop resistance to virtually all experimental therapeutics including compounds targeting host factors essential for the viral replication. Here we investigated in detail the development of enterovirus resistance to one of such compounds targeting a host protein GBF1 that activates small GTPases of the Arf family. We found that while the mutations in a resistant virus make it insensitive to the inhibition of GBF1, the virus acquired the capability of obtaining activated Arfs from other cellular sources and that the interaction of one of the viral proteins with activated Arfs is likely essential for the functioning of the replication complex. Thus, our work revealed that it is not GBF1 per se, but activated Arfs that are indispensable for viral replication, which provides new opportunities for the development of anti-enterovirus therapeutics refractory to the development of resistance. [ABSTRACT FROM AUTHOR]

As ultimate parasites, viruses depend on host factors for every step of their life cycle. On the other hand, cells evolved multiple mechanisms of detecting and interfering with viral replication. Yet, our understanding of the complex ensembles of pro- and anti-viral factors is very limited in virtually every virus-cell system. Here we investigated the proteins recruited to the replication organelles of poliovirus, a representative of the genus Enterovirus of the Picornaviridae family. We took advantage of a strict dependence of enterovirus replication on a host protein GBF1, and established a stable cell line expressing a truncated GBF1 fused to APEX2 peroxidase that effectively supported viral replication upon inhibition of the endogenous GBF1. This construct biotinylated multiple host and viral proteins on the replication organelles. Among the viral proteins, the polyprotein cleavage intermediates were overrepresented, suggesting that the GBF1 environment is linked to viral polyprotein processing. The proteomics characterization of biotinylated host proteins identified multiple proteins previously associated with enterovirus replication, as well as more than 200 new factors recruited to the replication organelles. RNA metabolism proteins, many of which normally localize in the nucleus, constituted the largest group, underscoring the massive release of nuclear factors into the cytoplasm of infected cells and their involvement in viral replication. Functional analysis of several newly identified proteins revealed both pro- and anti-viral factors, including a novel component of infection-induced stress granules. Depletion of these proteins similarly affected the replication of diverse enteroviruses indicating broad conservation of the replication mechanisms. Thus, our data significantly expand the knowledge of the composition of enterovirus replication organelles, provide new insights into viral replication, and offer a novel resource for identifying targets for anti-viral interventions. Author summary: Enteroviruses are arguably the most numerous group of viral pathogens infecting humans. Enterovirus infection can cause multiple complications including the development of asthma, type I diabetes, myocarditis, encephalitis, paralysis, and many others. Yet, there are no approved drugs against any of the pathogenic enteroviruses. The lack of effective anti-enterovirus measures is due in large part to insufficient understanding of molecular mechanisms supporting the development of enterovirus infections. Here, we developed a novel probe based on a host protein GBF1 that is universally required for enterovirus RNA replication to identify the proteins localized on enterovirus replication organelles, specialized membranous structures harboring the viral RNA replication complexes. Among the host proteins, we identified factors that promote and suppress the replication of diverse enteroviruses. Thus, our research provides new insights into molecular mechanisms of enterovirus replication and presents an important resource for the development of host-targeted anti-viral interventions. [ABSTRACT FROM AUTHOR]