The methyltransferase domain of dengue virus protein NS5 ensures efficient RNA synthesis initiation and elongation by the polymerase domain

International audienceViral RNA-dependent RNA polymerases (RdRps) responsible for the replication of single-strand RNA virus genomes exert their function in the context of complex replication machineries. Within these replication complexes the polymerase activity is often highly regulated by RNA elements, proteins or other domains of multi-domain polymerases. Here, we present data of the influence of the methyltrans-ferase domain (NS5-MTase) of dengue virus (DENV) protein NS5 on the RdRp activity of the polymerase domain (NS5-Pol). The steady-state polymerase activities of DENV-2 recombinant NS5 and NS5-Pol are compared using different biochemical assays allowing the dissection of the de novo initiation, transition and elongation steps of RNA synthesis. We show that NS5-MTase ensures efficient RdRp activity by stimulating the de novo initiation and the elongation phase. This stimulation is related to a higher affinity of NS5 toward the single-strand RNA template indicating NS5-MTase either completes a high-affinity RNA binding site and/or promotes the correct formation of the template tunnel. Furthermore, the NS5-MTase increases the affinity of the priming nucleotide ATP upon de novo initiation and causes a higher catalytic efficiency of the polymerase upon elongation. The complex stimulation pattern is discussed under the perspective that NS5 adopts several conforma-tions during RNA synthesis

Models of disability as distinguishing factor: a theoretical framework of inclusive education and the application to a literature review

This study reports on a newly developed framework of inclusive education, which sets out from three distinct models of disability (medical, relational, and social) and incorporates matching learning theory (behaviourist, cognitivist, and constructivist) and the placement of children with disabilities (exclusive, functional inclusive, full inclusive). Central to the framework is the contradiction between functional and full inclusive concepts, which are traced back to the conflict between a deterministic (medical and relational) and social model of disability. Applied to a complementary review of the literature published between 2006 and 2021, the framework sets the basis for structuring content analysis. An analysis of N ¼ 685 reports shows the coherence of the framework as well as an increase in total publications, especially with full inclusive concepts. Additionally, analysis of the applied methodology shows a predominant role of qualitative methods, which is coherent with the constructivist perception of full inclusion. Implications are discussed regarding inconsistencies and barriers to inclusive education

Extending the Variational Quantum Eigensolver to Finite Temperatures

We present a variational quantum thermalizer (VQT), called quantum-VQT (qVQT), which extends the variational quantum eigensolver (VQE) to finite temperatures. The qVQT makes use of an intermediate measurement between two variational circuits to encode a density matrix on a quantum device. A classical optimization provides the thermal state and, simultaneously, all associated excited states of a quantum mechanical system. We demonstrate the capabilities of the qVQT for two different spin systems. First, we analyze the performance of qVQT as a function of the circuit depth and the temperature for a 1-dimensional Heisenberg chain. Second, we use the excited states to map the complete, temperature dependent phase diagram of a 2-dimensional J1-J2 Heisenberg model. The numerical experiments demonstrate the efficiency of our approach, which can be readily applied to study various quantum many-body systems at finite temperatures on currently available NISQ devices.Comment: 10 pages, 7 figure

High-yield production of short GpppA- and (7Me)GpppA-capped RNAs and HPLC-monitoring of methyltransfer reactions at the guanine-N7 and adenosine-2′O positions

Many eukaryotic and viral mRNAs, in which the first transcribed nucleotide is an adenosine, are decorated with a cap-1 structure, (7Me)G(5′)-ppp(5′)-A(2′OMe). The positive-sense RNA genomes of flaviviruses (Dengue, West Nile virus) for example show strict conservation of the adenosine. We set out to produce GpppA- and (7Me)GpppA-capped RNA oligonucleotides for non-radioactive mRNA cap methyltransferase assays and, in perspective, for studies of enzyme specificity in relation to substrate length as well as for co-crystallization studies. This study reports the use of a bacteriophage T7 DNA primase fragment to synthesize GpppAC(n) and (7Me)GpppAC(n) (1 ≤ n ≤ 9) in a one-step enzymatic reaction, followed by direct on-line cleaning HPLC purification. Optimization studies show that yields could be modulated by DNA template, enzyme and substrate concentration adjustments and longer reaction times. Large-scale synthesis rendered pure (in average 99%) products (1 ≤ n ≤ 7) in quantities of up to 100 nmol starting from 200 nmol cap analog. The capped RNA oligonucleotides were efficient substrates of Dengue virus (nucleoside-2′-O-)-methyltransferase, and human (guanine-N7)-methyltransferase. Methyltransfer reactions were monitored by a non-radioactive, quantitative HPLC assay. Additionally, the produced capped RNAs may serve in biochemical, inhibition and structural studies involving a variety of eukaryotic and viral methyltransferases and guanylyltransferases

In Vitro Reconstitution of SARS-Coronavirus mRNA Cap Methylation

SARS-coronavirus (SARS-CoV) genome expression depends on the synthesis of a set of mRNAs, which presumably are capped at their 5′ end and direct the synthesis of all viral proteins in the infected cell. Sixteen viral non-structural proteins (nsp1 to nsp16) constitute an unusually large replicase complex, which includes two methyltransferases putatively involved in viral mRNA cap formation. The S-adenosyl-L-methionine (AdoMet)-dependent (guanine-N7)-methyltransferase (N7-MTase) activity was recently attributed to nsp14, whereas nsp16 has been predicted to be the AdoMet-dependent (nucleoside-2′O)-methyltransferase. Here, we have reconstituted complete SARS-CoV mRNA cap methylation in vitro. We show that mRNA cap methylation requires a third viral protein, nsp10, which acts as an essential trigger to complete RNA cap-1 formation. The obligate sequence of methylation events is initiated by nsp14, which first methylates capped RNA transcripts to generate cap-0 7MeGpppA-RNAs. The latter are then selectively 2′O-methylated by the 2′O-MTase nsp16 in complex with its activator nsp10 to give rise to cap-1 7MeGpppA2′OMe-RNAs. Furthermore, sensitive in vitro inhibition assays of both activities show that aurintricarboxylic acid, active in SARS-CoV infected cells, targets both MTases with IC50 values in the micromolar range, providing a validated basis for anti-coronavirus drug design

The who and what of inclusive education—Profiles of student teachers' attitudes toward inclusive education

The present study investigated the relationship between different attitudes toward inclusive education. It draws from the Framework of Inclusive Education by assuming a reciprocal relationship between learning theory beliefs, models of disability, and the assessment of joined education, resulting in consistent attitudes toward inclusion. The study investigated attitudes toward inclusion by applying a person-centered approach (latent profile analysis; LPA) to a sample of N = 138 student teachers. The results suggest a two-class solution: firstly, a consistent exclusive profile combining higher transmissive beliefs of learning and teaching and a preference for exclusion; secondly, a general inclusive profile that combines support for functional and full inclusion, relational and social models of disability, and a cognitive, constructivist learning theory. The profile distribution appeared to be related to teacher self-efficacy, but not to gender or the educational stage of prospective teaching practice

Dynamical Mean Field Theory for Real Materials on a Quantum Computer

Quantum computers (QC) could harbor the potential to significantly advance materials simulations, particularly at the atomistic scale involving strongly correlated fermionic systems where an accurate description of quantum many-body effects scales unfavorably with size. While a full-scale treatment of condensed matter systems with currently available noisy quantum computers remains elusive, quantum embedding schemes like dynamical mean-field theory (DMFT) allow the mapping of an effective, reduced subspace Hamiltonian to available devices to improve the accuracy of ab initio calculations such as density functional theory (DFT). Here, we report on the development of a hybrid quantum-classical DFT+DMFT simulation framework which relies on a quantum impurity solver based on the Lehmann representation of the impurity Green's function. Hardware experiments with up to 14 qubits on the IBM Quantum system are conducted, using advanced error mitigation methods and a novel calibration scheme for an improved zero-noise extrapolation to effectively reduce adverse effects from inherent noise on current quantum devices. We showcase the utility of our quantum DFT+DMFT workflow by assessing the correlation effects on the electronic structure of a real material, Ca2CuO2Cl2, and by carefully benchmarking our quantum results with respect to exact reference solutions and experimental spectroscopy measurements.Comment: 25 pages, 6 figures, supplementary informatio

Molecular Basis for Nucleotide Conservation at the Ends of the Dengue Virus Genome

International audienceThe dengue virus (DV) is an important human pathogen from the Flavivirus genus, whose genome- and antigenome RNAs start with the strictly conserved sequence pppAG. The RNA-dependent RNA polymerase (RdRp), a product of the NS5 gene, initiates RNA synthesis de novo, i.e., without the use of a pre-existing primer. Very little is known about the mechanism of this de novo initiation and how conservation of the starting adenosine is achieved. The polymerase domain NS5PolDV of NS5, upon initiation on viral RNA templates, synthesizes mainly dinucleotide primers that are then elongated in a processive manner. We show here that NS5PolDV contains a specific priming site for adenosine 59-triphosphate as the first transcribed nucleotide. Remarkably, in the absence of any RNA template the enzyme is able to selectively synthesize the dinucleotide pppAG when Mn 2+ is present as catalytic ion. The T794 to A799 priming loop is essential for initiation and provides at least part of the ATP-specific priming site. The H798 loop residue is of central importance for the ATP-specific initiation step. In addition to ATP selection, NS5PolDV ensures the conservation of the 59-adenosine by strongly discriminating against viral templates containing an erroneous 39-end nucleotide in the presence of Mg 2+. In the presence of Mn2+, NS5Pol DV is remarkably able to generate and elongate the correct pppAG primer on these erroneous templates. This can be regarded as a genomic/antigenomic RNA end repair mechanism. These conservational mechanisms, mediated by the polymerase alone, may extend to other RNA virus families having RdRps initiating RNA synthesis de novo

Synthesis and biological evaluation of novel flexible nucleoside analogues that inhibit flavivirus replication in vitro

Flaviviruses, such as Dengue (DENV) and Zika (ZIKV) viruses, represent a severe health burden. There are currently no FDA-approved treatments, and vaccines against most flaviviruses are still lacking. We have developed several flexible analogues (“fleximers”) of the FDA-approved nucleoside Acyclovir that exhibit activity against various RNA viruses, demonstrating their broad-spectrum potential. The current study reports activity against DENV and YFV, particularly for compound 1. Studies to elucidate the mechanism of action suggest the flex-analogue triphosphates, especially 1-TP, inhibit DENV and ZIKV methyltransferases. The results of these studies are reported herein

Recombination in West Nile Virus: minimal contribution to genomic diversity

Recombination is known to play a role in the ability of various viruses to acquire sequence diversity. We consequently examined all available West Nile virus (WNV) whole genome sequences both phylogenetically and with a variety of computational recombination detection algorithms. We found that the number of distinct lineages present on a phylogenetic tree reconstruction to be identical to the 6 previously reported. Statistically-significant evidence for recombination was only observed in one whole genome sequence. This recombination event was within the NS5 polymerase coding region. All three viruses contributing to the recombination event were originally isolated in Africa at various times, with the major parent (SPU116_89_B), minor parent (KN3829), and recombinant sequence (AnMg798) belonging to WNV taxonomic lineages 2, 1a, and 2 respectively. This one isolated recombinant genome was out of a total of 154 sequences analyzed. It therefore does not seem likely that recombination contributes in any significant manner to the overall sequence variation within the WNV genome