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Karen Beth G. Scholthof - One of the best experts on this subject based on the ideXlab platform.
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Brachypodium Phenylalanine Ammonia Lyase (PAL) Promotes Antiviral Defenses against Panicum Mosaic Virus and Its Satellites.
mBio, 2021Co-Authors: Shankar R. Pant, Karen Beth G. Scholthof, Sonia Irigoyen, Jiaxing Liu, Renesh Bedre, Shawn A. Christensen, Eric A. Schmelz, John C. Sedbrook, Kranthi K. MandadiAbstract:ABSTRACT Brachypodium distachyon has recently emerged as a premier model plant for monocot biology, akin to Arabidopsis thaliana. We previously reported genome-wide transcriptomic and alternative splicing changes occurring in Brachypodium during compatible infections with Panicum Mosaic Virus (PMV) and its satellite Virus (SPMV). Here, we dissected the role of Brachypodium phenylalanine ammonia lyase 1 (PAL1), a key enzyme for phenylpropanoid and salicylic acid (SA) biosynthesis and the induction of plant defenses. Targeted metabolomics profiling of PMV-infected and PMV- plus SPMV-infected (PMV/SPMV) Brachypodium plants revealed enhanced levels of multiple defense-related hormones and metabolites such as cinnamic acid, SA, and fatty acids and lignin precursors during disease progression. The Virus-induced accumulation of SA and lignin was significantly suppressed upon knockdown of B. distachyonPAL1 (BdPAL1) using RNA interference (RNAi). The compromised SA accumulation in PMV/SPMV-infected BdPAL1 RNAi plants correlated with weaker induction of multiple SA-related defense gene markers (pathogenesis related 1 [PR-1], PR-3, PR-5, and WRKY75) and enhanced susceptibility to PMV/SPMV compared to that of wild-type (WT) plants. Furthermore, exogenous application of SA alleviated the PMV/SPMV necrotic disease phenotypes and delayed plant death caused by single and mixed infections. Together, our results support an antiviral role for BdPAL1 during compatible host-Virus interaction, perhaps as a last resort attempt to rescue the infected plant. IMPORTANCE Although the role of plant defense mechanisms against Viruses are relatively well studied in dicots and in incompatible plant-microbe interactions, studies of their roles in compatible interactions and in grasses are lagging behind. In this study, we leveraged the emerging grass model Brachypodium and genetic resources to dissect Panicum Mosaic Virus (PMV)- and its satellite Virus (SPMV)-compatible grass-Virus interactions. We found a significant role for PAL1 in the production of salicylic acid (SA) in response to PMV/SPMV infections and that SA is an essential component of the defense response preventing the plant from succumbing to viral infection. Our results suggest a convergent role for the SA defense pathway in both compatible and incompatible plant-Virus interactions and underscore the utility of Brachypodium for grass-Virus biology.
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Panicum Mosaic Virus and Its Satellites Acquire RNA Modifications Associated with Host-Mediated Antiviral Degradation.
mBio, 2019Co-Authors: Jesse D. Pyle, Kranthi K. Mandadi, Karen Beth G. ScholthofAbstract:Positive-sense RNA Viruses in the Tombusviridae family have genomes lacking a 5' cap structure and prototypical 3' polyadenylation sequence. Instead, these Viruses utilize an extensive network of intramolecular RNA-RNA interactions to direct viral replication and gene expression. Here we demonstrate that the genomic RNAs of Panicum Mosaic Virus (PMV) and its satellites undergo sequence modifications at their 3' ends upon infection of host cells. Changes to the viral and subviral genomes arise de novo within Brachypodium distachyon (herein called Brachypodium) and proso millet, two alternative hosts of PMV, and exist in the infections of a native host, St. Augustinegrass. These modifications are defined by polyadenylation [poly(A)] events and significant truncations of the helper Virus 3' untranslated region-a region containing satellite RNA recombination motifs and conserved viral translational enhancer elements. The genomes of PMV and its satellite Virus (SPMV) were reconstructed from multiple poly(A)-selected Brachypodium transcriptome data sets. Moreover, the polyadenylated forms of PMV and SPMV RNAs copurify with their respective mature icosahedral virions. The changes to viral and subviral genomes upon infection are discussed in the context of a previously understudied poly(A)-mediated antiviral RNA degradation pathway and the potential impact on Virus evolution.IMPORTANCE The genomes of positive-sense RNA Viruses have an intrinsic capacity to serve directly as mRNAs upon viral entry into a host cell. These RNAs often lack a 5' cap structure and 3' polyadenylation sequence, requiring unconventional strategies for cap-independent translation and subversion of the cellular RNA degradation machinery. For tombusViruses, critical translational regulatory elements are encoded within the 3' untranslated region of the viral genomes. Here we describe RNA modifications occurring within the genomes of Panicum Mosaic Virus (PMV), a prototypical tombusVirus, and its satellite agents (i.e., satellite Virus and noncoding satellite RNAs), all of which depend on the PMV-encoded RNA polymerase for replication. The atypical RNAs are defined by terminal polyadenylation and truncation events within the 3' untranslated region of the PMV genome. These modifications are reminiscent of host-mediated RNA degradation strategies and likely represent a previously underappreciated defense mechanism against invasive nucleic acids.
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de novo generation of helper Virus satellite chimera rnas results in disease attenuation and satellite sequence acquisition in a host dependent manner
Virology, 2018Co-Authors: Jesse D. Pyle, Karen Beth G. ScholthofAbstract:Abstract Panicum Mosaic Virus (PMV) is a helper RNA Virus for satellite RNAs (satRNAs) and a satellite Virus (SPMV). Here, we describe modifications that occur at the 3′-end of a satRNA of PMV, satS. Co-infections of PMV+satS result in attenuation of the disease symptoms induced by PMV alone in Brachypodium distachyon and proso millet. The 375 nt satS acquires ~100–200 nts from the 3′-end of PMV during infection and is associated with decreased abundance of the PMV RNA and capsid protein in millet. PMV-satS chimera RNAs were isolated from native infections of St. Augustinegrass and switchgrass. Phylogenetic analyses revealed that the chimeric RNAs clustered according to the host species from which they were isolated. Additionally, the chimera satRNAs acquired non-viral "linker" sequences in a host-specific manner. These results highlight the dynamic regulation of viral pathogenicity by satellites, and the selective host-dependent, sequence-based pressures for driving satRNA generation and genome compositions.
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complete nucleotide sequences and virion particle association of two satellite rnas of Panicum Mosaic Virus
Virus Research, 2017Co-Authors: Jesse D. Pyle, Judit Monis, Karen Beth G. ScholthofAbstract:Over six decades ago, Panicum Mosaic Virus (PMV) was identified as the first viral pathogen of cultivated switchgrass (Panicum virgatum). Subsequently, PMV was demonstrated to support the replication of both a satellite RNA Virus (SPMV) and satellite RNA (satRNA) agents during natural infections of host grasses. In this study, we report the isolation and full-length sequences of two PMV satRNAs identified in 1988 from St. Augustinegrass (Stenotaphrum secundatum) and centipedegrass (Eremochloa ophiuroides) hosts. Each of these satellites have sequence relatedness at their 5'- and 3'-ends. In addition, satC has a region of ∼100 nt complementary to the 3'-end of the PMV genome. These agents are associated with purified virions of SPMV infections. Additionally, satS and satC RNAs contain conserved in-frame open reading frames in the complementary-sense sequences that could potentially generate 6.6- and 7.9-kDa proteins, respectively. In protoplasts and plants satS is infectious, when co-inoculated with the PMV RNA alone or PMV+SPMV RNAs, and negatively affects their accumulation.
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Biology and Pathogenesis of Satellite Viruses
Viroids and Satellites, 2017Co-Authors: Jesse D. Pyle, Karen Beth G. ScholthofAbstract:Abstract Satellite Viruses (SVs) are subviral pathogens that are entirely dependent upon the replication machinery of their helper Viruses. There are only four known plant SVs: satellite tobacco necrosis Virus, satellite tobacco Mosaic Virus, satellite Panicum Mosaic Virus, and satellite maize white line Mosaic Virus. These SVs have positive-sense single-stranded RNA genomes of 800–1400 nt that are encapsidated within ~17-nm T =1 icosahedral virions. SVs, in contrast to satellite-RNA or -DNA, encode a capsid protein for independent genome packaging of the cognate SV RNA. The unusually small and compact nature of these subviral agents has resulted in their use as models for fundamental virology studies, including gene expression, genome packaging, and virion structure.
Anne E Simon - One of the best experts on this subject based on the ideXlab platform.
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Concerted action of two 3' cap-independent translation enhancers increases the competitive strength of translated viral genomes.
Nucleic acids research, 2017Co-Authors: Olga M. Alekhina, Konstantin S. Vassilenko, Anne E SimonAbstract:Several families of plant Viruses evolved cap-independent translation enhancers (3'CITE) in the 3' untranslated regions of their genomic (g)RNAs to compete with ongoing cap-dependent translation of cellular mRNAs. UmbraVirus Pea enation Mosaic Virus (PEMV)2 is the only example where three 3'CITEs enhance translation: the eIF4E-binding Panicum Mosaic Virus-like translational enhancer (PTE) and ribosome-binding 3' T-shaped structure (TSS) have been found in Viruses of different genera, while the ribosome-binding kl-TSS that provides a long-distance interaction with the 5' end is unique. We report that the PTE is the key translation promoting element, but inhibits translation in cis and in trans in the absence of the kl-TSS by sequestering initiation factor eIF4G. PEMV2 strongly outcompeted a cellular mRNA mimic for translation, indicating that the combination of kl-TSS and PTE is highly efficient. Transferring the 3'-5' interaction from the kl-TSS to the PTE (to fulfill its functionality as found in other Viruses) supported translationin vitro, but gRNA did not accumulate to detectable levels in protoplasts in the absence of the kl-TSS. It was shown that the PTE in conjunction with the kl-TSS did not markedly affect the translation initiation rate but rather increased the number of gRNAs available for translation. A model is proposed to explain how 3'CITE-based regulation of ribosome recruitment enhances Virus fitness.
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the 3 untranslated region of pea enation Mosaic Virus contains two t shaped ribosome binding cap independent translation enhancers
Journal of Virology, 2014Co-Authors: Wojciech K. Kasprzak, Bruce A. Shapiro, Christine Szarko, Anne E SimonAbstract:ABSTRACT Many plant Viruses without 5′caps or 3′ poly(A) tails contain 3′ proximal, cap-independent translation enhancers (3′CITEs) that bind to ribosomal subunits or translation factors thought to assist in ribosome recruitment. Most 3′CITEs participate in a long-distance kissing-loop interaction with a 5′ proximal hairpin to deliver ribosomal subunits to the 5′ end for translation initiation. Pea Enation Mosaic Virus (PEMV) contains two adjacent 3′CITEs in the center of its 703-nucleotide 3′ untranslated region (3′UTR), the ribosome-binding, kissing-loop T-shaped structure (kl-TSS) and eukaryotic translation initiation factor 4E-binding Panicum Mosaic Virus-like translation enhance (PTE). We now report that PEMV contains a third, independent 3′CITE located near the 3′ terminus. This 3′CITE is composed of three hairpins and two pseudoknots, similar to the TSS 3′CITE of the carmoVirus Turnip crinkle Virus (TCV). As with the TCV TSS, the PEMV 3′TSS is predicted to fold into a T-shaped structure that binds to 80S ribosomes and 60S ribosomal subunits. A small hairpin (kl-H) upstream of the 3′TSS contains an apical loop capable of forming a kissing-loop interaction with a 5′ proximal hairpin and is critical for the accumulation of full-length PEMV in protoplasts. Although the kl-H and 3′TSS are dispensable for the translation of a reporter construct containing the complete PEMV 3′UTR in vitro , deleting the normally required kl-TSS and PTE 3′CITEs and placing the kl-H and 3′TSS proximal to the reporter termination codon restores translation to near wild-type levels. This suggests that PEMV requires three 3′CITEs for proper translation and that additional translation enhancers may have been missed if reporter constructs were used in 3′CITE identification. IMPORTANCE The rapid life cycle of Viruses requires efficient translation of viral-encoded proteins. Many plant RNA Viruses contain 3′ cap-independent translation enhancers (3′CITEs) to effectively compete with ongoing host translation. Since only single 3′CITEs have been identified for the vast majority of individual Viruses, it is widely accepted that this is sufficient for a Virus9s translational needs. Pea Enation Mosaic Virus possesses a ribosome-binding 3′CITE that can connect to the 5′ end through an RNA-RNA interaction and an adjacent eukaryotic translation initiation factor 4E-binding 3′CITE. We report the identification of a third 3′CITE that binds weakly to ribosomes and requires an upstream hairpin to form a bridge between the 3′ and 5′ ends. Although both ribosome-binding 3′CITEs are critical for Virus accumulation in vivo , only the CITE closest to the termination codon of a reporter open reading frame is active, suggesting that artificial constructs used for 3′CITE identification may underestimate the number of CITEs that participate in translation.
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The 3′ Untranslated Region of Pea Enation Mosaic Virus Contains Two T-Shaped, Ribosome-Binding, Cap-Independent Translation Enhancers
Journal of virology, 2014Co-Authors: Feng Gao, Wojciech K. Kasprzak, Bruce A. Shapiro, Christine Szarko, Anne E SimonAbstract:ABSTRACT Many plant Viruses without 5′caps or 3′ poly(A) tails contain 3′ proximal, cap-independent translation enhancers (3′CITEs) that bind to ribosomal subunits or translation factors thought to assist in ribosome recruitment. Most 3′CITEs participate in a long-distance kissing-loop interaction with a 5′ proximal hairpin to deliver ribosomal subunits to the 5′ end for translation initiation. Pea Enation Mosaic Virus (PEMV) contains two adjacent 3′CITEs in the center of its 703-nucleotide 3′ untranslated region (3′UTR), the ribosome-binding, kissing-loop T-shaped structure (kl-TSS) and eukaryotic translation initiation factor 4E-binding Panicum Mosaic Virus-like translation enhance (PTE). We now report that PEMV contains a third, independent 3′CITE located near the 3′ terminus. This 3′CITE is composed of three hairpins and two pseudoknots, similar to the TSS 3′CITE of the carmoVirus Turnip crinkle Virus (TCV). As with the TCV TSS, the PEMV 3′TSS is predicted to fold into a T-shaped structure that binds to 80S ribosomes and 60S ribosomal subunits. A small hairpin (kl-H) upstream of the 3′TSS contains an apical loop capable of forming a kissing-loop interaction with a 5′ proximal hairpin and is critical for the accumulation of full-length PEMV in protoplasts. Although the kl-H and 3′TSS are dispensable for the translation of a reporter construct containing the complete PEMV 3′UTR in vitro , deleting the normally required kl-TSS and PTE 3′CITEs and placing the kl-H and 3′TSS proximal to the reporter termination codon restores translation to near wild-type levels. This suggests that PEMV requires three 3′CITEs for proper translation and that additional translation enhancers may have been missed if reporter constructs were used in 3′CITE identification. IMPORTANCE The rapid life cycle of Viruses requires efficient translation of viral-encoded proteins. Many plant RNA Viruses contain 3′ cap-independent translation enhancers (3′CITEs) to effectively compete with ongoing host translation. Since only single 3′CITEs have been identified for the vast majority of individual Viruses, it is widely accepted that this is sufficient for a Virus9s translational needs. Pea Enation Mosaic Virus possesses a ribosome-binding 3′CITE that can connect to the 5′ end through an RNA-RNA interaction and an adjacent eukaryotic translation initiation factor 4E-binding 3′CITE. We report the identification of a third 3′CITE that binds weakly to ribosomes and requires an upstream hairpin to form a bridge between the 3′ and 5′ ends. Although both ribosome-binding 3′CITEs are critical for Virus accumulation in vivo , only the CITE closest to the termination codon of a reporter open reading frame is active, suggesting that artificial constructs used for 3′CITE identification may underestimate the number of CITEs that participate in translation.
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Position of the kissing-loop interaction associated with PTE-type 3'CITEs can affect enhancement of cap-independent translation.
Virology, 2014Co-Authors: Maitreyi Chattopadhyay, Micki M Kuhlmann, Kalyani Kumar, Anne E SimonAbstract:The Panicum Mosaic Virus-like translation enhancer (PTE) functions as a cap-independent translation enhancer (3'CITE) in members of several Tombusviridae genera including 7/19 carmoViruses. For nearly all PTE, a kissing-loop connects the element with a hairpin found in several conserved locations in the genomic RNA (5' terminal hairpin or ~100 nt from the 5' end) and small subgenomic RNA (~63 nt from the 5' end). Moving the interaction closer to the 5' end in reporter mRNAs using Saguaro cactus Virus (SCV) sequences had either a minimal or substantial negative effect on translation. Movement of the kissing loop from position 104 to the SCV 5' terminal hairpin also reduced translation by 4-fold. These results suggest that relocating the PTE kissing loop closer to the 5' end reduces PTE efficiency, in contrast to results for the Barley yellow dwarf BTE and Tomato bushy stunt Virus Y-shaped 3'CITEs, suggesting that different 3'CITEs have different bridging requirements.
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Position of the kissing-loop interaction associated with PTE-type 3'CITEs can affect enhancement of cap-independent translation.
Virology, 2014Co-Authors: Maitreyi Chattopadhyay, Micki M Kuhlmann, Kalyani Kumar, Anne E SimonAbstract:The Panicum Mosaic Virus-like translation enhancer (PTE) functions as a cap-independent translation enhancer (3'CITE) in members of several Tombusviridae genera including 7/19 carmoViruses. For nearly all PTE, a kissing-loop connects the element with a hairpin found in several conserved locations in the genomic RNA (5' terminal hairpin or ~100 nt from the 5' end) and small subgenomic RNA (~63 nt from the 5' end). Moving the interaction closer to the 5' end in reporter mRNAs using Saguaro cactus Virus (SCV) sequences had either a minimal or substantial negative effect on translation. Movement of the kissing loop from position 104 to the SCV 5' terminal hairpin also reduced translation by 4-fold. These results suggest that relocating the PTE kissing loop closer to the 5' end reduces PTE efficiency, in contrast to results for the Barley yellow dwarf BTE and Tomato bushy stunt Virus Y-shaped 3'CITEs, suggesting that different 3'CITEs have different bridging requirements.
Jesse D. Pyle - One of the best experts on this subject based on the ideXlab platform.
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Panicum Mosaic Virus and Its Satellites Acquire RNA Modifications Associated with Host-Mediated Antiviral Degradation.
mBio, 2019Co-Authors: Jesse D. Pyle, Kranthi K. Mandadi, Karen Beth G. ScholthofAbstract:Positive-sense RNA Viruses in the Tombusviridae family have genomes lacking a 5' cap structure and prototypical 3' polyadenylation sequence. Instead, these Viruses utilize an extensive network of intramolecular RNA-RNA interactions to direct viral replication and gene expression. Here we demonstrate that the genomic RNAs of Panicum Mosaic Virus (PMV) and its satellites undergo sequence modifications at their 3' ends upon infection of host cells. Changes to the viral and subviral genomes arise de novo within Brachypodium distachyon (herein called Brachypodium) and proso millet, two alternative hosts of PMV, and exist in the infections of a native host, St. Augustinegrass. These modifications are defined by polyadenylation [poly(A)] events and significant truncations of the helper Virus 3' untranslated region-a region containing satellite RNA recombination motifs and conserved viral translational enhancer elements. The genomes of PMV and its satellite Virus (SPMV) were reconstructed from multiple poly(A)-selected Brachypodium transcriptome data sets. Moreover, the polyadenylated forms of PMV and SPMV RNAs copurify with their respective mature icosahedral virions. The changes to viral and subviral genomes upon infection are discussed in the context of a previously understudied poly(A)-mediated antiviral RNA degradation pathway and the potential impact on Virus evolution.IMPORTANCE The genomes of positive-sense RNA Viruses have an intrinsic capacity to serve directly as mRNAs upon viral entry into a host cell. These RNAs often lack a 5' cap structure and 3' polyadenylation sequence, requiring unconventional strategies for cap-independent translation and subversion of the cellular RNA degradation machinery. For tombusViruses, critical translational regulatory elements are encoded within the 3' untranslated region of the viral genomes. Here we describe RNA modifications occurring within the genomes of Panicum Mosaic Virus (PMV), a prototypical tombusVirus, and its satellite agents (i.e., satellite Virus and noncoding satellite RNAs), all of which depend on the PMV-encoded RNA polymerase for replication. The atypical RNAs are defined by terminal polyadenylation and truncation events within the 3' untranslated region of the PMV genome. These modifications are reminiscent of host-mediated RNA degradation strategies and likely represent a previously underappreciated defense mechanism against invasive nucleic acids.
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de novo generation of helper Virus satellite chimera rnas results in disease attenuation and satellite sequence acquisition in a host dependent manner
Virology, 2018Co-Authors: Jesse D. Pyle, Karen Beth G. ScholthofAbstract:Abstract Panicum Mosaic Virus (PMV) is a helper RNA Virus for satellite RNAs (satRNAs) and a satellite Virus (SPMV). Here, we describe modifications that occur at the 3′-end of a satRNA of PMV, satS. Co-infections of PMV+satS result in attenuation of the disease symptoms induced by PMV alone in Brachypodium distachyon and proso millet. The 375 nt satS acquires ~100–200 nts from the 3′-end of PMV during infection and is associated with decreased abundance of the PMV RNA and capsid protein in millet. PMV-satS chimera RNAs were isolated from native infections of St. Augustinegrass and switchgrass. Phylogenetic analyses revealed that the chimeric RNAs clustered according to the host species from which they were isolated. Additionally, the chimera satRNAs acquired non-viral "linker" sequences in a host-specific manner. These results highlight the dynamic regulation of viral pathogenicity by satellites, and the selective host-dependent, sequence-based pressures for driving satRNA generation and genome compositions.
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complete nucleotide sequences and virion particle association of two satellite rnas of Panicum Mosaic Virus
Virus Research, 2017Co-Authors: Jesse D. Pyle, Judit Monis, Karen Beth G. ScholthofAbstract:Over six decades ago, Panicum Mosaic Virus (PMV) was identified as the first viral pathogen of cultivated switchgrass (Panicum virgatum). Subsequently, PMV was demonstrated to support the replication of both a satellite RNA Virus (SPMV) and satellite RNA (satRNA) agents during natural infections of host grasses. In this study, we report the isolation and full-length sequences of two PMV satRNAs identified in 1988 from St. Augustinegrass (Stenotaphrum secundatum) and centipedegrass (Eremochloa ophiuroides) hosts. Each of these satellites have sequence relatedness at their 5'- and 3'-ends. In addition, satC has a region of ∼100 nt complementary to the 3'-end of the PMV genome. These agents are associated with purified virions of SPMV infections. Additionally, satS and satC RNAs contain conserved in-frame open reading frames in the complementary-sense sequences that could potentially generate 6.6- and 7.9-kDa proteins, respectively. In protoplasts and plants satS is infectious, when co-inoculated with the PMV RNA alone or PMV+SPMV RNAs, and negatively affects their accumulation.
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Biology and Pathogenesis of Satellite Viruses
Viroids and Satellites, 2017Co-Authors: Jesse D. Pyle, Karen Beth G. ScholthofAbstract:Abstract Satellite Viruses (SVs) are subviral pathogens that are entirely dependent upon the replication machinery of their helper Viruses. There are only four known plant SVs: satellite tobacco necrosis Virus, satellite tobacco Mosaic Virus, satellite Panicum Mosaic Virus, and satellite maize white line Mosaic Virus. These SVs have positive-sense single-stranded RNA genomes of 800–1400 nt that are encapsidated within ~17-nm T =1 icosahedral virions. SVs, in contrast to satellite-RNA or -DNA, encode a capsid protein for independent genome packaging of the cognate SV RNA. The unusually small and compact nature of these subviral agents has resulted in their use as models for fundamental virology studies, including gene expression, genome packaging, and virion structure.
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Multi-Year Pathogen Survey of Biofuel Switchgrass Breeding Plots Reveals High Prevalence of Infections by Panicum Mosaic Virus and Its Satellite Virus.
Phytopathology, 2015Co-Authors: Catherine L. Stewart, Jesse D. Pyle, Charlene C. Jochum, Kenneth P. Vogel, Gary Y. Yuen, Karen Beth G. ScholthofAbstract:Switchgrass (Panicum virgatum) cultivars are currently under development as lignocellulosic feedstock. Here we present a survey of three established switchgrass experimental nurseries in Nebraska in which we identified Panicum Mosaic Virus (PMV) as the most prevalent Virus. In 2012, 72% of 139 symptomatic plants tested positive for PMV. Of the PMV-positive samples, 19% were coinfected with its satellite Virus (SPMV). Less than 14% of all sampled plants in 2012 were positive for four additional Viruses known to infect switchgrass. In 2013, randomized sampling of switchgrass individuals from the same 2012 breeding plots revealed that infection by PMV or PMV+SPMV was both more prevalent and associated with more severe symptoms in the cultivar Summer, and experimental lines with Summer parentage, than populations derived from the cultivar Kanlow. A 3-year analysis, from 2012 to 2014, showed that previously uninfected switchgrass plants acquire PMV or PMV+SPMV between harvest cycles. In contrast, some plants a...
Over Cabrera - One of the best experts on this subject based on the ideXlab platform.
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Genetic Diversity of Panicum Mosaic Virus Satellite RNAs in St. Augustinegrass.
Phytopathology, 2000Co-Authors: Over Cabrera, Marilyn J. Roossinck, Karen Beth G. ScholthofAbstract:ABSTRACT St. Augustine decline is a viral disease caused by Panicum Mosaic Virus (PMV) alone or in combination with a satellite Virus (SPMV) and/or satellite RNAs (satRNAs). A ribonuclease protection assay (RPA) was used to evaluate the genetic diversity of PMV satRNAs isolated from 100 naturally infected St. Augustinegrass plants (Stenotaphrum secundatum). Distinctive satRNA RPA profiles were observed for 40 of 52 samples from College Station (CS) and 37 of 48 samples from Corpus Christi (CC), Texas. A dendrogram constructed from the RPA data revealed that satRNAs were grouped in two distinct clusters based on their place of origin. From 100 samples, only 4 satRNAs from CS were placed in the CC group, and only 2 satRNAs from CC were placed in the CS group. The data show that there is genetic variability in PMV satRNAs in naturally occurring infections, and distinct geographically separate populations can be identified from CC and CS.
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The Complex Viral Etiology of St. Augustine Decline
Plant disease, 1999Co-Authors: Over Cabrera, Karen Beth G. ScholthofAbstract:St. Augustine decline is a viral disease of St. Augustinegrass, a turfgrass grown in the Gulf Coast region of the United States. Analyses of 204 plants in two locations in southeast Texas indicate that the disease is caused by an infection with Panicum Mosaic Virus (PMV), alone or in any combination with satellite Panicum Mosaic Virus (SPMV) and/or its satellite RNAs (satRNAs). This is the first report of the incidence of PMV satRNAs in field samples of St. Augustinegrass. Leaf symptoms of plants collected from the field ranged from severe bleaching to a mild chlorotic mottle, but after 5 months in the greenhouse, the plants had a relatively homogeneous chlorotic mottle phenotype, suggesting that environmental conditions have a significant influence on the development of this disease.
Alexander Mcpherson - One of the best experts on this subject based on the ideXlab platform.
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The crystallographic structure of Panicum Mosaic Virus (PMV).
Journal of structural biology, 2012Co-Authors: Debora L. Makino, Steven B. Larson, Alexander McphersonAbstract:The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9A resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7A, b=403.9A and c=412.5A, with β=89.7°. The asymmetric unit was two entire T=3 Virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacco Necrosis Virus (TNV), of ∼20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The Virus has Ca(++) ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1-53, 1-49 and 1-21 of the A, B and C subunits, respectively, and the four C-terminal residues (239-242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent "arm" that intertwines with symmetry equivalent "arms" at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A-B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other Viruses.
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Investigation of RNA structure in satellite Panicum Mosaic Virus.
Virology, 2006Co-Authors: Debora L. Makino, John Day, Steven B. Larson, Alexander McphersonAbstract:Three new crystal forms of satellite Panicum Mosaic Virus (SPMV) were grown and their structures solved from X-ray diffraction data using molecular replacement techniques. The crystals were grown under conditions of pH and ionic strength that were appreciably different then those used for the original structure determination. In rhombohedral crystals grown at pH 8.5 and low ionic strength PEG 3350 solutions, Fourier syntheses revealed segments, ten amino acid residues long, of amino-terminal polypeptides not previously seen, as well as masses of electron density within concavities on the interior of the capsid, which appeared in the neighborhoods of icosahedral five- and threefold axes. The densities were compatible with secondary structural domains of RNA, and they included a segment of double helical RNA of about four to five base pairs oriented, at least approximately, along the fivefold axes. The distribution of RNA observed for SPMV appears to be distinctly different than the encapsidated nucleic acid conformation previously suggested for another satellite Virus, satellite tobacco Mosaic Virus. This study further shows that analysis of Viruses in crystals grown under different chemical conditions may reveal additional information regarding the structure of encapsidated RNA.
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Preliminary analysis of crystals of Panicum Mosaic Virus (PMV) by X-ray diffraction and atomic force microscopy.
Acta Crystallographica Section D Biological Crystallography, 2005Co-Authors: Debora L. Makino, Steven B. Larson, Alexander McphersonAbstract:Panicum Mosaic Virus (PMV), a spherical Virus of diameter about 300 A, has been crystallized in a form suitable for high-resolution structural analysis. The crystals were grown from 15% PEG 400 at room temperature and could be flash-frozen directly from their mother liquor. The crystals diffracted to beyond 2.7 A resolution. A data set was collected at 100 K to an effective resolution of 3.2 A [Weiss (2001), J. Appl. Cryst. 34, 130-135]. The crystals belonged to space group P2(1), with unit-cell parameters a=411.7, b=403.9, c=412.5 A, beta=89.7 degrees . Self-rotation functions and molecular replacement with tobacco necrosis Virus as the probe model yielded tentative positions and orientations for the two entire Virus particles comprising the asymmetric unit and implied a pseudo-face-centered cubic packing arrangement. Investigation of lightly glutaraldehyde-fixed crystals in water using atomic force microscopy confirms the packing arrangement given by the molecular-replacement result. The images also show that contaminating virions of the satellite Virus to PMV, known as satellite Panicum Mosaic Virus (SPMV), can be incorporated into the PMV crystals by insertion into the interstices between PMV virions in the lattice. This is the first observation of such a phenomenon in macromolecular crystals.
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Structural comparison of the plant satellite Viruses
Virology, 1995Co-Authors: Nenad Ban, Steven B. Larson, Alexander McphersonAbstract:Detailed structures are now available for three plant satellite Viruses, satellite tobacco necrosis Virus (STNV), satellite tobacco Mosaic Virus (STMV), and satellite Panicum Mosaic Virus (SPMV). It is, therefore, possible to compare the tertiary structure of viral protein subunits, their quaternary interactions, and the interactions of protein subunits with the RNA genome. This analysis indicates that, in spite of common function and preservation of a "jelly-roll" motif in the protein monomer, the three Viruses are remarkably different. The differences include the arrangement of secondary structural elements, interactions of adjacent subunits, and the disposition of subunits relative to icosahedral symmetry axes. In each of the three Viruses, however, the narrow end of the jelly roll forms fivefold contacts. The fivefold protein interactions are organized about a Ca2+ ion for STNV, an anion for STMV, and, apparently, neither of these for SPMV. Low-resolution neutron diffraction studies using H2O/D2O solvent contrast variation revealed the general location of the RNA genome within the STNV. In the case of SPMV, regions of electron density on the interior of the capsid could be assigned to RNA, although it was not possible to model the nucleic acid. Only for STMV was nucleic acid visible in election density maps, and this was manifested as double-helical RNA segments associated with each coat protein dimer. The observations presented here provide no support for any common evolutionary relationship.
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The structure of satellite Panicum Mosaic Virus at 1.9 Å resolution
Nature Structural Biology, 1995Co-Authors: Nenad Ban, Alexander McphersonAbstract:The crystal structure of satellite Panicum Mosaic Virus (SPMV) has been solved by multiple isomorphous replacement and molecular replacement and refined at 1.9 Å resolution. SPMV, a T=1 icosahedral Virus, is the smallest Virus structure determined. The coat protein is an eight-stranded ‘jelly roll’ β-barrel with an amino-terminal strand that extends into the interior of the Virus, presumably interacting with the RNA. Regions of electron density on the interior of the protein capsid may be RNA, although it is not possible to construct any detailed model of the nucleic acid. Basic amino acid residues in contact with the nucleic acid show a considerable degree of disorder. The carboxy-terminal strand of the Virus coat protein interacts with adjacent subunits, forming an additional β-strand.
