RNA template-mediated inhibition of hepatitis C virus RNA-dependent RNA polymerase activity

The enzymatic activity of hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B is modulated by the molar ratio of NS5B enzyme and RNA template. Depending on the ratio, either template or enzyme can inhibit activity. Inhibition of NS5B activity by RNA template exhibited characteristics of substrate inhibition, suggesting the template binds to a secondary site on the enzyme forming an inactive complex. Template inhibition was modulated by primer. Increasing concentrations of primer restored NS5B activity and decreased the affinity of template for the secondary site. Conversely, increasing template concentration reduced the affinity of primer binding. The kinetic profiles suggest template inhibition results from the binding of template to a site that interferes with primer binding and the formation of productive replication complexes.     

Kinetic analysis of template-instructed and de novo RNA synthesis by Q beta replicase

The kinetics of template-free and template-instructed RNA synthesis by Q_β replicase were investigated. Template-instructed RNA synthesis has different growth rates in the exponential (excess enzyme) and the linear (excess template) phase of growth. In the absence of exogenous template, Q_β replicase synthesizes self-replicating RNA after an initial lag phase (“template-free” synthesis). The lag time can be determined by extrapolating the growth curve to the time of appearance of the first self-replicating strand. Growth rates in the exponential and linear phase, and especially the times of the lag phase for nucleotide incorporations under identical template-free conditions, show considerable scattering in contrast to the deterministic behavior of template-instructed synthesis. Evaluation of the kinetic data reveals that the time lag of template-free synthesis is strongly dependent on the concentration of the nucleoside triphosphate and the enzyme. The lag time is approximately inversely proportional to the powers 2.75 of the nucleotide and 2.5 of the enzyme concentration, respectively, both being lower limit values. The rate of template-instructed RNA synthesis is linearly proportional to the enzyme concentration and less than linearly proportional to the triphosphate concentration, in accordance with a substrate dependence of a Michaelis-Menten type of mechanism. The kinetic data cannot be reconciled with the proposition that template-free synthesis is due to low concentrations of templates present as impurities in the incorporation mixture and giving rise to autocatalytic RNA synthesis by a template-instructed mechanism. The data strongly favor the de novo mechanism proposed by Sumper &; Luce (1975).     

Kinetics and template-dependency of ribonucleic acid synthesis by bacterial ribonucleic acid polymerase.

The rate of RNA synthesis catalysed by DNA-dependent RNA polymerase shows a Michealis-Menten-type saturation curve with increasing template concentration. However, the apparent Km is proportional to enzyme concentration, indicating that the reaction does not obey a simple kinetic scheme. The action of inhibitors also indicates a more complex interaction between the enzyme and the DNA template; many inhibitors of RNA synthesis either decrease Vmax. without affecting Km, or increase Km without affecting Vmax. All of these observations can be accounted for quantitatively by a reaction pathway in which the non-specific binding sites of the viral DNA template inhibit competitively the binding of the enzyme to the initiation sites. In terms of this pathway the two classes of inhibitors of RNA synthesis must then act predominantly either on the rate of elongation or on the availability of the binding sites respectively.     

Faster rates with less catalyst in template-directed reactions

We have recently shown that the polycytidylic acid-directed polymerization of guanosine 5-monophosphate 2-methylimidazolide (2-McImpG) is amenable to kinetic study and that rate determinations as a function of 2-McImpG concentration can reveal much mechanistic detail (Kanavarioti et al. 1993). Here we report kinetic data which show that, once the reaction has been initiated by the formation of dimers, the elongation of dimers to form longer oligomers is accelerated by decreasing polycytidylate (poly(C)) concentration from 0.05 to 0.002 m. This result is consistent with the previously proposed mechanism. The increase in the observed pseudo-first order rate constant for formation of the trimer, k ₃ , and the corresponding constant for formation of oligomers longer than the trimer, k _i (k _i is independent of oligomer length for i 4), with decreasing template concentration for a given monomer concentration is attributed to an increase in template occupancy as template concentration is reduced.Correspondence to: A. Kanavarioti     

Kinetic analysis of artificial peptide self-replication. Part I: the homochiral case

Computational kinetic analysis of a lately discovered homochiral peptide self-replicator is presented. A 6-step kinetic model was designed that addresses the main reactions and hydrophobic interactions involved in this template-directed, autocatalytic system and that gave rise to excellent fitting of 4 previously published independent experimental series. The model sheds light on the mechanistic principle of the reaction system and illustrates directly a number of dynamic properties such as the observed autocatalytic efficiency. It was found that the dynamics are basically governed by two reversible hydrophobic interactions: between the template and a peptide fragment and between two template species. The later association was determined to be considerably more favored, which leads to the predominant presence of the catalytically inactive template dimer in the reaction system. Our results show that the involvement of a template trimer is not necessary to obtain the observed fittings.     

Mechanistic investigation of the bypass of a bulky aromatic DNA adduct catalyzed by a Y-family DNA polymerase

3-Nitrobenzanthrone (3-NBA), a nitropolyaromatic hydrocarbon (NitroPAH) pollutant in diesel exhaust, is a potent mutagen and carcinogen. After metabolic activation, the primary metabolites of 3-NBA react with DNA to form dG and dA adducts. One of the three major adducts identified is N-(2′-deoxyguanosin-8-yl)-3-aminobenzanthrone (dG^C8-N-ABA). This bulky adduct likely stalls replicative DNA polymerases but can be traversed by lesion bypass polymerases in vivo. Here, we employed running start assays to show that a site-specifically placed dG^C8-N-ABA is bypassed in vitro by Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase. However, the nucleotide incorporation rate of Dpo4 was significantly reduced opposite both the lesion and the template position immediately downstream from the lesion site, leading to two strong pause sites. To investigate the kinetic effect of dG^C8-N-ABA on polymerization, we utilized pre-steady-state kinetic methods to determine the kinetic parameters for individual nucleotide incorporations upstream, opposite, and downstream from the dG^C8-N-ABA lesion. Relative to the replication of the corresponding undamaged DNA template, both nucleotide incorporation efficiency and fidelity of Dpo4 were considerably decreased during dG^C8-N-ABA lesion bypass and the subsequent extension step. The lower nucleotide incorporation efficiency caused by the lesion is a result of a significantly reduced dNTP incorporation rate constant and modestly weaker dNTP binding affinity. At both pause sites, nucleotide incorporation followed biphasic kinetics with a fast and a slow phase and their rates varied with nucleotide concentration. In contrast, only the fast phase was observed with undamaged DNA. A kinetic mechanism was proposed for the bypass of dG^C8-N-ABA bypass catalyzed by Dpo4.     

Stereochemical specificity of Alzheimer's disease beta-peptide assembly

The formation and growth of insoluble amyloid deposits composed primarily of the human beta-amyloid peptide (A beta) in brain is an essentially invariant feature of Alzheimer's disease (AD) and is widely believed to contribute to the progressive neurodegeneration of the disorder. To probe the specificity of amyloid formation and growth, we synthesized and examined the self-assembly of D- and L-stereoisomers of A beta in vitro. While both enantiomers formed insoluble aggregates at similar rates with amyloid-like fibrillar morphology, deposition of soluble A beta peptide onto preexisting A beta aggregates was stereospecific. Although the L-peptide deposited readily onto immobilized L-A beta aggregates with first-order kinetic dependence on soluble peptide concentration, essentially no association between the D-peptide and L-template was observed. Similarly, the D-peptide deposited with first-order kinetics onto a D-A beta aggregate template but did not deposit onto a similar template composed of aggregates of the L-enantiomer. Furthermore, although the L-A beta isomer deposited onto authentic AD amyloid in preparations of unfixed AD brain, no focal association between the D-peptide and brain amyloid was detected. These results establish that deposition of soluble A beta onto preexisting amyloid template is stereospecific, likely involving direct docking interactions between peptide backbone and/or side chains rather than simple hydrophobic association.     

Reduced dNTP interaction of human immunodeficiency virus type 1 reverse transcriptase promotes strand transfer

We have recently demonstrated that HIV-1 RT mutants characterized by low dNTP binding affinity display significantly reduced dNTP incorporation kinetics in comparison to wild-type RT. This defect is particularly emphasized at low dNTP concentrations where WT RT remains capable of efficient synthesis. Kinetic interference in DNA synthesis can induce RT pausing and slow down the synthesis rate. RT stalling and slow synthesis rate can enhance RNA template cleavage by RT-RNase H, facilitating transfer of the primer to a homologous template. We therefore hypothesized that reduced dNTP binding RT mutants can promote template switching during minus strand synthesis more efficiently than WT HIV-1 RT at low dNTP concentrations. To test this hypothesis, we employed two dNTP binding HIV-1 RT mutants, Q151N and V148I. Indeed, as the dNTP concentration was decreased, the template switching frequency progressively increased for both WT and mutant RTs. However, as predicted, the RT mutants promoted more transfers compared with WT RT. The WT and mutant RTs were similar in their intrinsic RNase H activity, supporting that the elevated template switching efficiency of the mutants was not the result of the mutations enhancing RNase H activity. Rather, kinetic interference leading to stalled DNA synthesis likely enhanced transfers. These results suggest that the RT-dNTP substrate interaction mechanistically influences strand transfer and recombination of HIV-1 RT.     

A continuous nonradioactive assay for RNA-dependent RNA polymerase activity

Current assays for the activity of viral RNA-dependent RNA polymerases (RdRps) are inherently end-point measurements, often requiring the use of radiolabeled or chemically modified nucleotides to detect reaction products. In an effort to improve the characterization of polymerases that are essential to the life cycle of RNA viruses and develop antiviral therapies that target these enzymes, a continuous nonradioactive assay was developed to monitor the activity of RdRps by measuring the release of pyrophosphate (PP(i)) generated during nascent strand synthesis. A coupled-enzyme assay method based on the chemiluminescent detection of PP(i), using ATP sulfurylase and firefly luciferase, was adapted to monitor poliovirus 3D polymerase (3D(pol)) and the hepatitis C virus nonstructural protein 5B (NS5B) RdRp reactions. Light production was dependent on RdRp and sensitive to the concentration of oligonucleotide primer directing RNA synthesis. The assay system was found to be amenable to sensitive kinetic studies of RdRps, requiring only 6nM 3D(pol) to obtain a reliable estimate of the initial velocity in as little as 4 min. The assay can immediately accommodate the use of both homopolymer and heteropolymer RNA templates lacking uridylates and can be adapted to RNA templates containing uridine by substituting alpha-thio ATP for ATP. The low background signal produced by other NTPs can be corrected from no enzyme (RdRp) controls. The effect of RdRp/RNA template preincubation was assessed using NS5B and a homopolymer RNA template and a time-dependent increase of RdRp activity was observed. Progress curves for a chain terminator (3(')-deoxyguanosine 5(')-triphosphate) and an allosteric NS5B inhibitor demonstrated the predicted time- and dose-dependent reductions in signal. This assay should facilitate detailed kinetic studies of RdRps and their potential inhibitors using either standard or single-nucleotide approaches.     

Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase

During DNA replication replicative polymerases move in discrete mechanical steps along the DNA template. To address how the chemical cycle is coupled to mechanical motion of the enzyme, here we use optical tweezers to study the translocation mechanism of individual bacteriophage Phi29 DNA polymerases during processive DNA replication. We determine the main kinetic parameters of the nucleotide incorporation cycle and their dependence on external load and nucleotide (dNTP) concentration. The data is inconsistent with power stroke models for translocation, instead supports a loose-coupling mechanism between chemical catalysis and mechanical translocation during DNA replication. According to this mechanism the DNA polymerase works by alternating between a dNTP/PPi-free state, which diffuses thermally between pre- and post-translocated states, and a dNTP/PPi-bound state where dNTP binding stabilizes the post-translocated state. We show how this thermal ratchet mechanism is used by the polymerase to generate work against large opposing loads (∼50 pN).     

Sub-exponential growth and coexistence of non-enzymatically replicating templates

The experimentally reported kinetic behaviour (sub-exponential but supra-linear growth) of non-enzymatic template replication is incorporated into a simple model of template competition. Sub-exponential growth is shown to lead to coexistence invariably. Thus coexistence of different non-enzymatically replicating sequences is predicted. This type of coexistence could have been important in maintaining a sufficient diversity of RNA modules used later to build functional molecules such as ribozymes. Experimental tests of this theoretical prediction are possible.     

Preferential incorporation of G opposite template T by the low-fidelity human DNA polymerase iota

DNA polymerase activity is essential for replication, recombination, repair, and mutagenesis. All DNA polymerases studied so far from any biological source synthesize DNA by the Watson-Crick base-pairing rule, incorporating A, G, C, and T opposite the templates T, C, G, and A, respectively. Non-Watson-Crick base pairs would lead to mutations. In this report, we describe the ninth human DNA polymerase, Pol(iota), encoded by the RAD30B gene. We show that human Pol(iota) violates the Watson-Crick base-pairing rule opposite template T. During base selection, human Pol(iota) preferred T-G base pairing, leading to G incorporation opposite template T. The resulting T-G base pair was less efficiently extended by human Pol(iota) compared to the Watson-Crick base pairs. Consequently, DNA synthesis frequently aborted opposite template T, a property we designated the T stop. This T stop restricted human Pol(iota) to a very short stretch of DNA synthesis. Furthermore, kinetic analyses show that human Pol(iota) copies template C with extraordinarily low fidelity, misincorporating T, A, and C with unprecedented frequencies of 1/9, 1/10, and 1/11, respectively. Human Pol(iota) incorporated one nucleotide opposite a template abasic site more efficiently than opposite a template T, suggesting a role for human Pol(iota) in DNA lesion bypass. The unique features of preferential G incorporation opposite template T and T stop suggest that DNA Pol(iota) may additionally play a specialized function in human biology.