The Experts below are selected from a list of 161745 Experts worldwide ranked by ideXlab platform
Alexander E Gorbalenya - One of the best experts on this subject based on the ideXlab platform.
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Picornavirales, a proposed order of Positive-Sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture
Archives of Virology, 2008Co-Authors: Olivier Gall, Peter Christian, Andrew M Q King, Glyn Stanway, Nobuhiko Nakashima, Claude M Fauquet, Nick J Knowles, Alexander E GorbalenyaAbstract:Despite the apparent natural grouping of “picorna-like” viruses, the taxonomical significance of this putative “supergroup” was never addressed adequately. We recently proposed to the ICTV that an order should be created and named Picornavirales , to include viruses infecting eukaryotes that share similar properties: (i) a Positive-Sense RNA genome, usually with a 5′-bound VPg and 3′-polyadenylated, (ii) genome translation into autoproteolytically processed polyprotein(s), (iii) capsid proteins organized in a module containing three related jelly-roll domains which form small icosahedral, non-enveloped particles with a pseudo-T = 3 symmetry, and (iv) a three-domain module containing a superfamily III helicase, a (cysteine) proteinase with a chymotrypsin-like fold and an RNA-dependent RNA polymerase. According to the above criteria, the order Picornavirales includes the families Picornaviridae, Comoviridae , Dicistroviridae, Marnaviridae, Sequiviridae and the unassigned genera Cheravirus , Iflavirus and Sadwavirus . Other taxa of “picorna-like” viruses, e.g. Potyviridae , Caliciviridae , Hypoviridae , do not conform to several of the above criteria and are more remotely related: therefore they are not being proposed as members of the new order. Newly described viruses, not yet assigned to an existing taxon by ICTV, may belong to the proposed order.
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picornavirales a proposed order of Positive Sense single stranded rna viruses with a pseudo t 3 virion architecture
Archives of Virology, 2008Co-Authors: Olivier Le Gall, Peter Christian, Andrew M Q King, Glyn Stanway, Nobuhiko Nakashima, Claude M Fauquet, Nick J Knowles, Alexander E GorbalenyaAbstract:Despite the apparent natural grouping of “picorna-like” viruses, the taxonomical significance of this putative “supergroup” was never addressed adequately. We recently proposed to the ICTV that an order should be created and named Picornavirales, to include viruses infecting eukaryotes that share similar properties: (i) a Positive-Sense RNA genome, usually with a 5′-bound VPg and 3′-polyadenylated, (ii) genome translation into autoproteolytically processed polyprotein(s), (iii) capsid proteins organized in a module containing three related jelly-roll domains which form small icosahedral, non-enveloped particles with a pseudo-T = 3 symmetry, and (iv) a three-domain module containing a superfamily III helicase, a (cysteine) proteinase with a chymotrypsin-like fold and an RNA-dependent RNA polymerase. According to the above criteria, the order Picornavirales includes the families Picornaviridae, Comoviridae, Dicistroviridae, Marnaviridae, Sequiviridae and the unassigned genera Cheravirus, Iflavirus and Sadwavirus. Other taxa of “picorna-like” viruses, e.g. Potyviridae, Caliciviridae, Hypoviridae, do not conform to several of the above criteria and are more remotely related: therefore they are not being proposed as members of the new order. Newly described viruses, not yet assigned to an existing taxon by ICTV, may belong to the proposed order.
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Picornavirales, a proposed order of Positive-Sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture
Archives of Virology, 2008Co-Authors: Olivier Gall, Peter Christian, Andrew M Q King, Glyn Stanway, Nobuhiko Nakashima, Claude M Fauquet, Nick J Knowles, Alexander E GorbalenyaAbstract:Despite the apparent natural grouping of “picorna-like” viruses, the taxonomical significance of this putative “supergroup” was never addressed adequately. We recently proposed to the ICTV that an order should be created and named Picornavirales, to include viruses infecting eukaryotes that share similar properties: (i) a Positive-Sense RNA genome, usually with a 5′-bound VPg and 3′-polyadenylated, (ii) genome translation into autoproteolytically processed polyprotein(s), (iii) capsid proteins organized in a module containing three related jelly-roll domains which form small icosahedral, non-enveloped particles with a pseudo-T = 3 symmetry, and (iv) a three-domain module containing a superfamily III helicase, a (cysteine) proteinase with a chymotrypsin-like fold and an RNA-dependent RNA polymerase. According to the above criteria, the order Picornavirales includes the families Picornaviridae, Comoviridae, Dicistroviridae, Marnaviridae, Sequiviridae and the unassigned genera Cheravirus, Iflavirus and Sadwavirus. Other taxa of “picorna-like” viruses, e.g. Potyviridae, Caliciviridae, Hypoviridae, do not conform to several of the above criteria and are more remotely related: therefore they are not being proposed as members of the new order. Newly described viruses, not yet assigned to an existing taxon by ICTV, may belong to the proposed order.
Tomas Canto - One of the best experts on this subject based on the ideXlab platform.
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Effects of simultaneously elevated temperature and CO2 levels on Nicotiana benthamiana and its infection by different Positive-Sense RNA viruses are cumulative and virus type-specific.
Virology, 2017Co-Authors: Francisco J. Del Toro, F. Rakhshandehroo, Beatriz Larruy, Emmanuel Aguilar, Francisco Tenllado, Tomas CantoAbstract:Abstract We have studied how simultaneously elevated temperature and CO 2 levels [climate change-related conditions (CCC) of 30 °C, 970 parts- per -million (ppm) of CO 2 vs. standard conditions (SC) of 25 °C, ~ 405 ppm CO 2 ] affect physiochemical properties of Nicotiana benthamiana leaves , and also its infection by several Positive-Sense RNA viruses. In previous works we had studied effects of elevated temperature, CO 2 levels separately. Under CCC, leaves of healthy plants almost doubled their area relative to SC but contained less protein/unit-of-area, similarly to what we had found under conditions of elevated CO 2 alone. CCC also affected the sizes/numbers of different foliar cell types differently. Under CCC, infection outcomes in titers and symptoms were virus type-specific, broadly similar to those observed under elevated temperature alone. Under either condition, infections did not significantly alter the protein content of leaf discs. Therefore, effects of elevated temperature and CO 2 combined on properties of the pathosystems studied were overall cumulative.
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High Temperature, High Ambient CO2 Affect the Interactions between Three Positive-Sense RNA Viruses and a Compatible Host Differentially, but not Their Silencing Suppression Efficiencies
PloS one, 2015Co-Authors: Francisco J. Del Toro, Emmanuel Aguilar, Francisco Tenllado, Francisco J. Hernández-walias, Bong-nam Chung, Tomas CantoAbstract:We compared infection of Nicotiana benthamiana plants by the Positive-Sense RNA viruses Cucumber mosaic virus (CMV), Potato virus Y (PVY), and by a Potato virus X (PVX) vector, the latter either unaltered or expressing the CMV 2b protein or the PVY HCPro suppressors of silencing, at 25°C vs. 30°C, or at standard (~401 parts per million, ppm) vs. elevated (970 ppm) CO2 levels. We also assessed the activities of their suppressors of silencing under those conditions. We found that at 30°C, accumulation of the CMV isolate and infection symptoms remained comparable to those at 25°C, whereas accumulation of the PVY isolate and those of the three PVX constructs decreased markedly, even when expressing the heterologous suppressors 2b or HCPro, and plants had either very attenuated or no symptoms. Under elevated CO2 plants grew larger, but contained less total protein/unit of leaf area. In contrast to temperature, infection symptoms remained unaltered for the five viruses at elevated CO2 levels, but viral titers in leaf disks as a proportion of the total protein content increased in all cases, markedly for CMV, and less so for PVY and the PVX constructs. Despite these differences, we found that neither high temperature nor elevated CO2 prevented efficient suppression of silencing by their viral suppressors in agropatch assays. Our results suggest that the strength of antiviral silencing at high temperature or CO2 levels, or those of the viral suppressors that counteract it, may not be the main determinants of the observed infection outcomes.
Ricardo Rajsbaum - One of the best experts on this subject based on the ideXlab platform.
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Topoisomerase III-β is required for efficient replication of Positive-Sense RNA viruses.
Antiviral research, 2020Co-Authors: K. Reddisiva Prasanth, Minato Hirano, W. Samuel Fagg, Eileen T. Mcanarney, Chao Shan, Xuping Xie, Adam Hage, Colette A. Pietzsch, Alexander Bukreyev, Ricardo RajsbaumAbstract:Based on genome-scale loss-of-function screens we discovered that Topoisomerase III-s (TOP3B), a human topoisomerase that acts on DNA and RNA, is required for yellow fever virus and dengue virus-2 replication. Remarkably, we found that TOP3B is required for efficient replication of all Positive-Sense-single stranded RNA viruses tested, including SARS-CoV-2. While there are no drugs that specifically inhibit this topoisomerase, we posit that TOP3B is an attractive anti-viral target.
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Topoisomerase III-ß is required for efficient replication of Positive-Sense RNA viruses.
bioRxiv : the preprint server for biology, 2020Co-Authors: K. Reddisiva Prasanth, Minato Hirano, W. Samuel Fagg, Eileen T. Mcanarney, Chao Shan, Xuping Xie, Adam Hage, Colette A. Pietzsch, Alexander Bukreyev, Ricardo RajsbaumAbstract:Based on genome-scale loss-of-function screens we discovered that Topoisomerase III-s (TOP3B), a human topoisomerase that acts on DNA and RNA, is required for yellow fever virus and dengue virus-2 replication. Remarkably, we found that TOP3B is required for efficient replication of all Positive-Sense-single stranded RNA viruses tested, including SARS-CoV-2. While there are no drugs that specifically inhibit this topoisomerase, we posit that TOP3B is an attractive anti-viral target.
Yves Rouillé - One of the best experts on this subject based on the ideXlab platform.
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Investigation of the role of GBF1 in the replication of Positive-Sense single-stranded RNA viruses
Journal of General Virology, 2018Co-Authors: Juliette Ferlin, Rayan Farhat, Sandrine Belouzard, Laurence Cocquerel, Antoine Bertin, Didier Hober, Jean Dubuisson, Yves RouilléAbstract:GBF1 has emerged as a host factor required for the replication of Positive-Sense single-stranded RNA viruses of different families, but its mechanism of action is still unknown. GBF1 is a guanine nucleotide exchange factor for Arf family members. Recently, we identified Arf4 and Arf5 (class II Arfs) as host factors required for the replication of hepatitis C virus (HCV), a GBF1-dependent virus. To assess whether a GBF1/class II Arf pathway is conserved among Positive-Sense single-stranded RNA viruses, we investigated yellow fever virus (YFV), Sindbis virus (SINV), coxsackievirus B4 (CVB4) and human coronavirus 229E (HCoV-229E). We found that GBF1 is involved in the replication of these viruses. However, using siRNA or CRISPR-Cas9 technologies, it was seen that the depletion of Arf1, Arf3, Arf4 or Arf5 had no impact on viral replication. In contrast, the depletion of Arf pairs suggested that class II Arfs could be involved in HCoV-229E, YFV and SINV infection, as for HCV, but not in CVB4 infection. In addition, another Arf pair, Arf1 and Arf4, appears to be essential for YFV and SINV infection, but not for infection by other viruses. Finally, CVB4 infection was not inhibited by any combination of Arf depletion. We conclude that the mechanism of action of GBF1 in viral replication appears not to be conserved, and that a subset of Positive-Sense single-stranded RNA viruses from different families might require class II Arfs for their replication.
Andrew E Firth - One of the best experts on this subject based on the ideXlab platform.
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A case for a negative-strand coding sequence in a group of Positive-Sense RNA viruses.
Virus evolution, 2020Co-Authors: Adam M. Dinan, Nina I. Lukhovitskaya, Ingrida Olendraite, Andrew E FirthAbstract:Positive-Sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-Sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-Sense RNA viruses are generally accepted to encode proteins solely on the Positive strand. However, we previously identified a surprisingly long (∼1,000-codon) open reading frame (ORF) on the negative strand of some members of the family Narnaviridae which, together with RNA bacteriophages of the family Leviviridae, form a sister group to all other Positive-Sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungal, and plant transcriptomic data sets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95 per cent of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA, and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a Positive-Sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and de novo origin of genes.
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A case for a reverse-frame coding sequence in a group of Positive-Sense RNA viruses
bioRxiv, 2019Co-Authors: Adam M. Dinan, Nina I. Lukhovitskaya, Ingrida Olendraite, Andrew E FirthAbstract:Positive-Sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-Sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-Sense RNA viruses are generally accepted to encode proteins solely on the Positive strand. However, we previously identified a surprisingly long (~1000 codons) open reading frame (ORF) on the negative strand of some members of the family Narnaviridae which, together with RNA bacteriophages of the family Leviviridae, form a sister group to all other Positive-Sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungi and plant transcriptomic datasets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95% of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a Positive-Sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and de novo origin of genes.
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transcriptional slippage in the Positive Sense rna virus family potyviridae
EMBO Reports, 2015Co-Authors: Allan Olspert, Betty Y W Chung, John F Atkins, John P Carr, Andrew E FirthAbstract:The family Potyviridae encompasses ~30% of plant viruses and is responsible for significant economic losses worldwide. Recently, a small overlapping coding sequence, termed pipo, was found to be conserved in the genomes of all potyvirids. PIPO is expressed as part of a frameshift protein, P3N-PIPO, which is essential for virus cell-to-cell movement. However, the frameshift expression mechanism has hitherto remained unknown. Here, we demonstrate that transcriptional slippage, specific to the viral RNA polymerase, results in a population of transcripts with an additional “A” inserted within a highly conserved GAAAAAA sequence, thus enabling expression of P3N-PIPO. The slippage efficiency is ~2% in Turnip mosaic virus and slippage is inhibited by mutations in the GAAAAAA sequence. While utilization of transcriptional slippage is well known in negative-Sense RNA viruses such as Ebola, mumps and measles, to our knowledge this is the first report of its widespread utilization for gene expression in Positive-Sense RNA viruses.
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Transcriptional slippage in the Positive‐Sense RNA virus family Potyviridae
EMBO reports, 2015Co-Authors: Allan Olspert, Betty Y W Chung, John F Atkins, John P Carr, Andrew E FirthAbstract:The family Potyviridae encompasses ~30% of plant viruses and is responsible for significant economic losses worldwide. Recently, a small overlapping coding sequence, termed pipo, was found to be conserved in the genomes of all potyvirids. PIPO is expressed as part of a frameshift protein, P3N-PIPO, which is essential for virus cell-to-cell movement. However, the frameshift expression mechanism has hitherto remained unknown. Here, we demonstrate that transcriptional slippage, specific to the viral RNA polymerase, results in a population of transcripts with an additional “A” inserted within a highly conserved GAAAAAA sequence, thus enabling expression of P3N-PIPO. The slippage efficiency is ~2% in Turnip mosaic virus and slippage is inhibited by mutations in the GAAAAAA sequence. While utilization of transcriptional slippage is well known in negative-Sense RNA viruses such as Ebola, mumps and measles, to our knowledge this is the first report of its widespread utilization for gene expression in Positive-Sense RNA viruses.
