Journal articles: 'RDRL'

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Hua, Xia, Nathan D. Berkowitz, Matthew R. Willmann, Xiang Yu, Eric Lyons, and Brian D. Gregory. "Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis." Non-Coding RNA 7, no. 2 (April 27, 2021): 28. http://dx.doi.org/10.3390/ncrna7020028.

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RNA silencing pathways control eukaryotic gene expression transcriptionally or posttranscriptionally in a sequence-specific manner. In RNA silencing, the production of double-stranded RNA (dsRNA) gives rise to various classes of 20–24 nucleotide (nt) small RNAs (smRNAs). In Arabidopsis thaliana, smRNAs are often derived from long dsRNA molecules synthesized by one of the six genomically encoded RNA-dependent RNA Polymerase (RDR) proteins. However, the full complement of the RDR-dependent smRNAs and functions that these proteins and their RNA-binding cofactors play in plant RNA silencing has not been fully uncovered. To address this gap, we performed a global genomic analysis of all six RDRs and two of their cofactors to find new substrates for RDRs and targets of the resulting RDR-derived siRNAs to uncover new functions for these proteins in plants. Based on these analyses, we identified substrates for the three RDRγ clade proteins (RDR3–5), which had not been well-characterized previously. We also identified new substrates for the other three RDRs (RDR1, RDR2, and RDR6) as well as the RDR2 cofactor RNA-directed DNA methylation 12 (RDM12) and the RDR6 cofactor suppressor of gene silencing 3 (SGS3). These findings revealed that the target substrates of SGS3 are not limited to those solely utilized by RDR6, but that this protein seems to be a more general cofactor for the RDR family of proteins. Additionally, we found that RDR6 and SGS3 are involved in the production of smRNAs that target transcripts related to abiotic stresses, including water deprivation, salt stress, and ABA response, and as expected the levels of these mRNAs are increased in rdr6 and sgs3 mutant plants. Correspondingly, plants that lack these proteins (rdr6 and sgs3 mutants) are hypersensitive to ABA treatment, tolerant to high levels of PEG8000, and have a higher survival rate under salt treatment in comparison to wild-type plants. In total, our analyses have provided an extremely data-rich resource for uncovering new functions of RDR-dependent RNA silencing in plants, while also revealing a previously unexplored link between the RDR6/SGS3-dependent pathway and plant abiotic stress responses.

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Wang, Lei, Neil A. Smith, Lan Zhang, Elizabeth S. Dennis, Peter M. Waterhouse, Peter J. Unrau, and Ming-Bo Wang. "Synthesis of complementary RNA by RNA-dependent RNA polymerases in plant extracts is independent of an RNA primer." Functional Plant Biology 35, no. 11 (2008): 1091. http://dx.doi.org/10.1071/fp08118.

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RNA-dependent RNA polymerase (RDR) activities were readily detected in extracts from cauliflower and broccoli florets, Arabidopsis thaliana (L.) Heynh callus tissue and broccoli nuclei. The synthesis of complementary RNA (cRNA) was independent of a RNA primer, whether or not the primer contained a 3′ terminal 2′-O-methyl group or was phosphorylated at the 5′ terminus. cRNA synthesis in plant extracts was not affected by loss-of-function mutations in the DICER-LIKE (DCL) proteins DCL2, DCL3, and DCL4, indicating that RDRs function independently of these DCL proteins. A loss-of-function mutation in RDR1, RDR2 or RDR6 did not significantly reduce the amount of cRNA synthesis. This indicates that these RDRs did not account for the bulk RDR activities in plant extracts, and suggest that either the individual RDRs each contribute a fraction of polymerase activity or another RDR(s) is predominant in the plant extract.

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Qu, Feng. "Antiviral Role of Plant-Encoded RNA-Dependent RNA Polymerases Revisited with Deep Sequencing of Small Interfering RNAs of Virus Origin." Molecular Plant-Microbe Interactions® 23, no. 10 (October 2010): 1248–52. http://dx.doi.org/10.1094/mpmi-06-10-0124.

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Several recent studies profiled virus-specific small interfering RNAs (vsRNAs) using next generation sequencing platforms and compellingly implicated plant-encoded RNA-dependent RNA polymerases (RDR) in vsRNA biogenesis and vsRNA-mediated antiviral defense. Specifically, both RDR1 and RDR6 were found to contribute to the accumulation of vsRNAs in virus-infected cells. While RDR1 was responsible for the majority of vsRNAs in plants infected with three different viruses, RDR6 acted as a surrogate when RDR1 function was disrupted. Mechanistically, vsRNAs associated with RDR1 mostly mapped to viral RNA regions close to the 5′ ends, whereas those associated with RDR6 mapped to more 3′ regions and appeared to be dependent on higher viral RNA concentrations. Knocking out both RDR1 and RDR6 led to drastically diminished vsRNA levels concomitant with enhanced viral RNA accumulation. In conclusion, these studies established that RDR1 and RDR6 function synergistically to contain RNA virus infections through the RNA silencing–based antiviral defense.

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Adkar-Purushothama, Charith Raj, and Jean-Pierre Perreault. "Suppression of RNA-Dependent RNA Polymerase 6 Favors the Accumulation of Potato Spindle Tuber Viroid in Nicotiana Benthamiana." Viruses 11, no. 4 (April 14, 2019): 345. http://dx.doi.org/10.3390/v11040345.

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To date, two plant genes encoding RNA-dependent RNA polymerases (RdRs) that play major roles in the defense against RNA viruses have been identified: (i) RdR1, which is responsible for the viral small RNAs (vsRNAs) found in virus-infected plants, and, (ii) RdR6, which acts as a surrogate in the absence of RdR1. In this study, the role of RdR6 in the defense against viroid infection was examined by knock-down of RdR6 followed by potato spindle tuber viroid (PSTVd) infection. The suppression of RdR6 expression increased the plant’s growth, as was illustrated by the plant’s increased height. PSTVd infection of RdR6 compromised plants resulted in an approximately three-fold increase in the accumulation of viroid RNA as compared to that seen in control plants. Additionally, RNA gel blot assay revealed an increase in the number of viroids derived small RNAs in RdR6 suppressed plants as compared to control plants. These data provide a direct correlation between RdR6 and viroid accumulation and indicate the role of RDR6 in the plant’s susceptibility to viroid infection.

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Chen, Miaojiang, Anfeng Liu, Wei Liu, Kaoru Ota, Mianxiong Dong, and Neal N. Xiong. "RDRL: A Recurrent Deep Reinforcement Learning Scheme for Dynamic Spectrum Access in Reconfigurable Wireless Networks." IEEE Transactions on Network Science and Engineering 9, no. 2 (March 1, 2022): 364–76. http://dx.doi.org/10.1109/tnse.2021.3117565.

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Chen, Miaojiang, Anfeng Liu, Wei Liu, Kaoru Ota, Mianxiong Dong, and Neal N. Xiong. "RDRL: A Recurrent Deep Reinforcement Learning Scheme for Dynamic Spectrum Access in Reconfigurable Wireless Networks." IEEE Transactions on Network Science and Engineering 9, no. 2 (March 1, 2022): 364–76. http://dx.doi.org/10.1109/tnse.2021.3117565.

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Donaire, Livia, Daniel Barajas, Belén Martínez-García, Llucia Martínez-Priego, Israel Pagán, and César Llave. "Structural and Genetic Requirements for the Biogenesis of Tobacco Rattle Virus-Derived Small Interfering RNAs." Journal of Virology 82, no. 11 (March 19, 2008): 5167–77. http://dx.doi.org/10.1128/jvi.00272-08.

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ABSTRACT In plants, small RNA-guided processes referred to as RNA silencing control gene expression and serve as an efficient antiviral mechanism. Plant viruses are inducers and targets of RNA silencing as infection involves the production of functional virus-derived small interfering RNAs (siRNAs). Here we investigate the structural and genetic components influencing the formation of Tobacco rattle virus (TRV)-derived siRNAs. TRV siRNAs are mostly 21 nucleotides in length and derive from positive and negative viral RNA strands, although TRV siRNAs of positive polarity are significantly more abundant. This asymmetry appears not to correlate with the presence of highly structured regions of single-stranded viral RNA. The Dicer-like enzyme DCL4, DCL3, or DCL2 targets, alone or in combination, viral templates to promote synthesis of siRNAs of both polarities from all regions of the viral genome. The heterogeneous distribution profile of TRV siRNAs reveals differential contributions throughout the TRV genome to siRNA formation. Indirect evidence suggests that DCL2 is responsible for production of a subset of siRNAs derived from the 3′ end region of TRV. TRV siRNA biogenesis and antiviral silencing are strongly dependent on the combined activity of the host-encoded RNA-dependent RNA polymerases RDR1, RDR2, and RDR6, thus providing evidence that perfectly complementary double-stranded RNA serves as a substrate for siRNA production. We conclude that the overall composition of viral siRNAs in TRV-infected plants reflects the combined action of several interconnected pathways involving different DCL and RDR activities.

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Guo, Zhongxin, Jinfeng Lu, Xianbing Wang, Binhui Zhan, Wanxiang Li, and Shou-Wei Ding. "Lipid flippases promote antiviral silencing and the biogenesis of viral and host siRNAs in Arabidopsis." Proceedings of the National Academy of Sciences 114, no. 6 (January 25, 2017): 1377–82. http://dx.doi.org/10.1073/pnas.1614204114.

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Dicer-mediated processing of virus-specific dsRNA into short interfering RNAs (siRNAs) in plants and animals initiates a specific antiviral defense by RNA interference (RNAi). In this study, we developed a forward genetic screen for the identification of host factors required for antiviral RNAi in Arabidopsis thaliana. Using whole-genome sequencing and a computational pipeline, we identified aminophospholipid transporting ATPase 2 (ALA2) and the related ALA1 in the type IV subfamily of P-type ATPases as key components of antiviral RNAi. ALA1 and ALA2 are flippases, which are transmembrane lipid transporter proteins that transport phospholipids across cellular membranes. We found that the ala1/ala2 single- and double-mutant plants exhibited enhanced disease susceptibility to cucumber mosaic virus when the virus-encoded function to suppress RNAi was disrupted. Notably, the antiviral activity of both ALA1 and ALA2 was abolished by a single amino acid substitution known to inactivate the flippase activity. Genetic analysis revealed that ALA1 and ALA2 acted to enhance the amplification of the viral siRNAs by RNA-dependent RNA polymerase (RdRP) 1 (RDR1) and RDR6 and of the endogenous virus-activated siRNAs by RDR1. RNA virus replication by plant viral RdRPs occurs inside vesicle-like membrane invaginations induced by the recruitment of the viral RdRP and host factors to subcellular membrane microdomains enriched with specific phospholipids. Our results suggest that the phospholipid transporter activity of ALA1/ALA2 may be necessary for the formation of similar invaginations for the synthesis of dsRNA precursors of highly abundant viral and host siRNAs by the cellular RdRPs.

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Wang, Mian, Shanwei Li, Haifang Yang, Zheng Gao, Changai Wu, and Xingqi Guo. "Characterization and functional analysis of GhRDR6, a novel RDR6 gene from cotton (Gossypium hirsutum L.)." Bioscience Reports 32, no. 2 (November 21, 2011): 139–51. http://dx.doi.org/10.1042/bsr20100086.

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RDR6 (RNA-dependent RNA polymerase 6) is not only involved in virus resistance but also plays an important role in natural plant development. In the present study, a novel RDR gene, named GhRDR6 (Gossypium hirsutum RDR6), was isolated from cotton (G. hirsutum L.). Alignment and evolutionary relationship analyses showed that GhRDR6 was more closely related to RDR6 than to other RDRs. Expression analysis indicated that this single-copy gene is constitutively expressed in the roots, stems and leaves. Semi-quantitative RT–PCR (reverse transcription–PCR) showed that GhRDR6 was up-regulated by the application of various phytohormones, including MeJA [methyl JA (jasmonate)], ABA (abscisic acid), JA, α-naphthylacetic acid, gibberellins and ET (ethylene). In addition, GhRDR6 expression increased in response to wounding, cold (4°C) and NaCl treatments, but not by drought. Furthermore, overexpression of GhRDR6 in transgenic Nicotiana benthamiana plants resulted in root lengths longer than the wide-type during the seeding stage. Interestingly, the GhRDR6-overexpressing plants displayed reduced tolerance to oxidative damage, resulting in reduced ABA-sensitivity, but they tolerated freezing. Moreover, resistance to potato virus Y was enhanced in transgenic N. benthamiana plants. These results suggest that GhRDR6 may play an important role in plant defence responses and a pivotal role in plant development.

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Polydore, Seth, and Michael J. Axtell. "Analysis of RDR1 /RDR2 /RDR6 -independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals unexplained types of short interfering RNA loci." Plant Journal 94, no. 6 (May 13, 2018): 1051–63. http://dx.doi.org/10.1111/tpj.13919.

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Karunanithi, Sivarajan, Vidya Oruganti, Simone Marker, Angela M. Rodriguez-Viana, Franziska Drews, Marcello Pirritano, Karl Nordström, Martin Simon, and Marcel H. Schulz. "Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium." Nucleic Acids Research 47, no. 15 (June 28, 2019): 8036–49. http://dx.doi.org/10.1093/nar/gkz553.

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Abstract Extensive research has characterized distinct exogenous RNAi pathways interfering in gene expression during vegetative growth of the unicellular model ciliate Paramecium. However, role of RNAi in endogenous transcriptome regulation, and environmental adaptation is unknown. Here, we describe the first genome-wide profiling of endogenous sRNAs in context of different transcriptomic states (serotypes). We developed a pipeline to identify, and characterize 2602 siRNA producing clusters (SRCs). Our data show no evidence that SRCs produce miRNAs, and in contrast to other species, no preference for strand specificity of siRNAs. Interestingly, most SRCs overlap coding genes and a separate group show siRNA phasing along the entire open reading frame, suggesting that the mRNA transcript serves as a source for siRNAs. Integrative analysis of siRNA abundance and gene expression levels revealed surprisingly that mRNA and siRNA show negative as well as positive associations. Two RNA-dependent RNA Polymerase mutants, RDR1 and RDR2, show a drastic loss of siRNAs especially in phased SRCs accompanied with increased mRNA levels. Importantly, most SRCs depend on both RDRs, reminiscent to primary siRNAs in the RNAi against exogenous RNA, indicating mechanistic overlaps between exogenous and endogenous RNAi contributing to flexible transcriptome adaptation.

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Jauvion, Vincent, Maud Rivard, Nathalie Bouteiller, Taline Elmayan, and Hervé Vaucheret. "RDR2 Partially Antagonizes the Production of RDR6-Dependent siRNA in Sense Transgene-Mediated PTGS." PLoS ONE 7, no. 1 (January 5, 2012): e29785. http://dx.doi.org/10.1371/journal.pone.0029785.

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Rakhshandehroo, Farshad, Minoru Takeshita, Julie Squires, and Peter Palukaitis. "The Influence of RNA-Dependent RNA Polymerase 1 on Potato virus Y Infection and on Other Antiviral Response Genes." Molecular Plant-Microbe Interactions® 22, no. 10 (October 2009): 1312–18. http://dx.doi.org/10.1094/mpmi-22-10-1312.

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The gene encoding RNA-dependent RNA polymerase 1 (RDR1) is involved in basal resistance to several viruses. Expression of the RDR1 gene also is induced in resistance to Tobacco mosaic virus (TMV) mediated by the N gene in tobacco (Nicotiana tabacum cv. Samsun NN) in an incompatible hypersensitive response, as well as in a compatible response against Potato virus Y (PVY). Reducing the accumulation of NtRDR1 transcripts by RNA inhibition mediated by transgenic expression of a double-stranded RNA hairpin corresponding to part of the RDR1 gene resulted in little or no induction of accumulation of RDR1 transcripts after infection by PVY. Plants with lower accumulation of RDR1 transcripts showed much higher accumulation levels of PVY. Reduced accumulation of NtRDR1 transcripts also resulted in lower or no induced expression of three other antiviral, defense-related genes after infection by PVY. These genes encoded a mitochondrial alternative oxidase, an inhibitor of virus replication (IVR), and a transcription factor, ERF5, all involved in resistance to infection by TMV, as well as RDR6, involved in RNA silencing. The extent of the effect on the induced NtIVR and NtERF5 genes correlated with the extent of suppression of the NtRDR1 gene.

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Sakurai, Yuriki, Kyungmin Baeg, Andy Y. W. Lam, Keisuke Shoji, Yukihide Tomari, and Hiro-oki Iwakawa. "Cell-free reconstitution reveals the molecular mechanisms for the initiation of secondary siRNA biogenesis in plants." Proceedings of the National Academy of Sciences 118, no. 31 (July 30, 2021): e2102889118. http://dx.doi.org/10.1073/pnas.2102889118.

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Secondary small interfering RNA (siRNA) production, triggered by primary small RNA targeting, is critical for proper development and antiviral defense in many organisms. RNA-dependent RNA polymerase (RDR) is a key factor in this pathway. However, how RDR specifically converts the targets of primary small RNAs into double-stranded RNA (dsRNA) intermediates remains unclear. Here, we develop an in vitro system that allows for dissection of the molecular mechanisms underlying the production of trans-acting siRNAs, a class of plant secondary siRNAs that play roles in organ development and stress responses. We find that a combination of the dsRNA-binding protein, SUPPRESSOR OF GENE SILENCING3; the putative nuclear RNA export factor, SILENCING DEFECTIVE5, primary small RNA, and Argonaute is required for physical recruitment of RDR6 to target RNAs. dsRNA synthesis by RDR6 is greatly enhanced by the removal of the poly(A) tail, which can be achieved by the cleavage at a second small RNA-binding site bearing appropriate mismatches. Importantly, when the complementarity of the base pairing at the second target site is too strong, the small RNA–Argonaute complex remains at the cleavage site, thereby blocking the initiation of dsRNA synthesis by RDR6. Our data highlight the light and dark sides of double small RNA targeting in the secondary siRNA biogenesis.

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Kreitman, R. J., and I. Pastan. "Importance of the glutamate residue of KDEL in increasing the cytotoxicity of Pseudomonas exotoxin derivatives and for increased binding to the KDEL receptor." Biochemical Journal 307, no. 1 (April 1, 1995): 29–37. http://dx.doi.org/10.1042/bj3070029.

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It was previously shown that amino acids 609-613 (REDLK) at the C-terminus of Pseudomonas exotoxin (PE) are necessary for cytotoxicity, presumably by directing the toxin to the endoplasmic reticulum (ER) [Chaudhary, Jinno, FitzGerald and Pastan (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 308-312]. Using the anti-[interleukin 2 receptor (IL2R)] immunotoxin anti-Tac(Fv)-PE38 (AT-PE38REDLK), it was found that removing the terminal lysine did not alter the activity, but replacing REDL with KDEL, the most common ER retention sequence, increased activity. To determine which amino acid in KDEL was responsible for the increase in activity, we tested eight C-terminal mutants of AT-PE38REDLK. Using IL2R-bearing MT-1 cells, we found that the glutamate residue of KDEL was required for high activity, as the cytotoxicity of AT-PE38 ending in KDEL, RDEL, KEEL or REEL was much greater than that of AT-PE38 ending in REDL, KEDL, RDDL or KDDL. Using freshly isolated lymphocytic leukaemia cells, AT-PE38 ending in KDEL, REEL or RDEL was more than 100-fold more cytotoxic than AT-PE38 ending in KEDL, REDL, RDDL or the native sequence REDLK. The RDEL sequence also improved the cytotoxic activity of an interleukin 4-PE38 toxin fusion protein. Improved cytotoxic activity correlated with improved binding of the C-termini to the KDEL receptor on rat Golgi membranes. These data indicate that the glutamate residue of KDEL improves the cytotoxicity of PE by increasing binding to a sorting receptor which transports the toxin from the transreticular Golgi apparatus to the ER, where it is translocated to the cytosol and inhibits protein synthesis.

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Khan, Shahid, Muhammad Amir Khan, Muhammad Anab, Safdar Nawaz Khan Marwat, Naveed Jan, and Rania M. Ghoniem. "Wideband Singly Fed Compact Circularly Polarized Rectangular Dielectric Resonator Antenna for X-Band Wireless Applications." Electronics 11, no. 20 (October 12, 2022): 3281. http://dx.doi.org/10.3390/electronics11203281.

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This work focuses on a compact circularly polarized wideband rectangular dielectric resonator antenna (RDRA) for X-band wireless applications. The wideband response of the RDRA is initially generated by a coaxial probe, a compact RDR, an air gap in the DR and a slot of rectangular shape in the ground. The circular polarization is achieved via incorporation of a unique feeding mechanism. The edge feeding of the RDRA with a coaxial probe generates the orthogonal modes in RDRA that make the design polarized circularly. The axial ratio performance is improved by adding a copper strip on the top of the DR. To validate the simulated results, the prototype design is fabricated and measured results are noted. For −10 dB reference value, the prototype has 59.74% impedance bandwidth (8.45–14.09 GHz). For 3 dB reference value of the axial ratio, the prototype has 9.24% Circular Polarization (CP) performance (10.084–11.084 GHz). The design has 6.5 dBic peak gain and 95.5% peak efficiency. Results show that simulated results are in close agreement with the measured results.

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Selvaraju, Raghuraman, Muhammad Ramlee Kamarudin, Mohsen Khalily, Mohd Haizal Jamaluddin, and Jamal Nasir. "Dual-Port MIMO Rectangular Dielectric Resonator Antenna for 4G-LTE Application." Applied Mechanics and Materials 781 (August 2015): 24–27. http://dx.doi.org/10.4028/www.scientific.net/amm.781.24.

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A Multi Input Multi Output (MIMO) Rectangular Dielectric Resonator Antenna (RDRA) for 1.8 GHz Long Term Evolution (LTE) applications is investigated and presented. The antenna consisting of two rectangular dielectric resonator elements, both resonators are fed by microstrip feed line is etched on FR4 substrate. The simulated impedance bandwidth for port1 and port2 is 26.38% (1.6176-2.1093 GHz) and 26.80% (1.6146-2.1143GHz) respectively for |S11| ≤ -6dB, which can operate on LTE band 1-4,9,10,35-37 and 39. The gain of the MIMO RDRA is 3.2 dBi and 3.1 dBi at 1.8 GHz for port 1and port 2, respectively. The S-parameters, isolation, gain, and MIMO performance such as correlation coefficient and diversity gain of the presented RDR Antenna have been studied.

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Taochy, Christelle, Agnès Yu, Nicolas Bouché, Nathalie Bouteiller, Taline Elmayan, Uwe Dressel, Bernard J. Carroll, and Hervé Vaucheret. "Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis." Nucleic Acids Research 47, no. 17 (August 2, 2019): 9104–14. http://dx.doi.org/10.1093/nar/gkz636.

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Abstract Spontaneous post-transcriptional silencing of sense transgenes (S-PTGS) is established in each generation and is accompanied by DNA methylation, but the pathway of PTGS-dependent DNA methylation is unknown and so is its role. Here we show that CHH and CHG methylation coincides spatially and temporally with RDR6-dependent products derived from the central and 3′ regions of the coding sequence, and requires the components of the RNA-directed DNA methylation (RdDM) pathway NRPE1, DRD1 and DRM2, but not CLSY1, NRPD1, RDR2 or DCL3, suggesting that RDR6-dependent products, namely long dsRNAs and/or siRNAs, trigger PTGS-dependent DNA methylation. Nevertheless, none of these RdDM components are required to establish S-PTGS or produce a systemic silencing signal. Moreover, preventing de novo DNA methylation in non-silenced transgenic tissues grafted onto homologous silenced tissues does not inhibit the triggering of PTGS. Overall, these data indicate that gene body DNA methylation is a consequence, not a cause, of PTGS, and rule out the hypothesis that a PTGS-associated DNA methylation signal is transmitted independent of a PTGS signal.

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Sánchez, Ricardo J., Joseph B. Evans, Gary J. Minden, Victor S. Frost, and K. Sam Shanmugan. "RDRN." ACM SIGMOBILE Mobile Computing and Communications Review 2, no. 2 (April 1998): 15–22. http://dx.doi.org/10.1145/584017.584019.

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Qu, Feng, Xiaohong Ye, Guichuan Hou, Shirley Sato, Thomas E. Clemente, and T. Jack Morris. "RDR6 Has a Broad-Spectrum but Temperature-Dependent Antiviral Defense Role in Nicotiana benthamiana." Journal of Virology 79, no. 24 (December 15, 2005): 15209–17. http://dx.doi.org/10.1128/jvi.79.24.15209-15217.2005.

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ABSTRACT SDE1/SGS2/RDR6, a putative RNA-dependent RNA polymerase (RdRP) from Arabidopsis thaliana, has previously been found to be indispensable for maintaining the posttranscriptional silencing of transgenes, but it is seemingly redundant for antiviral defense. To elucidate the antiviral role of this RdRP in a different host plant and to evaluate whether plant growth conditions affect its role, we down-regulated expression of the Nicotiana benthamiana homolog, NbRDR6, and examined the plants for altered susceptibility to various viruses at different growth temperatures. The results we describe here clearly show that plants with reduced expression of NbRDR6 were more susceptible to all viruses tested and that this effect was more pronounced at higher growth temperatures. Diminished expression of NbRDR6 also permitted efficient multiplication of tobacco mosaic virus in the shoot apices, leading to serious disruption with microRNA-mediated developmental regulation. Based on these results, we propose that NbRDR6 participates in the antiviral RNA silencing pathway that is stimulated by rising temperatures but suppressed by virus-encoded silencing suppressors. The relative strengths of these two factors, along with other plant defense components, critically influence the outcome of virus infections.

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Devert, Anthony, Nicolas Fabre, Maïna Floris, Bruno Canard, Christophe Robaglia, and Patrice Crété. "Primer-Dependent and Primer-Independent Initiation of Double Stranded RNA Synthesis by Purified Arabidopsis RNA-Dependent RNA Polymerases RDR2 and RDR6." PLOS ONE 10, no. 3 (March 20, 2015): e0120100. http://dx.doi.org/10.1371/journal.pone.0120100.

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Amvongo-Adjia, Nathalie, Jacob M. Riveron, Flobert Njiokou, Samuel Wanji, and Charles S. Wondji. "Influence of a Major Mountainous Landscape Barrier (Mount Cameroon) on the Spread of Metabolic (GSTe2) and Target-Site (Rdl) Resistance Alleles in the African Malaria Vector Anopheles funestus." Genes 11, no. 12 (December 11, 2020): 1492. http://dx.doi.org/10.3390/genes11121492.

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Increased levels of insecticide resistance in major malaria vectors such as Anopheles funestus threaten the effectiveness of insecticide-based control programmes. Understanding the landscape features impacting the spread of resistance makers is necessary to design suitable resistance management strategies. Here, we examined the influence of the highest mountain in West Africa (Mount Cameroon; 4095 m elevation) on the spread of metabolic and target-site resistance alleles in An. funestus populations. Vector composition varied across the four localities surveyed along the altitudinal cline with major vectors exhibiting high parity rate (80.5%). Plasmodium infection rates ranged from 0.79% (An. melas) to 4.67% (An. funestus). High frequencies of GSTe2R (67–81%) and RdlR (49–90%) resistance alleles were observed in An. funestus throughout the study area, with GSTe2R frequency increasing with altitude, whereas the opposite is observed for RdlR. Patterns of genetic diversity and population structure analyses revealed high levels of polymorphisms with 12 and 16 haplotypes respectively for GSTe2 and Rdl. However, the reduced diversity patterns of resistance allele carriers revealed signatures of positive selection on the two genes across the study area irrespective of the altitude. Despite slight variations associated with the altitude, the spread of resistance alleles suggest that control strategies could be implemented against malaria vectors across mountainous landscapes.

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Kumakura, Naoyoshi, Atsushi Takeda, Yoichiro Fujioka, Hiroyasu Motose, Ryo Takano, and Yuichiro Watanabe. "SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6-bodies." FEBS Letters 583, no. 8 (March 28, 2009): 1261–66. http://dx.doi.org/10.1016/j.febslet.2009.03.055.

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Cho, Jane. "Study of Asian RDR based on re3data." Electronic Library 37, no. 2 (April 1, 2019): 302–13. http://dx.doi.org/10.1108/el-01-2019-0016.

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Purpose RDR has become an essential academic infrastructure in an atmosphere that facilitates the openness of research output granted by public research funds. This study aims to understand operational status of 152 Asian data repositories on re3data and cluster repositories into four groups according to their operational status. In addition, identify the main subject areas of RDRs in Asian countries and try to understand what topic correlations exist between data archived in Asian countries. Design/methodology/approach This study extracts metadata from re3data and analyzes it in various ways to grasp the current status of research data repositories in Asian countries. The author clusters the repositories into four groups using hierarchical cluster analysis according to the level of operation. In addition, for identifying the main subject areas of RDRs in Asian countries, extracted the keywords of the subject field assigned to the each repository, and Pathfinder Network (PFNET) analysis is performed. Findings About 70 per cent of the Asian-country repositories are those where licenses or policies are declared but not granted permanent identifiers and international-level certification. As a result of the subject domain analysis, eight clusters are formed centering on life sciences and natural sciences. Originality/value The research output in developing countries, especially non-English-speaking countries, tends not to be smoothly circulated in the international community due to the immaturity of the open-access culture, as well as linguistic and technical problems. This study has value, in that it investigates the status of Asian countries’ research data management and global distribution infrastructure in global open-science trends.

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McGonigle, Ian, and Sarah C. R. Lummis. "RDL receptors." Biochemical Society Transactions 37, no. 6 (November 19, 2009): 1404–6. http://dx.doi.org/10.1042/bst0371404.

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RDL receptors are invertebrate members of the Cys-loop family of ligand-gated ion channels. They are GABA (γ-aminobutyric acid)-activated chloride-selective receptors that are closely related to their vertebrate orthologues, the GABAA receptors, as well as other Cys-loop receptors such as the ionotropic glycine, nicotinic acetylcholine and 5-HT3 receptors. RDL receptors are widely expressed throughout the insect CNS (central nervous system) and are important in inhibitory neurotransmission. They are therefore a major insecticidal target site.

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Chou, Shihyu, Eric Jui-Lin Lu, and Yi-Hui Chen. "X-RDR." ACM SIGOPS Operating Systems Review 39, no. 1 (January 2005): 4–21. http://dx.doi.org/10.1145/1044552.1044553.

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Prakash, Ved, and Supriya Chakraborty. "Identification of transcription factor binding sites on promoter of RNA dependent RNA polymerases (RDRs) and interacting partners of RDR proteins through in silico analysis." Physiology and Molecular Biology of Plants 25, no. 4 (May 6, 2019): 1055–71. http://dx.doi.org/10.1007/s12298-019-00660-w.

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Garo, Eliane, Gary R. Eldridge, Matt G. Goering, Elinor DeLancey Pulcini, Martin A. Hamilton, John W. Costerton, and Garth A. James. "Asiatic Acid and Corosolic Acid Enhance the Susceptibility of Pseudomonas aeruginosa Biofilms to Tobramycin." Antimicrobial Agents and Chemotherapy 51, no. 5 (March 12, 2007): 1813–17. http://dx.doi.org/10.1128/aac.01037-06.

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ABSTRACT Asiatic acid and corosolic acid are two natural products identified as biofilm inhibitors in a biofilm inhibition assay. We evaluated the activities of these two compounds on Pseudomonas aeruginosa biofilms grown in rotating disk reactors (RDRs) in combination with tobramycin and ciprofloxacin. To determine the ruggedness of our systems, the antibiotic susceptibilities of these biofilms were assessed with tobramycin and ciprofloxacin. The biofilm bacteria produced in the RDR were shown to display remarkable tolerance to 10 μg/ml of ciprofloxacin, thus mimicking the tolerance observed in recalcitrant bacterial infections. These studies further demonstrate that a nonmucoid strain of P. aeruginosa can form a biofilm that tolerates ciprofloxacin at clinically relevant concentrations. Neither asiatic acid nor corosolic acid reduced the viable cell density of P. aeruginosa biofilms. However, both compounds increased the susceptibility of biofilm bacteria to subsequent treatment with tobramycin, suggesting asiatic acid and corosolic acid to be compounds that potentiate the activity of antibiotics. A similar statistical interaction was observed between ciprofloxacin and subsequent treatment with tobramycin.

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Jang, Woong Sik, Da Hye Lim, Jung Yoon, Ahran Kim, Minsup Lim, Jeonghun Nam, Richard Yanagihara, et al. "Development of a multiplex Loop-Mediated Isothermal Amplification (LAMP) assay for on-site diagnosis of SARS CoV-2." PLOS ONE 16, no. 3 (March 3, 2021): e0248042. http://dx.doi.org/10.1371/journal.pone.0248042.

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A newly identified coronavirus, designated as severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), has spread rapidly from its epicenter in China to more than 150 countries across six continents. In this study, we have designed three reverse-transcription loop-mediated isothermal amplification (RT-LAMP) primer sets to detect the RNA-dependent RNA polymerase (RdRP), Envelope (E) and Nucleocapsid protein (N) genes of SARS CoV-2. For one tube reaction, the detection limits for five combination SARS CoV-2 LAMP primer sets (RdRP/E, RdRP/N, E/N, RdRP/E/N and RdRP/N/Internal control (actin beta)) were evaluated with a clinical nasopharyngeal swab sample. Among the five combination, the RdRP/E and RdRP/N/IC multiplex LAMP assays showed low detection limits. The sensitivity and specificity of the RT-LAMP assay were evaluated and compared to that of the widely used Allplex™ 2019-nCoV Assay (Seegene, Inc., Seoul, South Korea) and PowerChek™ 2019-nCoV Real-time PCR kit (Kogenebiotech, Seoul, South Korea) for 130 clinical samples from 91 SARS CoV-2 patients and 162 NP specimens from individuals with (72) and without (90) viral respiratory infections. The multiplex RdRP (FAM)/N (CY5)/IC (Hex) RT-LAMP assay showed comparable sensitivities (RdRP: 93.85%, N: 94.62% and RdRP/N: 96.92%) to that of the Allplex™ 2019-nCoV Assay (100%) and superior to those of PowerChek™ 2019-nCoV Real-time PCR kit (RdRP: 92.31%, E: 93.85% and RdRP/E: 95.38%).

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Min, Jung Sun, Geon-Woo Kim, Sunoh Kwon, and Young-Hee Jin. "A Cell-Based Reporter Assay for Screening Inhibitors of MERS Coronavirus RNA-Dependent RNA Polymerase Activity." Journal of Clinical Medicine 9, no. 8 (July 27, 2020): 2399. http://dx.doi.org/10.3390/jcm9082399.

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Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19) are emerging zoonotic diseases caused by coronavirus (CoV) infections. The viral RNA-dependent RNA polymerase (RdRp) has been suggested as a valuable target for antiviral therapeutics because the sequence homology of CoV RdRp is highly conserved. We established a cell-based reporter assay for MERS-CoV RdRp activity to test viral polymerase inhibitors. The cell-based reporter system was composed of the bicistronic reporter construct and the MERS-CoV nsp12 plasmid construct. Among the tested nine viral polymerase inhibitors, ribavirin, sofosbuvir, favipiravir, lamivudine, zidovudine, valacyclovir, vidarabine, dasabuvir, and remdesivir, only remdesivir exhibited a dose-dependent inhibition. Meanwhile, the Z-factor and Z′-factor of this assay for screening inhibitors of MERS-CoV RdRp activity were 0.778 and 0.782, respectively. Ribavirin and favipiravir did not inhibit the MERS-CoV RdRp activity, and non-nucleoside HCV RdRp inhibitor, dasabuvir, partially inhibited MERS-CoV RdRp activity. Taken together, the cell-based reporter assay for MERS-CoV RdRp activity confirmed remdesivir as a direct inhibitor of MERS-CoV RdRp in cells. A cell-based MERS-CoV RdRp activity reporter assay is reliable and accurate for screening MERS-CoV RdRp-specific inhibitors. It may provide a valuable platform for developing antiviral drugs for emerging CoV infections.

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Zhou, Nan, Yue Huang, Lu Zhou, Mingma Li, and Hui Jin. "Molecular Evolution of RNA-Dependent RNA Polymerase Region in Norovirus Genogroup I." Viruses 15, no. 1 (January 5, 2023): 166. http://dx.doi.org/10.3390/v15010166.

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Norovirus is the leading viral agent of gastroenteritis in humans. RNA-dependent RNA polymerase (RdRp) is essential in the replication of norovirus RNA. Here, we present a comprehensive evolutionary analysis of the norovirus GI RdRp gene. Our results show that the norovirus GI RdRp gene can be divided into three groups, and that the most recent common ancestor was 1484. The overall evolutionary rate of GI RdRp is 1.821 × 10−3 substitutions/site/year. Most of the amino acids of the GI RdRp gene were under negative selection, and only a few positively selected sites were recognized. Amino acid substitutions in the GI RdRp gene accumulated slowly over time. GI.P1, GI.P3 and GI.P6 owned the higher evolutionary rates. GI.P11 and GI.P13 had the faster accumulation rate of amino acid substitutions. GI.P2, GI.P3, GI.P4, GI.P6 and GI.P13 presented a strong linear evolution. These results reveal that the norovirus GI RdRp gene evolves conservatively, and that the molecular evolutionary characteristics of each P-genotype are diverse. Sequencing in RdRp and VP1 of norovirus should be advocated in the surveillance system to explore the effect of RdRp on norovirus activity.

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Pogany, Judit, and Peter D. Nagy. "Activation ofTomato Bushy Stunt VirusRNA-Dependent RNA Polymerase by Cellular Heat Shock Protein 70 Is Enhanced by PhospholipidsIn Vitro." Journal of Virology 89, no. 10 (March 11, 2015): 5714–23. http://dx.doi.org/10.1128/jvi.03711-14.

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ABSTRACTSimilar to other positive-strand RNA viruses, tombusviruses are replicated by the membrane-bound viral replicase complex (VRC). The VRC consists of the p92 virus-coded RNA-dependent RNA polymerase (RdRp), the viral p33 RNA chaperone, and several co-opted host proteins. In order to become a functional RdRp after its translation, the p92 replication protein should be incorporated into the VRC, followed by its activation. We have previously shown in a cell-free yeast extract-based assay that the activation of theTomato bushy stunt virus(TBSV) RdRp requires a soluble host factor(s). In this article, we identify the cellular heat shock protein 70 (Hsp70) as the co-opted host factor required for the activation of an N-terminally truncated recombinant TBSV RdRp. In addition, small-molecule-based blocking of Hsp70 function inhibits RNA synthesis by the tombusvirus RdRpin vitro. Furthermore, we show that neutral phospholipids, namely, phosphatidylethanolamine (PE) and phosphatidylcholine (PC), enhance RdRp activationin vitro. In contrast, phosphatidylglycerol (PG) shows a strong and dominant inhibitory effect onin vitroRdRp activation. We also demonstrate that PE and PC stimulate RdRp-viral plus-strand RNA [(+)RNA] interaction, while PG inhibits the binding of the viral RNA to the RdRp. Based on the stimulatory versus inhibitory roles of various phospholipids in tombusvirus RdRp activation, we propose that the lipid composition of targeted subcellular membranes might be utilized by tombusviruses to regulate new VRC assembly during the course of infection.IMPORTANCEThe virus-coded RNA-dependent RNA polymerase (RdRp), which is responsible for synthesizing the viral RNA progeny in infected cells of several positive-strand RNA viruses, is initially inactive. This strategy is likely to avoid viral RNA synthesis in the cytosol that would rapidly lead to induction of RNA-triggered cellular antiviral responses. During the assembly of the membrane-bound replicase complex, the viral RdRp becomes activated through an incompletely understood process that makes the RdRp capable of RNA synthesis. By using TBSV RdRp, we show that the co-opted cellular Hsp70 chaperone and neutral phospholipids facilitate RdRp activationin vitro. In contrast, phosphatidylglycerol (PG) has a dominant inhibitory effect onin vitroRdRp activation and RdRp-viral RNA interaction, suggesting that the membranous microdomain surrounding the RdRp greatly affects its ability for RNA synthesis. Thus, the activation of the viral RdRp likely depends on multiple host components in infected cells.

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Min, Jung Sun, Sunoh Kwon, and Young-Hee Jin. "SARS-CoV-2 RdRp Inhibitors Selected from a Cell-Based SARS-CoV-2 RdRp Activity Assay System." Biomedicines 9, no. 8 (August 11, 2021): 996. http://dx.doi.org/10.3390/biomedicines9080996.

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The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), urgently needs effective prophylactic and therapeutic drugs. RNA-dependent RNA polymerase (RdRp), essential for replicating and transcribing a viral RNA genome, is highly conserved in coronaviruses; thus, it is a potential target for inhibiting coronavirus infection. In this study, we generated the cell-based SARS-CoV-2 RdRp activity assay system by modifying a previously reported cell-based MERS-CoV RdRp activity assay system to screen for SARS-CoV-2 RdRp inhibitors. The assay system consisted of an expression plasmid encoding SARS-CoV-2 RdRp and an RdRp activity reporter plasmid. RdRp activity in the cells could be conveniently detected by luminescence after transfection. We confirmed that SARS-CoV-2 RdRp replicated double-stranded RNA using immunofluorescence staining and the inhibition of RdRp activity by remdesivir and lycorine using this system. Moreover, the Z-factor of this system was calculated to be 0.798, suggesting the reproducibility and reliability of the high-throughput screening system. Finally, we screened nucleoside and nucleotide analogs and identified adefovir dipivoxil, emtricitabine, telbivudine, entecavir hydrate, moroxydine and rifampin as novel SARS-CoV-2 RdRp inhibitors and therapeutic candidates for COVID-19 This system provides an effective high-throughput screening system platform for developing potential prophylactic and therapeutic drugs for COVID-19 and emerging coronavirus infections.

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Mohammad, Anwar, Fahd Al-Mulla, Dong-Qing Wei, and Jehad Abubaker. "Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type." Biomolecules 11, no. 7 (June 22, 2021): 919. http://dx.doi.org/10.3390/biom11070919.

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SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) protein is the target for the antiviral drug Remdesivir (RDV). With RDV clinical trials on COVID-19 patients showing a reduced hospitalisation time. During the spread of the virus, the RdRp has developed several mutations, with the most frequent being A97V and P323L. The current study sought to investigate whether A97V and P323L mutations influence the binding of RDV to the RdRp of SARS-CoV-2 compared to wild-type (WT). The interaction of RDV with WT-, A97V-, and P323L-RdRp were measured using molecular dynamic (MD) simulations, and the free binding energies were extracted. Results showed that RDV that bound to WT- and A97V-RdRp had a similar dynamic motion and internal residue fluctuations, whereas RDV interaction with P323L-RdRp exhibited a tighter molecular conformation, with a high internal motion near the active site. This was further corroborated with RDV showing a higher binding affinity to P323L-RdRp (−24.1 kcal/mol) in comparison to WT-RdRp (−17.3 kcal/mol). This study provides insight into the potential significance of administering RDV to patients carrying the SARS-CoV-2 P323L-RdRp mutation, which may have a more favourable chance of alleviating the SARS-CoV-2 illness in comparison to WT-RdRp carriers, thereby suggesting further scientific consensus for the usage of Remdesivir as clinical candidate against COVID-19.

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Niyomrattanakit, Pornwaratt, Yen-Liang Chen, Hongping Dong, Zheng Yin, Min Qing, J. Frasier Glickman, Kai Lin, et al. "Inhibition of Dengue Virus Polymerase by Blocking of the RNA Tunnel." Journal of Virology 84, no. 11 (March 17, 2010): 5678–86. http://dx.doi.org/10.1128/jvi.02451-09.

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ABSTRACT Dengue virus (DENV) is the most prevalent mosquito-borne viral pathogen in humans. Neither vaccine nor antiviral therapy is currently available for DENV. We report here that N-sulfonylanthranilic acid derivatives are allosteric inhibitors of DENV RNA-dependent RNA polymerase (RdRp). The inhibitor was identified through high-throughput screening of one million compounds using a primer extension-based RdRp assay [substrate poly(C)/oligo(G)20]. Chemical modification of the initial “hit” improved the compound potency to an IC50 (that is, a concentration that inhibits 50% RdRp activity) of 0.7 μM. In addition to suppressing the primer extension-based RNA elongation, the compound also inhibited de novo RNA synthesis using a DENV subgenomic RNA, but at a lower potency (IC50 of 5 μM). Remarkably, the observed anti-polymerase activity is specific to DENV RdRp; the compound did not inhibit WNV RdRp and exhibited IC50s of >100 μM against hepatitis C virus RdRp and human DNA polymerase α and β. UV cross-linking and mass spectrometric analysis showed that a photoreactive inhibitor could be cross-linked to Met343 within the RdRp domain of DENV NS5. On the crystal structure of DENV RdRp, Met343 is located at the entrance of RNA template tunnel. Biochemical experiments showed that the order of addition of RNA template and inhibitor during the assembly of RdRp reaction affected compound potency. Collectively, the results indicate that the compound inhibits RdRp through blocking the RNA tunnel. This study has provided direct evidence to support the hypothesis that allosteric pockets from flavivirus RdRp could be targeted for antiviral development.

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Tanimoto, Shoichi, Satoru G. Itoh, and Hisashi Okumura. "State-of-the-Art Molecular Dynamics Simulation Studies of RNA-Dependent RNA Polymerase of SARS-CoV-2." International Journal of Molecular Sciences 23, no. 18 (September 8, 2022): 10358. http://dx.doi.org/10.3390/ijms231810358.

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Molecular dynamics (MD) simulations are powerful theoretical methods that can reveal biomolecular properties, such as structure, fluctuations, and ligand binding, at the level of atomic detail. In this review article, recent MD simulation studies on these biomolecular properties of the RNA-dependent RNA polymerase (RdRp), which is a multidomain protein, of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are presented. Although the tertiary structures of RdRps in SARS-CoV-2 and SARS-CoV are almost identical, the RNA synthesis activity of RdRp of SARS-CoV is higher than SARS-CoV-2. Recent MD simulations observed a difference in the dynamic properties of the two RdRps, which may cause activity differences. RdRp is also a drug target for Coronavirus disease 2019 (COVID-19). Nucleotide analogs, such as remdesivir and favipiravir, are considered to be taken up by RdRp and inhibit RNA replication. Recent MD simulations revealed the recognition mechanism of RdRp for these drug molecules and adenosine triphosphate (ATP). The ligand-recognition ability of RdRp decreases in the order of remdesivir, favipiravir, and ATP. As a typical recognition process, it was found that several lysine residues of RdRp transfer these ligand molecules to the binding site such as a “bucket brigade.” This finding will contribute to understanding the mechanism of the efficient ligand recognition by RdRp. In addition, various simulation studies on the complexes of SARS-CoV-2 RdRp with several nucleotide analogs are reviewed, and the molecular mechanisms by which these compounds inhibit the function of RdRp are discussed. The simulation studies presented in this review will provide useful insights into how nucleotide analogs are recognized by RdRp and inhibit the RNA replication.

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Fukushi, Shuetsu, Shigeyuki Kojima, Reiko Takai, Fuminori B. Hoshino, Tomoichiro Oka, Naokazu Takeda, Kazuhiko Katayama, and Tsutomu Kageyama. "Poly(A)- and Primer-Independent RNA Polymerase of Norovirus." Journal of Virology 78, no. 8 (April 15, 2004): 3889–96. http://dx.doi.org/10.1128/jvi.78.8.3889-3896.2004.

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ABSTRACT Replication of positive-strand caliciviruses is mediated by a virus-encoded RNA-dependent RNA polymerase (RdRp). To study the replication of Norovirus (NV), a member of the family Caliciviridae, we used a recombinant baculovirus system to express an enzymatically active RdRp protein from the 3D region of the NV genome and defined conditions for optimum enzymatic activity. Using an RNA template from the NV 3′ genomic region, we observed similar levels of enzymatic activity in assays with and without a poly(A) tail. RdRp activity was not significantly affected by the addition of an RNA primer to the reaction mixture. Thus, the NV RdRp exhibited primer- and poly(A)-independent RNA polymerase activity. While the RdRp inhibitor phosphonoacetic acid inhibited NV RdRp activity, another gliotoxin did not. The active recombinant NV RdRp will be of benefit to studies of NV replication and will facilitate the development of specific inhibitors of NV proliferation.

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Weng, Leiyun, Yuichi Hirata, Masaaki Arai, Michinori Kohara, Takaji Wakita, Koichi Watashi, Kunitada Shimotohno, Ying He, Jin Zhong, and Tetsuya Toyoda. "Sphingomyelin Activates Hepatitis C Virus RNA Polymerase in a Genotype-Specific Manner." Journal of Virology 84, no. 22 (September 15, 2010): 11761–70. http://dx.doi.org/10.1128/jvi.00638-10.

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ABSTRACT Hepatitis C virus (HCV) replication and infection depend on the lipid components of the cell, and replication is inhibited by inhibitors of sphingomyelin biosynthesis. We found that sphingomyelin bound to and activated genotype 1b RNA-dependent RNA polymerase (RdRp) by enhancing its template binding activity. Sphingomyelin also bound to 1a and JFH1 (genotype 2a) RdRps but did not activate them. Sphingomyelin did not bind to or activate J6CF (2a) RdRp. The sphingomyelin binding domain (SBD) of HCV RdRp was mapped to the helix-turn-helix structure (residues 231 to 260), which was essential for sphingomyelin binding and activation. Helix structures (residues 231 to 241 and 247 to 260) are important for RdRp activation, and 238S and 248E are important for maintaining the helix structures for template binding and RdRp activation by sphingomyelin. 241Q in helix 1 and the negatively charged 244D at the apex of the turn are important for sphingomyelin binding. Both amino acids are on the surface of the RdRp molecule. The polarity of the phosphocholine of sphingomyelin is important for HCV RdRp activation. However, phosphocholine did not activate RdRp. Twenty sphingomyelin molecules activated one RdRp molecule. The biochemical effect of sphingomyelin on HCV RdRp activity was virologically confirmed by the HCV replicon system. We also found that the SBD was the lipid raft membrane localization domain of HCV NS5B because JFH1 (2a) replicon cells harboring NS5B with the mutation A242C/S244D moved to the lipid raft while the wild type did not localize there. This agreed with the myriocin sensitivity of the mutant replicon. This sphingomyelin interaction is a target for HCV infection because most HCV RdRps have 241Q.

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Shang, Xiaopu, Xue Feng, and Jun Wang. "A Novel Interval-Valued q-Rung Dual Hesitant Linguistic Multi-Attribute Decision-Making Method Based on Linguistic Scale Functions and Power Hamy Mean." Entropy 24, no. 2 (January 22, 2022): 166. http://dx.doi.org/10.3390/e24020166.

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The interval-valued q-rung dual hesitant linguistic (IVq-RDHL) sets are widely used to express the evaluation information of decision makers (DMs) in the process of multi-attribute decision-making (MADM). However, the existing MADM method based on IVq-RDHL sets has obvious shortcomings, i.e., the operational rules of IVq-RDHL values have some weaknesses and the existing IVq-RDHL aggregation operators are incapable of dealing with some special decision-making situations. In this paper, by analyzing these drawbacks, we then propose the operations for IVq-RDHL values based on a linguistic scale function. After it, we present novel aggregation operators for IVq-RDHL values based on the power Hamy mean and introduce the IVq-RDHL power Hamy mean operator and IVq-RDHL power weighted Hamy mean operator. Properties of these new aggregation operators are also studied. Based on these foundations, we further put forward a MADM method, which is more reasonable and rational than the existing one. Our proposed method not only provides a series of more reasonable operational laws but also offers a more powerful manner to fuse attribute values. Finally, we apply the new MADM method to solve the practical problem of patient admission evaluation. The performance and advantages of our method are illustrated in the comparative analysis with other methods.

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Rajendran, K. S., J. Pogany, and P. D. Nagy. "Comparison of Turnip Crinkle Virus RNA-Dependent RNA Polymerase Preparations Expressed in Escherichia coli or Derived from Infected Plants." Journal of Virology 76, no. 4 (February 15, 2002): 1707–17. http://dx.doi.org/10.1128/jvi.76.4.1707-1717.2002.

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ABSTRACT Turnip crinkle virus (TCV) is a small, plus-sense, single-stranded RNA virus of plants. A virus-coded protein, p88, which is required for replication has been expressed and purified from Escherichia coli. In vitro assays revealed that the recombinant p88 has an RNA-dependent RNA polymerase (RdRp) activity and can also bind to RNA. Deletion of the N-terminal region in p88 resulted in a more active RdRp, while further deletions abolished RdRp activity. Comparison of the E. coli-expressed p88, the N-terminal deletion mutant of p88, and a TCV RdRp preparation obtained from infected plants revealed that these preparations show remarkable similarities in RNA template recognition and usage. Both the recombinant and the plant TCV RdRp preparations are capable of de novo initiation on both plus- and minus-strand satC and satD templates, which are small parasitic RNAs associated with TCV infections. In addition, these RdRp preparations can efficiently recognize the related Tomato bushy stunt virus promoter sequences, including the minus- and plus-strand initiation promoters. Heterologous viral and artificial promoters are recognized poorly by the recombinant and the plant TCV RdRps. Further comparison of the single-component recombinant TCV RdRp and the multicomponent plant TCV RdRp will help dissect the functions of various components of the TCV replicase.

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Hall, Roy A., Si En Tan, Barbara Selisko, Rachael Slade, Jody Hobson-Peters, Bruno Canard, Megan Hughes, et al. "Monoclonal antibodies to the West Nile virus NS5 protein map to linear and conformational epitopes in the methyltransferase and polymerase domains." Journal of General Virology 90, no. 12 (December 1, 2009): 2912–22. http://dx.doi.org/10.1099/vir.0.013805-0.

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The West Nile virus (WNV) NS5 protein contains a methyltransferase (MTase) domain involved in RNA capping and an RNA-dependent RNA polymerase (RdRp) domain essential for virus replication. Crystal structures of individual WNV MTase and RdRp domains have been solved; however, the structure of full-length NS5 has not been determined. To gain more insight into the structure of NS5 and interactions between the MTase and RdRp domains, we generated a panel of seven monoclonal antibodies (mAbs) to the NS5 protein of WNV (Kunjin strain) and mapped their binding sites using a series of truncated NS5 proteins and synthetic peptides. Binding sites of four mAbs (5D4, 4B6, 5C11 and 6A10) were mapped to residues 354–389 in the fingers subdomain of the RdRp. This is consistent with the ability of these mAbs to inhibit RdRp activity in vitro and suggests that this region represents a potential target for RdRp inhibitors. Using a series of synthetic peptides, we also identified a linear epitope (bound by mAb 5H1) that mapped to a 13 aa stretch surrounding residues 47 and 49 in the MTase domain, a region predicted to interact with the palm subdomain of the RdRp. The failure of one mAb (7G6) to bind both N- and C-terminally truncated NS5 recombinants indicates that the antibody recognizes a conformational epitope that requires the presence of residues in both the MTase and RdRp domains. These data support a structural model of the full-length NS5 molecule that predicts a physical interaction between the MTase and the RdRp domains.

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Lee, Ji-Hye, Yeon Bin Chung, Jong Hyeon Seok, Kang Rok Han, Sella Kim, and Kyung Hyun Kim. "Structural basis for VPg-induced formation of RNA-dependent RNA polymerase multimeric complexes." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1601. http://dx.doi.org/10.1107/s2053273314083983.

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Norovirus is the leading cause of epidemic acute, nonbacterial gastroenteritis, and adopts de novo and VPg (Virion protein genome linked)-primed RNA synthesis by RNA-dependent RNA polymerase (RdRp). To understand the interaction between RdRp and VPg in replication of murine norovirus-1 (MNV-1), we determined the crystal structure of MNV-1 RdRp-VPg(1-73)-RNA complex. VPg was bound to the base of the palm domain and the tip of the fingers domain of RdRp simultaneously, but RNA template could not be modeled. The binding affinity constants (Kd) for RdRp-VPg was 3.7411.57 nM and VPg(1-73) showed approximately 90-fold less affinity than that of full-length VPg. In addition to this multiple binding mode, VPg enhanced the interactions of RdRp hexamers, leading to the formation of high-order multimers or tubular fibrils with significantly increased polymerase activity, confirmed by electron microscopic and biochemical studies. Our data indicated that MNV-1 VPg with helical structure was bound to RdRp at multiple sites and induces RdRp multimerization in viral replication. The multimers of RdRp-VPg-RNA can provide a mechanistic understanding of viral polymerase multimeric arrays and a new tool for development of antivirals to control norovirus outbreaks. This work was supported by a grant of the Korea Healthcare Technology R&D Project, Ministry of Health, Welfare and Family Affairs (A085119 K.H.K), Basic Science Research Program through the National Research Foundation (NRF-2013R1A1A2064940, L.J-H), Korea University Grant (L.J-H), and the BK21 plus program of the Ministry of Education, Korea.

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Zhan, Binhui, Mengji Cao, Kaina Wang, Xifeng Wang, and Xueping Zhou. "Detection and Characterization of Cucumis melo Cryptic Virus, Cucumis melo Amalgavirus 1, and Melon Necrotic Spot Virus in Cucumis melo." Viruses 11, no. 1 (January 18, 2019): 81. http://dx.doi.org/10.3390/v11010081.

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Three RNA viruses—Cucumis melo cryptic virus (CmCV), Cucumis melo amalgavirus 1 (CmAV1), and melon necrotic spot virus (MNSV)—were identified from a melon (Cucumis melo) transcriptome dataset. CmCV has two dsRNA genome segments; dsRNA-1 is 1592 bp in size, containing a conserved RNA-dependent RNA polymerase (RdRp), and dsRNA-2 is 1715 bp in size, and encodes a coat protein (CP). The sequence alignment and phylogenetic analyses of the CmCV RdRp and CP indicated CmCV clusters with approved or putative deltapartitiviruses in well-supported monophyletic clade. The RdRp of CmCV shared an amino acid sequence identity of 60.7% with the closest RdRp of beet cryptic virus 3, and is <57% identical to other partitiviruses. CmAV1 is a nonsegmented dsRNA virus with a genome of 3424 bp, including two partially overlapping open reading frames (ORFs) encoding a putative CP and RdRp. The sequence alignment and phylogenetic analyses of CmAV1 RdRp revealed that it belongs to the genus Amalgavirus in the family Amalgaviridae. The RdRp of CmAV1 shares 57.7% of its amino acid sequence identity with the most closely related RdRp of Phalaenopsis equestris amalgavirus 1, and is <47% identical to the other reported amalgaviruses. These analyses suggest that CmCV and CmAV1 are novel species in the genera Amalgavirus and Deltapartitivirus, respectively. These findings enrich our understanding of new plant dsRNA virus species.

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Cooper, Carly, Bruce Frey, Haiying Long, and Charles Day. "A Confirmatory Factor Analysis of the ‘Return to Duty Readiness Questionnaire’." Healthcare 11, no. 1 (December 23, 2022): 41. http://dx.doi.org/10.3390/healthcare11010041.

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The Readiness to Return to Duty Questionnaire (RDRQ) is a recently developed screening instrument for detecting fear-avoidance behavior in a military musculoskeletal pain population. The RDRQ was developed based on the Fear-Avoidance Model which postulates four factors resulting in overall fear-avoidance behavior. While research investigating the factor structure of the RDRQ does not exist, research investigating the factor structure of other measures of fear avoidance have found evidence of one and two factor solutions. In the present paper we assess the adequacy of the proposed factor structure of the RDRQ using confirmatory factor analysis. The results favor a three-factor model. Theoretical implications for research using the RDRQ are discussed.

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Levanova, Alesia A., Eeva J. Vainio, Jarkko Hantula, and Minna M. Poranen. "RNA-Dependent RNA Polymerase from Heterobasidion RNA Virus 6 Is an Active Replicase In Vitro." Viruses 13, no. 9 (August 31, 2021): 1738. http://dx.doi.org/10.3390/v13091738.

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Heterobasidion RNA virus 6 (HetRV6) is a double-stranded (ds)RNA mycovirus and a member of the recently established genus Orthocurvulavirus within the family Orthocurvulaviridae. The purpose of the study was to determine the biochemical requirements for RNA synthesis catalyzed by HetRV6 RNA-dependent RNA polymerase (RdRp). HetRV6 RdRp was expressed in Escherichia coli and isolated to near homogeneity using liquid chromatography. The enzyme activities were studied in vitro using radiolabeled UTP. The HetRV6 RdRp was able to initiate RNA synthesis in a primer-independent manner using both virus-related and heterologous single-stranded (ss)RNA templates, with a polymerization rate of about 46 nt/min under optimal NTP concentration and temperature. NTPs with 2′-fluoro modifications were also accepted as substrates in the HetRV6 RdRp-catalyzed RNA polymerization reaction. HetRV6 RdRp transcribed viral RNA genome via semi-conservative mechanism. Furthermore, the enzyme demonstrated terminal nucleotidyl transferase (TNTase) activity. Presence of Mn2+ was required for the HetRV6 RdRp catalyzed enzymatic activities. In summary, our study shows that HetRV6 RdRp is an active replicase in vitro that can be potentially used in biotechnological applications, molecular biology, and biomedicine.

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Rao, Dongning, and Zhihua Jiang. "Learning Planning Domain Descriptions in RDDL." International Journal on Artificial Intelligence Tools 24, no. 03 (June 2015): 1550002. http://dx.doi.org/10.1142/s0218213015500025.

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Recently, there is increasing interest in action model learning. However, most previous studies focused on learning effect-based action models. On the other hand, a rule-based planning domain description language was proposed in the latest planning competition. That is the Relational Dynamic Influence Diagram Language (RDDL). It uses rules to describe transitions instead of action models. In this paper, we build a system to learn planning domain descriptions in the RDDL. There are three major parts of an RDDL domain description: constraints, transitions and rewards. We first take advantage of the finite state machine analysis to identify constraints. Then, we employ the inductive learning technique to learn transitions. At last, we use regression to fix rewards. The evaluation was performed on benchmarks from planning competitions. It showed that our system can learn domain descriptions in the RDDL with low error rates. Moreover, our system is developed based on classical approaches. It implicates that the RDDL roots in previous planning languages. Therefore, more classical approaches could be useful in the RDDL domains.

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Singh, P. K., S. Pathania, and R. K. Rawal. "Exploring RdRp–remdesivir interactions to screen RdRp inhibitors for the management of novel coronavirus 2019-nCoV." SAR and QSAR in Environmental Research 31, no. 11 (October 26, 2020): 857–67. http://dx.doi.org/10.1080/1062936x.2020.1825014.

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Xu, Hong-Tao, Susan P. Colby-Germinario, Said Hassounah, Peter K. Quashie, Yingshan Han, Maureen Oliveira, Brent R. Stranix, and Mark A. Wainberg. "Identification of a Pyridoxine-Derived Small-Molecule Inhibitor Targeting Dengue Virus RNA-Dependent RNA Polymerase." Antimicrobial Agents and Chemotherapy 60, no. 1 (November 16, 2015): 600–608. http://dx.doi.org/10.1128/aac.02203-15.

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ABSTRACTThe viral RNA-dependent RNA polymerase (RdRp) activity of the dengue virus (DENV) NS5 protein is an attractive target for drug design. Here, we report the identification of a novel class of inhibitor (i.e., an active-site metal ion chelator) that acts against DENV RdRp activity. DENV RdRp utilizes a two-metal-ion mechanism of catalysis; therefore, we constructed a small library of compounds, through mechanism-based drug design, aimed at chelating divalent metal ions in the catalytic site of DENV RdRp. We now describe a pyridoxine-derived small-molecule inhibitor that targets DENV RdRp and show that 5-benzenesulfonylmethyl-3-hydroxy-4-hydroxymethyl-pyridine-2-carboxylic acid hydroxyamide (termed DMB220) inhibited the RdRp activity of DENV serotypes 1 to 4 at low micromolar 50% inhibitory concentrations (IC50sof 5 to 6.7 μM) in an enzymatic assay. The antiviral activity of DMB220 against DENV infection was also verified in a cell-based assay and showed a 50% effective concentration (EC50) of <3 μM. Enzyme assays proved that DMB220 was competitive with nucleotide incorporation. DMB220 did not inhibit the enzymatic activity of recombinant HIV-1 reverse transcriptase and showed only weak inhibition of HIV-1 integrase strand transfer activity, indicating high specificity for DENV RdRp. S600T substitution in the DENV RdRp, which was previously shown to confer resistance to nucleoside analogue inhibitors (NI), conferred 3-fold hypersusceptibility to DMB220, and enzymatic analyses showed that this hypersusceptibility may arise from the decreased binding/incorporation efficiency of the natural NTP substrate without significantly impacting inhibitor binding. Thus, metal ion chelation at the active site of DENV RdRp represents a viable anti-DENV strategy, and DMB220 is the first of a new class of DENV inhibitor.

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Haddad, Abderrahim, Mohssin Aoutoul, Mohamed Essaaidi, Khalid Sabri, Abdelaziz Khoukh, Youssef Errami, Anas Had, Fadwa El Moukhtafi, and Redouane Jouali. "1×16 Rectangular dielectric resonator antenna array for 24 Ghz automotive radar system." Bulletin of Electrical Engineering and Informatics 11, no. 4 (August 1, 2022): 2115–23. http://dx.doi.org/10.11591/eei.v11i4.3068.

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This paper presents the design of a 1×16-elements RDRA array for anti-collision radar SRR application at 24 GHz. A single RDRA with high dielectric constant of 41, fed by a simple microstrip line feeding technique, is initially designed to operate around 24 GHz. The RDRA element is further used within an array network structure made up of 16 linear antenna elements to cover the same frequency band. The simulated 1×16 RDRA array can reach a high gain, up to18.6 dB, very high radiation efficiency (97%), and ensure enough directional radiation pattern properties for radar applications with a 3-dB angular beam width of 6°. To validate our design, RDRA array’ radiation pattern computed results are compared to an equivalent fabricated patch antenna array reported in the literature.

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Maio, Nunziata, Bernard A. P. Lafont, Debangsu Sil, Yan Li, J. Martin Bollinger, Carsten Krebs, Theodore C. Pierson, W. Marston Linehan, and Tracey A. Rouault. "Fe-S cofactors in the SARS-CoV-2 RNA-dependent RNA polymerase are potential antiviral targets." Science 373, no. 6551 (June 3, 2021): 236–41. http://dx.doi.org/10.1126/science.abi5224.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19, uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes. We found that the catalytic subunit of the RdRp, nsp12, ligates two iron-sulfur metal cofactors in sites that were modeled as zinc centers in the available cryo–electron microscopy structures of the RdRp complex. These metal binding sites are essential for replication and for interaction with the viral helicase. Oxidation of the clusters by the stable nitroxide TEMPOL caused their disassembly, potently inhibited the RdRp, and blocked SARS-CoV-2 replication in cell culture. These iron-sulfur clusters thus serve as cofactors for the SARS-CoV-2 RdRp and are targets for therapy of COVID-19.

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Journal articles on the topic 'RDRL'

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