The Experts below are selected from a list of 123 Experts worldwide ranked by ideXlab platform
Joh F Atkins - One of the best experts on this subject based on the ideXlab platform.
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stimulation of stop codon readthrough frequent presence of an extended 3 rna structural element
Nucleic Acids Research, 2011Co-Authors: Andrew E Firth, Raymond F Gesteland, Norma M Wills, Joh F AtkinsAbstract:In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3'-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the ∼ 150 nt 3'-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem-loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem-loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3' RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis.
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Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element
Nucleic acids research, 2011Co-Authors: Andrew E Firth, Raymond F Gesteland, Norma M Wills, Joh F AtkinsAbstract:In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3'-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the ∼ 150 nt 3'-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem-loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem-loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3' RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis.
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Stimulation of stop codon readthrough: frequent presence of an extended 39 RNA structural element
2011Co-Authors: Andrew E Firth, Norma M Wills, Raymond F. Gestel, Joh F AtkinsAbstract:In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 30-adjacent to the UGA. However, analysis of vari-ability at synonymous sites revealed strikingly enhanced conservation within the 150nt 30-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem–loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem–loop increases readthrough by up to 10-fold. The same computa-tional analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 30 RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis
Andrew E Firth - One of the best experts on this subject based on the ideXlab platform.
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stimulation of stop codon readthrough frequent presence of an extended 3 rna structural element
Nucleic Acids Research, 2011Co-Authors: Andrew E Firth, Raymond F Gesteland, Norma M Wills, Joh F AtkinsAbstract:In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3'-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the ∼ 150 nt 3'-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem-loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem-loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3' RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis.
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Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element
Nucleic acids research, 2011Co-Authors: Andrew E Firth, Raymond F Gesteland, Norma M Wills, Joh F AtkinsAbstract:In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3'-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the ∼ 150 nt 3'-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem-loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem-loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3' RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis.
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Stimulation of stop codon readthrough: frequent presence of an extended 39 RNA structural element
2011Co-Authors: Andrew E Firth, Norma M Wills, Raymond F. Gestel, Joh F AtkinsAbstract:In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 30-adjacent to the UGA. However, analysis of vari-ability at synonymous sites revealed strikingly enhanced conservation within the 150nt 30-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem–loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem–loop increases readthrough by up to 10-fold. The same computa-tional analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 30 RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis
Norma M Wills - One of the best experts on this subject based on the ideXlab platform.
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stimulation of stop codon readthrough frequent presence of an extended 3 rna structural element
Nucleic Acids Research, 2011Co-Authors: Andrew E Firth, Raymond F Gesteland, Norma M Wills, Joh F AtkinsAbstract:In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3'-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the ∼ 150 nt 3'-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem-loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem-loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3' RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis.
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Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element
Nucleic acids research, 2011Co-Authors: Andrew E Firth, Raymond F Gesteland, Norma M Wills, Joh F AtkinsAbstract:In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3'-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the ∼ 150 nt 3'-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem-loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem-loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3' RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis.
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Stimulation of stop codon readthrough: frequent presence of an extended 39 RNA structural element
2011Co-Authors: Andrew E Firth, Norma M Wills, Raymond F. Gestel, Joh F AtkinsAbstract:In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 30-adjacent to the UGA. However, analysis of vari-ability at synonymous sites revealed strikingly enhanced conservation within the 150nt 30-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem–loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem–loop increases readthrough by up to 10-fold. The same computa-tional analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 30 RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis
Jan Kreuze - One of the best experts on this subject based on the ideXlab platform.
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Virgaviridae: a new family of rod-shaped plant viruses
Archives of Virology, 2009Co-Authors: Michael J. Adams, John F. Antoniw, Jan KreuzeAbstract:The new plant virus family Virgaviridae is described. The family is named because its members have rod-shaped virions (from the Latin virga = rod), and it includes the genera Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus and Tobravirus . The chief characteristics of members of the family are presented with phylogenetic analyses of selected genes to support the creation of the family. Species demarcation criteria within the genera are examined and discussed.
C. Fritsch - One of the best experts on this subject based on the ideXlab platform.
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Intracellular Localization of the Peanut Clump Virus Replication Complex in Tobacco BY-2 Protoplasts Containing Green Fluorescent Protein-Labeled Endoplasmic Reticulum or Golgi Apparatus
Journal of Virology, 2002Co-Authors: Patrice Dunoyer, Odile Hemmer, Christophe Ritzenthaler, Pierre Michler, C. FritschAbstract:Replication is a key event of the viral multiplication cycle that ultimately determines the success of the viral infection. For positive-stranded viruses, replication is thought to occur in complexes containing viral RNA template, viral RNA-dependent RNA polymerase (RdRp), cellular factors, and, in some cases, virus-encoded accessory proteins (27, 57). All results obtained so far show that RNA replication occurs in close association with intracellular membranes, which generally undergo extensive reorganization in the virus-infected cell (9). Depending upon the virus, the membrane component of the replication complex may be of different origins: membranes of the endoplasmic reticulum (ER) are implicated in viral replication of picorna-like viruses such as comoviruses (11) and potyviruses (50) and of alpha-like viruses such as tobamoviruses (42) and bromoviruses (44, 45). Cytoplasmic invaginations of chloroplast membranes are associated with Tymovirus replication complexes (18, 41), and multivesicular bodies derived from peroxisomes, mitochondria, or vacuoles are the sites of replication for other viruses: cucumber mosaic and tomato aspermy viruses (21), Tomato bushy stunt virus (52), Cymbidium ringspot virus and Carnation Italian ringspot virus (47), and Alfalfa mosaic virus (AMV) (55). In animal cells, the replication of viruses of the Togaviridae and Coronaviridae families occurs in modified endosomes or lysosomes (17, 30, 40, 56). Flavivirus RNA synthesis is thought to occur in vesicle packets derived from the trans-Golgi membranes (29, 58), whereas membranes of the ER, of the Golgi apparatus, and of lysosomes have been detected in the vesicles generated by poliovirus replication (51). In a number of cases (e.g., poliovirus, alphaviruses, and Brome mosaic virus), all of the viral replication proteins are localized within the replication complex (2, 3, 5, 6, 17, 39, 45). On the other hand, for Flavivirus Kunjin, the replicative proteins and RNA viral synthesis sites colocalize in vesicle packets, while other nonstructural proteins are associated with modified membranes from the intermediate compartment (29). For Tobacco etch virus, only the 6-kDa protein and the viral RNA replication complex were associated with vesicles derived from the ER, whereas NIa and NIb, which are also required for replication, predominantly accumulated in the nucleus (43, 50). To gain insight into the interactions between viral and host factors during Peanut clump virus (PCV) RNA replication, we have investigated the in situ localization of the replicase proteins and the RNA synthesis sites. PCV, a type member of the Pecluvirus genus, is a positive-strand RNA virus of the alphavirus-like family. The PCV genome is composed of two molecules of RNA. RNA-1 is able to replicate independently of RNA-2 in protoplasts, but both RNAs are indispensable for plant infection (25). Two N-terminally overlapping proteins encoded by RNA-1 (P131 and P191) are essential replication proteins. P131 contains sequence motifs common to methyltransferases and helicases, while P191 contains the signature motifs of RNA-dependent RNA polymerases in its C-terminal extension (20, 24). The RNA-1-encoded protein P15, on the other hand, is not an essential replication factor but is required for efficient viral RNA accumulation. This protein was not detected near the sites of viral RNA synthesis (15) and therefore is probably not a component of the replication complex. In the present study, we have further investigated the localization of the viral RNA replication complex and provide evidence that both P131 and P191 are present at the replication sites. Using protoplasts from transgenic lines of tobacco BY-2 cells, we demonstrate that the ER, but not the Golgi apparatus, undergoes extensive reorganization upon PCV infection, and we show that the viral RNA replication complex is associated with the modified ER membranes.
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Identification, subcellular localization and some properties of a cysteine-rich suppressor of gene silencing encoded by peanut clump virus
The Plant journal : for cell and molecular biology, 2002Co-Authors: Patrice Dunoyer, C. Fritsch, Odile Hemmer, Sébastien Pfeffer, Olivier Voinnet, Kenneth RichardsAbstract:In plants, post-transcriptional gene silencing (PTGS) is part of a defence mechanism against virus infection. Several plant viruses have been shown to encode proteins which can counteract PTGS. In this paper it is demonstrated that P15 of peanut clump Pecluvirus (PCV) has anti-PTGS activity. P15 is a small cysteine-rich protein with no sequence similarity to previously described PTGS-suppressor proteins which has several novel properties. It possesses four C-terminal proximal heptad repeats that can potentially mediate a coiled-coil interaction and is targeted to peroxisomes via a C-terminal SKL motif. The coiled-coil sequence is necessary for the anti-PTGS activity of P15, but the peroxisomal localization signal is not, although it is required for efficient intercellular movement of the virus.
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Peanut Clump Virus RNA-1-Encoded P15 Regulates Viral RNA Accumulation but Is Not Abundant at Viral RNA Replication Sites
Journal of virology, 2001Co-Authors: Patrice Dunoyer, Odile Hemmer, Christophe Ritzenthaler, Etienne Herzog, C. FritschAbstract:RNA-1 of peanut clump Pecluvirus (PCV) encodes N-terminally overlapping proteins which contain helicase-like (P131) and polymerase-like (P191) domains and is able to replicate in the absence of RNA-2 in protoplasts of tobacco BY-2 cells. RNA-1 also encodes P15, which is expressed via a subgenomic RNA. To investigate the role of P15, we analyzed RNA accumulation in tobacco BY-2 protoplasts inoculated with RNA-1 containing mutations in P15. For all the mutants, the amount of progeny RNA-1 produced was significantly lower than that obtained for wild-type RNA-1. If RNA-2 was included in the inoculum, the accumulation of both progeny RNAs was diminished, but near-normal yields of both could be recovered if the inoculum was supplemented with a small, chimeric viral replicon expressing P15, demonstrating that P15 has an effect on viral RNA accumulation. To further analyze the role of P15, transcripts were produced expressing P15 fused to enhanced green fluorescent protein (EGFP). Following inoculation to protoplasts, epifluorescence microscopy revealed that P15 accumulated as spots around the nucleus and in the cytoplasm. Intracellular sites of viral RNA synthesis were visualized by laser scanning confocal microscopy of infected protoplasts labeled with 5-bromouridine 5′-triphosphate (BrUTP). BrUTP labeling also occured in spots distributed within the cytoplasm and around the nucleus. However, the BrUTP-labeled RNA and EGFP/P15 very rarely colocalized, suggesting that P15 does not act primarily at sites of viral replication but intervenes indirectly to control viral accumulation levels.
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Identification of Genes Involved in Replication and Movement of Peanut Clump Virus
Virology, 1998Co-Authors: Etienne Herzog, Odile Hemmer, S. Bouzoubaa, S. Hauser, G. Meyer, C. FritschAbstract:Abstract The genome of peanut clump Pecluvirus (PCV) consists of two messenger RNA components which contain, respectively, three and five open reading frames (ORFs). Inoculation of transcripts from full-length cDNA clones derived from the PCV RNAs showed that RNA-1 is able to replicate in the absence of RNA-2 in protoplasts, but both RNAs are necessary for plant infection. To investigate the role of different gene products in viral RNA replication and movement, transcripts from mutant cDNA clones were inoculated to protoplasts and to Chenopodium quinoa or Nicotiana benthamiana plants, and progeny RNA was detected by Northern blot analysis. The protein P15, encoded by the third ORF of RNA-1, is essential for efficient replication of the viral genome. The three proteins, P51, P14, and P17, of the triple gene block contained in RNA-2 are involved in localized movement of the viral genome, whereas the coat protein (P23) is also required for vascular movement. Insertion of the β-glucuronidase reporter gene (GUS) in place of the P23 or P39 genes (the first and the second genes of RNA-2) allows visualization of the virus infection in inoculated leaves. Although the presence of the GUS gene resulted in a lower accumulation of progeny RNA and, despite instability of the construct in planta, histochemical detection of PCV multiplication was more sensitive than Northern blot detection.