In RNA-directed silencing pathways, ternary complexes result from small RNA-guided ARGONAUTE (AGO) associating with target transcripts. Target transcripts are often silenced through direct cleavage (slicing), destabilization through slicerindependent turnover mechanisms, and translational repression. Here, wild-type and active-site defective forms of several Arabidopsis thaliana AGO proteins involved in posttranscriptional silencing were used to examine several AGO functions, including small RNA binding, interaction with target RNA, slicing or destabilization of target RNA, secondary small interfering RNA formation, and antiviral activity. Complementation analyses in ago mutant plants revealed that the catalytic residues of AGO1, AGO2, and AGO7 are required to restore the defects of Arabidopsis ago1-25, ago2-1, and zip-1 (AGO7-defective) mutants, respectively. AGO2 had slicer activity in transient assays but could not trigger secondary small interfering RNA biogenesis, and catalytically active AGO2 was necessary for local and systemic antiviral activity against Turnip mosaic virus. Slicer-defective AGOs associated with miRNAs and stabilized AGO-miRNA-target RNA ternary complexes in individual target coimmunoprecipitation assays. In genome-wide AGO-miRNA-target RNA coimmunoprecipitation experiments, slicerdefective AGO1-miRNA associated with target RNA more effectively than did wild-type AGO1-miRNA. These data not only reveal functional roles for AGO1, AGO2, and AGO7 slicer activity, but also indicate an approach to capture ternary complexes more efficiently for genome-wide analyses.

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Recently, a benzo-1,2,4-thiadiazine antiviral agent (C 21 H 21 N 3 O 4 S; compound 4) was shown to be a potent, highly specific inhibitor of the primary catalytic enzyme of the hepatitis C virus (HCV) replicase complex. In this study, we selected for resistance to confirm the mechanism of action for compound 4 in HCV replicon cells. As expected, spontaneous mutations or fluidity in the HCV polymerase (NS5B) coding sequence occurred upon routine passage of the HCV replicon cells in the absence of compound 4. After 1 month of culture in the presence of 10 M compound 4, or 20 times the 50% inhibitory concentration of the replicon, replicon cells were almost 20-fold less susceptible to compound 4. Twenty-one NS5B cDNA clones were generated from the resistant replicon cells. Five mutations in the 21 NS5B clones were present at frequencies higher than that of control replicon cells, and no clone contained more than a single mutation within the polymerase gene. RNA-dependent RNA polymerase studies using purified recombinant NS5B containing these single point mutations allowed the identification of residue 414 as sufficient for biochemical resistance to compound 4. Further, the contribution of this residue to confer cell-based resistance to compound 4 was validated using a stable recombinant mutant replicon cell line which harbors a methionine-to-threonine change at residue 414. The potential for additional mutations in other nonstructural genes of HCV to contribute to the resistance profile of compound 4 is discussed.Hepatitis C virus (HCV), a positive-strand RNA virus of the Flaviviridae family, represents the major etiological agent of posttransfusion and sporadic non-A, non-B hepatitis (4). The nonstructural protein 5B (NS5B) encodes the catalytic polymerase which is responsible for RNA-dependent RNA polymerase (RdRp) activity (1, 12) and terminal transferase activity (15). Flaviviridae RdRps have been shown to initiate RNA synthesis via a de novo mechanism based on in vitro assays (10,11,14,16,18), a process that is also presumed to occur in HCV-infected cells (9).Recent structural analysis (3) and cell-based replicon systems have advanced our understanding of HCV replication. These systems rely upon the nonstructural proteins to stably replicate subgenomic viral RNA in Huh-7 cells (2, 13), and they have been used to evaluate antiviral agents. Recently, a benzothiadiazine compound was shown to have highly specific antiviral activity against the HCV RdRp, inhibiting viral RNA synthesis in both biochemical and cell-based replicon systems (5). Further, this agent shows synergy with interferon-alpha (IFN-␣) in the replicon system, confirming a distinct mode of action (V. K. Johnston, D. Maley, R. Gagnon, C. W. Grassmann, S.-E. Behrens, and R. T. Sarisky, unpublished data). Although HCV replication is sensitive to IFN-␣ with a 50% inhibitory concentration (IC 50 ) of less than 10 U/ml, long-term treatment with up to 1,000 U/ml in the presence of G418 to maintain the replicon RNA did not yield IFN-resistant variants (7)....

Virology 132:26-37, 1984). Typically, these resistance mutations map to the thymidine kinase (TK) gene and render the virus TK deficient. To examine this process more closely, a plating efficiency assay was used to determine whether the frequencies of naturally occurring mutations in populations of the laboratory strains HSV-1 SC16, HSV-2 SB5, and HSV-2 333 grown in MRC-5 cells were similar when scored for resistance to penciclovir (PCV) and ACV. Our results indicate that (i) HSV mutants resistant to PCV and those resistant to ACV accumulate at approximately equal frequencies during replication in cell culture, (ii) the spontaneous mutation frequency for the HSV-1 strain SC16 is similar to that previously reported for HSV-1 laboratory strains KOS and Cl101, and (iii) spontaneous mutations in the laboratory HSV-2 strains examined were 9-to 16-fold more frequent than those in the HSV-1 strain SC16. These observations were confirmed and extended for a group of eight clinical isolates in which the HSV-2 mutation frequency was approximately 30 times higher than that for HSV-1 isolates. In conclusion, our results indicate that the frequencies of naturally occurring, or spontaneous, HSV mutants resistant to PCV and those resistant to ACV are similar. However, HSV-2 strains may have a greater propensity to generate drug-resistant mutants than do HSV-1 strains.The antiviral drug standard for the treatment of herpes simplex virus (HSV) infections including herpes labialis and genital herpes for almost 2 decades has been acyclovir (ACV) [9-(2-hydroxyethoxymethyl)guanine]. However, with the more recent introduction of penciclovir (PCV) (BRL 39123) [9-(4-hydroxy-3-hydroxymethylbut-1-yl)guanine] and its oral prodrug, famciclovir, the usage of antivirals alternative to ACV for the management of herpesvirus infections has also increased. Identical activation pathways and similar modes of action suggest that the mechanisms of HSV resistance to PCV and ACV are likely to be analogous (2, 40). An assumption that the frequency with which resistance in HSV arises is identical for PCV and ACV can be based on the biochemical similarities of the two compounds and the cross-resistance of thymidine kinase (TK)-negative mutants; however, direct genetic evidence is not available.A low level of replication errors is typically associated with DNA synthesis (10, 33). Resistance to PCV or ACV can arise by a single base mutation in the DNA encoding the HSV TK protein which activates the antiviral agent (6, 23, 29). These spontaneous mutations occur during DNA replication and are independent of the presence of antiviral drug (16). These errors, or random mutations, provide genetic diversity to facilitate the adaptation and evolution of an organism (15). Data from a study of the molecular evolution of HSV type 1 (HSV-1) show that its evolution is slow; the mutation rate was estimated to be 3.5 ϫ 10 Ϫ8 substitutions per site per year (36). Mispaired deoxyribonucleoside triphosphates are often removed by the HSV polymerase (Pol) through its associat...

In this study, we present several lines of evidence to demonstrate that this inhibitor interferes with the initiation step of RNA synthesis rather than acting as an elongation inhibitor. Inhibition of initial phosphodiester bond formation occurred regardless of whether replication was initiated by primer-dependent or de novo mechanisms. Filter binding studies using increasing concentrations of compound 4 did not interfere with the ability of ⌬21 HCV RdRp to interact with nucleic acid. Furthermore, varying the order of reagent addition in the primer extension assay showed no distinct differences in inhibition profile. Finally, surface plasmon resonance analyses provided evidence that a ternary complex is capable of forming between the RNA template, RdRp, and compound 4. Together, these data suggest that this heterocyclic agent interacts with the apoenzyme, as well as with the RNAbound form of ⌬21 HCV RdRp, and therefore does not directly interfere with the RdRp-RNA interaction to mediate inhibition.