The 335 exoribonucleases, RNase II and polynucleotide phosphorylase (PNPase), play an essential role in degrading fragments of mRNA generated by prior cleavages by endonucleases. We have assessed the ability of small RNA substrates containing defined stem-loop structures and variable 3 extensions to impede the exonucleolytic activity of these enzymes. We find that stem-loops containing five G-C base pairs do not block either enzyme; in contrast, more stable stem-loops of 7, 9, or 11 bp block the processive action of both enzymes. Under conditions where enzyme activity is limiting, both enzymes stall and dissociate from their substrates six to nine residues, on average, from the base of a stable stem-loop structure. Our data provide a clear mechanistic explanation for the previous observation that RNase II and PNPase behave as functionally redundant.In the bacterium Escherichia coli, degradation of mRNA is almost always initiated by an endoribonuclease, usually RNase E (1, 26). At least two 3Ј exoribonucleases subsequently attack the newly created 3Ј termini generated by RNase E. One of these, RNase II, a monomer with a molecular mass of 72.5 kDa, is hydrolytic (31) and accounts for up to 90% of the exoribonucleolytic activity in crude extracts (12). The other, polynucleotide phosphorylase (PNPase), a trimer with 78-kDa subunits, is phosphorolytic and accounts for the remaining 10% of the exoribonuclease activity in E. coli extracts (12). Although strains singly mutated in the genes encoding RNase II (rnb) or PNPase (pnp) exhibit a mild phenotype, double mutants deficient in both PNPase and RNase II are inviable (13). This finding has been interpreted to indicate that these exonucleases are functionally redundant but collectively essential. Other data, however, suggest that RNase II and PNPase are not functionally equivalent but are differentially sensitive to RNA secondary structure (3,7,8,16,19,24,28). In such cases, PNPase is required for the degradation of highly structured RNAs and RNase II cannot substitute (7,8,19). Moreover, RNase II, but not PNPase, may actually stabilize some RNAs (3,28). In addition, while RNase II behaves as a soluble monomeric enzyme (31), PNPase can be assembled into a multienzyme complex, the degradosome (5, 27, 29). In the complex, PNPase can degrade extensively structured RNA substrates in concert with RhlB, a putative DEAD-box RNA helicase (10, 29). Alternatively, the action of PNPase against folded RNAs can be stimulated by prior 3Ј polyadenylation of such substrates (2, 33). RNase II can also be stimulated by polyadenylation in vitro, but to a more limited extent (7).In order to resolve the paradoxical properties of RNase II and PNPase, we compared their abilities to degrade short synthetic RNA substrates containing a single stem-loop of defined size and thermal stability. This would permit us to test directly whether both enzymes are functionally equivalent. In addition, we could measure the minimum size of base-paired stems which would stall each enzyme and consequently pred...

The protein NPR1/NIM1 is required for the induction of systemic acquired resistance (SAR) in plants and has been shown to interact with members of the TGA/OBF family of basic leucine zipper (bZIP) transcription factors. However, to date, there is no method available to monitor such interactions in plant cells. We report here an in vivo protein fragment complementation assay (PCA), based on association of reconstituted murine dihydrofolate reductase (mDHFR) with a fluorescent probe to detect protein-protein interaction in planta. We demonstrate that the interaction between Arabidopsis NPR1/NIM1 and the bZIP factor TGA2 is induced by the regulators of SAR, salicylic acid (SA), and its analog 2,6-dichloroisonicotinic acid (INA) with distinct species-specific responses. Furthermore, the induced interaction is localized predominantly in the nucleus. Protein fragment complementation assays could be of value to agricultural research by providing a system for high-throughput biochemical pathway mapping and for screening of small molecules that modulate protein interactions.

Human rhinovirus (HRV) is the predominant cause of the common cold, but more importantly, infection may have serious repercussions in asthmatics and chronic obstructive pulmonary disorder (COPD) patients. A cell-based antiviral screen against HRV was performed with a subset of our proprietary compound collection, and an aminothiazole series with pan-HRV species and enteroviral activity was identified. The series was found to act at the level of replication in the HRV infectious cycle. In vitro selection and sequencing of aminothiazole series-resistant HRV variants revealed a single-nucleotide mutation leading to the amino acid change I42V in the essential HRV 3A protein. This same mutation has been previously implicated in resistance to enviroxime, a former clinical-stage antipicornavirus agent. Enviroxime-like compounds have recently been shown to target the lipid kinase phosphatidylinositol 4-kinase III beta (PI4KIII␤). A good correlation between PI4KIII␤ activity and HRV antiviral potency was found when analyzing the data over 80 compounds of the aminothiazole series, covering a 750-fold potency range. The mechanism of action through PI4KIII␤ inhibition was further demonstrated by small interfering RNA (siRNA) knockdown of PI4KB, which reduced HRV replication and also increased the potency of the PI4KIII␤ inhibitors. Inhibitors from two different structural classes with promising pharmacokinetic profiles and with very good selectivity for PI4KIII␤ were used to dissociate compound-related toxicity from target-related toxicity. Mortality was seen in all dosing groups of mice treated with either compound, therefore suggesting that short-term inhibition of PI4KIII␤ is deleterious.

The in vitro resistance profile of BI 201335 was evaluated through selection and characterization of variants in genotype 1a (GT 1a) and genotype 1b (GT 1b) replicons. NS3 R155K and D168V were the most frequently observed resistant variants. Phenotypic characterization of the mutants revealed shifts in sensitivity specific to BI 201335 that did not alter susceptibility to alpha interferon. In contrast to macrocyclic and covalent protease inhibitors, changes at V36, T54, F43, and Q80 did not confer resistance to BI 201335.T he hepatitis C virus (HCV)-encoded NS3 protease is essential for viral replication and has long been considered an attractive target in drug design efforts (3, 5). NS3 protease inhibitors (PIs) can induce substantial reductions in HCV RNA plasma levels, and several candidates have progressed through clinical development to offer improved treatment options (for a review, see reference 27). Two PIs, boceprevir and telaprevir, were recently approved for use in combination with pegylated interferon (Peg-IFN) and ribavirin (1,6,7,19). The selection of drug-resistant variants is commonly observed in patients experiencing virologic rebound during treatment with PIs (16,[20][21][22]24).BI 201335 is a potent HCV NS3/4A PI (15, 28) currently in phase 3 clinical trials in combination with Peg-IFN and ribavirin as well as phase 2 assessment with other HCV direct acting antivirals in IFN-sparing regimens. BI 201335 exhibited a profound reduction in viral load when administered for 14 days as monotherapy in treatment-naïve patients or for 28 days in combination with Peg-IFN and ribavirin in treatment-experienced patients (16). In these studies, viral breakthrough was observed in most patients on monotherapy, whereas breakthrough was less frequent in patients undergoing combination treatment. Distinct resistant NS3 variants R155K and D168V predominated for genotype 1a and 1b (GT 1a and GT 1b), respectively (8,16).This study was designed to evaluate the genotypic and phenotypic profiles of the resistant variants that emerged during in vitro selection in the presence of BI 201335 in the replicon system and to relate these results to clinical observations. Replicons resistant to BI 201335 were selected in GT 1a H77 and GT 1b CON-1 replicon cell lines in the presence of 2 concentrations (100ϫ and 1,000ϫ drug concentration required to reduce HCV RNA or the luciferase reporter levels by 50% [EC 50 ]) of drug for 3 weeks and G-418 as previously described (9). With the lower concentration of BI 201335, resistant variants encoding NS3 changes at residues 155, 156, and 168 were selected with the GT 1b replicon, with D168G as the predominant variant (55%). R155K was the predominant variant (68%) selected with the GT 1a replicon (Table 1) and is consistent with the predominant variant selected in GT 1a HCV-infected patients (16). At the higher concentration of BI 201335, essentially only D168 variants were selected with D168 A and V as the predominant variants in both genotypes.In order to confirm that the mutations ob...

RNA vaccines have demonstrated efficacy against SARS-CoV-2 in humans and the technology, is being leveraged for rapid emergency response. In this report, we assessed immunogenicity, and, for the first time, toxicity, biodistribution and protective efficacy in preclinical models of a two-dose self-amplifying messenger RNA (SAM) vaccine, encoding a prefusion stabilized Spike antigen of SARS-CoV-2 Wuhan-Hu-1 strain and delivered by lipid nanoparticles (LNP). In mice, one immunization with the SAM vaccine elicited a robust Spike-specific antibody response, which was further boosted by a second immunization, and effectively neutralized the matched SARS-CoV-2 Wuhan strain as well as B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta) variants. High frequencies of Spike-specific germinal center B, Th0/Th1 CD4, and CD8 T cell responses were observed in mice. Local tolerance, potential systemic toxicity, and biodistribution of the vaccine were characterized in rats. In hamsters, the vaccine candidate was well-tolerated, markedly reduced viral load in the upper and lower airways, and protected animals against disease in a dose-dependent manner, with no evidence of disease enhancement following SARS-CoV-2 challenge. Therefore, the SARS-CoV-2 SAM (LNP) vaccine candidate has a favorable safety profile, elicits robust protective immune responses against multiple SARS-CoV-2 variants, and has been advanced to Phase-1 clinical evaluation (NCT04758962).