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Denis Fargette - One of the best experts on this subject based on the ideXlab platform.
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Biological and molecular characterization of a putative new Sobemovirus infecting Imperata cylindrica and maize in Africa
Archives of Virology, 2008Co-Authors: Drissa Sérémé, Denis Fargette, S Everine Lacombe, Moumouni Konaté, Agnès Pinel-galzi, Valentin Stanislas Edgar Traoré, Eugénie Hébrard, Oumar Traoré, Christophe Brugidou, Gnissa KonatéAbstract:A new virus was isolated from both the grass Imperata cylindrica and maize plants that had yellow mottle symptoms in Burkina Faso, West Africa. The virus has isometric particles ca. 32 nm in diameter. The experimental host range was restricted to Rottboellia exaltata . Virions were isolated from leaves of systemically infected maize plants. Koch’s postulates were completed by mechanically inoculating uninfected Imperata or maize with either purified virus or sap from infected Imperata plants. Virion preparations were used to produce a specific polyclonal antiserum, and an enzyme-linked immunosorbent assay test was set up. The full genome of the virus was sequenced, and it comprised 4,547 nucleotides. Phylogenetic studies indicated that the virus is closely related to rice yellow mottle virus, a Sobemovirus that infects monocotyledons in Africa, and is more distantly related to cocksfoot mottle virus, another Sobemovirus that infects monocotyledons. Although the virus can infect R. exaltata experimentally, it differs from Rottboellia yellow mottle virus , a member of a tentative species of the genus Sobemovirus that also infects monocotyledons in Africa. Particle morphology, serological properties, genomic organization, and phylogenetic analysis are all consistent with assignment of the new virus to the genus Sobemovirus . The name Imperata yellow mottle virus is proposed.
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virulence domain of the rymv genome linked viral protein vpg towards rice rymv1 2 mediated resistance
Archives of Virology, 2008Co-Authors: Eugénie Hébrard, Agnes Pinelgalzi, Denis FargetteAbstract:Virulent variants of Rice yellow mottle virus (genus Sobemovirus) can emerge on the highly resistant rice cultivars Gigante and Bekarosaka. Non-synonymous mutations responsible for the breakdown of the recessive resistance gene rymv1–2 were located in the VPg after determination of its termini in the polyprotein P2a. The secondary structure of this protein was predicted to include a central α-helix. The two major amino acids related to virulence are located on the same side of this helix. The 3D topology and the biochemical properties of virulence mutations both suggested a direct site-to-site interaction between RYMV VPg and rice eIF(iso)4G encoded by rymv1.
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Diversification of Rice Yellow Mottle Virus and Related Viruses Spans the History of Agriculture from the Neolithic to the Present
2008Co-Authors: Denis Fargette, Drissa Sérémé, S Everine Lacombe, Agnès Pinel-galzi, Eugénie Hébrard, Gnissa KonatéAbstract:The mechanisms of evolution of plant viruses are being unraveled, yet the timescale of their evolution remains an enigma. To address this critical issue, the divergence time of plant viruses at the intra- and inter-specific levels was assessed. The time of the most recent common ancestor (TMRCA) of Rice yellow mottle virus (RYMV; genus Sobemovirus) was calculated by a Bayesian coalescent analysis of the coat protein sequences of 253 isolates collected between 1966 and 2006 from all over Africa. It is inferred that RYMV diversified approximately 200 years ago in Africa, i.e., centuries after rice was domesticated or introduced, and decades before epidemics were reported. The divergence time of Sobemoviruses and viruses of related genera was subsequently assessed using the age of RYMV under a relaxed molecular clock for calibration. The divergence time between Sobemoviruses and related viruses was estimated to be approximately 9,000 years, that between Sobemoviruses and poleroviruses approximately 5,000 years, and that among Sobemoviruses approximately 3,000 years. The TMRCA of closely related pairs of Sobemoviruses, poleroviruses, and luteoviruses was approximately 500 years, which is a measure of the time associated with plant virus speciation. It is concluded that the diversification of RYMV and relate
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Emergence of a resistance breaking isolate of Rice yellow mottle virus during serial inoculations is due to a single substitution in the genome-linked viral protein VPg
Journal of General Virology, 2006Co-Authors: Eugénie Hébrard, Agnès Pinel-galzi, Anne Bersoult, Christelle Siré, Denis FargetteAbstract:The recessive gene rymv-1 responsible for the high resistance of Oryza sativa cultivar Gigante to Rice yellow mottle virus (Sobemovirus) was overcome by the variant CI4* which emerged after serial inoculations of the non-resistance-breaking (nRB) isolate CI4. By comparison of the full-length sequences of CI4 and CI4*, we identified a non-synonymous mutation at position 1729 localised in the putative VPg domain and developed an assay based on this single nucleotide polymorphism. The mutation G1729T was detected as early as the first passage in resistant plants and was found in all subsequent passages. Neither reversion nor additional mutation were observed. The substitution G1729T introduced by mutagenesis in the VPg of an nRB infectious clone is sufficient to induce symptoms in non-inoculated leaves of cultivar Gigante. This is the first evidence that VPg is a virulence factor in plants with recessive resistance against viruses outside the family Potyviridae.
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inferring the evolutionary history of rice yellow mottle virus from genomic phylogenetic and phylogeographic studies
Journal of Virology, 2004Co-Authors: Denis Fargette, Eugénie Hébrard, Oumar Traoré, Christophe Brugidou, A Pinel, Zakia Abubakar, Sorho Fatogoma, Marc Choisy, Yacouba Sere, Claude M FauquetAbstract:Fourteen isolates of Rice yellow mottle virus (RYMV) were selected as representative of the genetic variability of the virus in Africa from a total set of 320 isolates serologically typed or partially sequenced. The 14 isolates were fully sequenced and analyzed together with two previously reported sequences. RYMV had a genomic organization similar to that of Cocksfoot mottle Sobemovirus. The average nucleotide diversity among the 16 isolates of RYMV was 7%, and the maximum diversity between any two isolates was 10%. A strong conservative selection was apparent on both synonymous and nonsynonymous substitutions, through the amino acid replacement pattern, on the genome size, and through the limited number of indel events. Furthermore, there was a lack of positive selection on single amino acid sites and no evidence of recombination events. RYMV diversity had a pronounced and characteristic geographic structure. The branching order of the clades correlated with the geographic origin of the isolates along an east-to-west transect across Africa, and there was a marked decrease in nucleotide diversity moving westward across the continent. The insertion-deletion polymorphism was related to virus phylogeny. There was a partial phylogenetic incongruence between the coat protein gene and the rest of the genome. Overall, our results support the hypothesis that RYMV originated in East Africa and then dispersed and differentiated gradually from the east to the west of the continent.
Eugénie Hébrard - One of the best experts on this subject based on the ideXlab platform.
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Intrinsic disorder in Viral Proteins Genome-Linked: experimental and predictive analyses
Virology Journal, 2009Co-Authors: Eugénie Hébrard, Vladimir N Uversky, Sonia Longhi, Yannick Bessin, Thierry Michon, François Delalande, Alain Van Dorsselaer, Pedro Romero, Jocelyne Walter, Nathalie DeclerckAbstract:Background VPgs are viral proteins linked to the 5' end of some viral genomes. Interactions between several VPgs and eukaryotic translation initiation factors eIF4Es are critical for plant infection. However, VPgs are not restricted to phytoviruses, being also involved in genome replication and protein translation of several animal viruses. To date, structural data are still limited to small picornaviral VPgs. Recently three phytoviral VPgs were shown to be natively unfolded proteins. Results In this paper, we report the bacterial expression, purification and biochemical characterization of two phytoviral VPgs, namely the VPgs of Rice yellow mottle virus (RYMV, genus Sobemovirus ) and Lettuce mosaic virus (LMV, genus Potyvirus ). Using far-UV circular dichroism and size exclusion chromatography, we show that RYMV and LMV VPgs are predominantly or partly unstructured in solution, respectively. Using several disorder predictors, we show that both proteins are predicted to possess disordered regions. We next extend theses results to 14 VPgs representative of the viral diversity. Disordered regions were predicted in all VPg sequences whatever the genus and the family. Conclusion Based on these results, we propose that intrinsic disorder is a common feature of VPgs. The functional role of intrinsic disorder is discussed in light of the biological roles of VPgs.
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Biological and molecular characterization of a putative new Sobemovirus infecting Imperata cylindrica and maize in Africa
Archives of Virology, 2008Co-Authors: Drissa Sérémé, Denis Fargette, S Everine Lacombe, Moumouni Konaté, Agnès Pinel-galzi, Valentin Stanislas Edgar Traoré, Eugénie Hébrard, Oumar Traoré, Christophe Brugidou, Gnissa KonatéAbstract:A new virus was isolated from both the grass Imperata cylindrica and maize plants that had yellow mottle symptoms in Burkina Faso, West Africa. The virus has isometric particles ca. 32 nm in diameter. The experimental host range was restricted to Rottboellia exaltata . Virions were isolated from leaves of systemically infected maize plants. Koch’s postulates were completed by mechanically inoculating uninfected Imperata or maize with either purified virus or sap from infected Imperata plants. Virion preparations were used to produce a specific polyclonal antiserum, and an enzyme-linked immunosorbent assay test was set up. The full genome of the virus was sequenced, and it comprised 4,547 nucleotides. Phylogenetic studies indicated that the virus is closely related to rice yellow mottle virus, a Sobemovirus that infects monocotyledons in Africa, and is more distantly related to cocksfoot mottle virus, another Sobemovirus that infects monocotyledons. Although the virus can infect R. exaltata experimentally, it differs from Rottboellia yellow mottle virus , a member of a tentative species of the genus Sobemovirus that also infects monocotyledons in Africa. Particle morphology, serological properties, genomic organization, and phylogenetic analysis are all consistent with assignment of the new virus to the genus Sobemovirus . The name Imperata yellow mottle virus is proposed.
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virulence domain of the rymv genome linked viral protein vpg towards rice rymv1 2 mediated resistance
Archives of Virology, 2008Co-Authors: Eugénie Hébrard, Agnes Pinelgalzi, Denis FargetteAbstract:Virulent variants of Rice yellow mottle virus (genus Sobemovirus) can emerge on the highly resistant rice cultivars Gigante and Bekarosaka. Non-synonymous mutations responsible for the breakdown of the recessive resistance gene rymv1–2 were located in the VPg after determination of its termini in the polyprotein P2a. The secondary structure of this protein was predicted to include a central α-helix. The two major amino acids related to virulence are located on the same side of this helix. The 3D topology and the biochemical properties of virulence mutations both suggested a direct site-to-site interaction between RYMV VPg and rice eIF(iso)4G encoded by rymv1.
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Diversification of Rice Yellow Mottle Virus and Related Viruses Spans the History of Agriculture from the Neolithic to the Present
2008Co-Authors: Denis Fargette, Drissa Sérémé, S Everine Lacombe, Agnès Pinel-galzi, Eugénie Hébrard, Gnissa KonatéAbstract:The mechanisms of evolution of plant viruses are being unraveled, yet the timescale of their evolution remains an enigma. To address this critical issue, the divergence time of plant viruses at the intra- and inter-specific levels was assessed. The time of the most recent common ancestor (TMRCA) of Rice yellow mottle virus (RYMV; genus Sobemovirus) was calculated by a Bayesian coalescent analysis of the coat protein sequences of 253 isolates collected between 1966 and 2006 from all over Africa. It is inferred that RYMV diversified approximately 200 years ago in Africa, i.e., centuries after rice was domesticated or introduced, and decades before epidemics were reported. The divergence time of Sobemoviruses and viruses of related genera was subsequently assessed using the age of RYMV under a relaxed molecular clock for calibration. The divergence time between Sobemoviruses and related viruses was estimated to be approximately 9,000 years, that between Sobemoviruses and poleroviruses approximately 5,000 years, and that among Sobemoviruses approximately 3,000 years. The TMRCA of closely related pairs of Sobemoviruses, poleroviruses, and luteoviruses was approximately 500 years, which is a measure of the time associated with plant virus speciation. It is concluded that the diversification of RYMV and relate
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Emergence of a resistance breaking isolate of Rice yellow mottle virus during serial inoculations is due to a single substitution in the genome-linked viral protein VPg
Journal of General Virology, 2006Co-Authors: Eugénie Hébrard, Agnès Pinel-galzi, Anne Bersoult, Christelle Siré, Denis FargetteAbstract:The recessive gene rymv-1 responsible for the high resistance of Oryza sativa cultivar Gigante to Rice yellow mottle virus (Sobemovirus) was overcome by the variant CI4* which emerged after serial inoculations of the non-resistance-breaking (nRB) isolate CI4. By comparison of the full-length sequences of CI4 and CI4*, we identified a non-synonymous mutation at position 1729 localised in the putative VPg domain and developed an assay based on this single nucleotide polymorphism. The mutation G1729T was detected as early as the first passage in resistant plants and was found in all subsequent passages. Neither reversion nor additional mutation were observed. The substitution G1729T introduced by mutagenesis in the VPg of an nRB infectious clone is sufficient to induce symptoms in non-inoculated leaves of cultivar Gigante. This is the first evidence that VPg is a virulence factor in plants with recessive resistance against viruses outside the family Potyviridae.
Handanahal S. Savithri - One of the best experts on this subject based on the ideXlab platform.
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Interaction of Sesbania mosaic virus movement protein with VPg and P10: implication to specificity of genome recognition.
PloS one, 2011Co-Authors: Soumya Roy Chowdhury, Handanahal S. SavithriAbstract:Sesbania mosaic virus (SeMV) is a single strand positive-sense RNA plant virus that belongs to the genus Sobemovirus. The mechanism of cell-to-cell movement in Sobemoviruses has not been well studied. With a view to identify the viral encoded ancillary proteins of SeMV that may assist in cell-to-cell movement of the virus, all the proteins encoded by SeMV genome were cloned into yeast Matchmaker system 3 and interaction studies were performed. Two proteins namely, viral protein genome linked (VPg) and a 10-kDa protein (P10) c v gft encoded by OFR 2a, were identified as possible interacting partners in addition to the viral coat protein (CP). Further characterization of these interactions revealed that the movement protein (MP) recognizes cognate RNA through interaction with VPg, which is covalently linked to the 5' end of the RNA. Analysis of the deletion mutants delineated the domains of MP involved in the interaction with VPg and P10. This study implicates for the first time that VPg might play an important role in specific recognition of viral genome by MP in SeMV and shed light on the possible role of P10 in the viral movement.
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Sesbania mosaic virus (SeMV) infectious clone: possible mechanism of 3' and 5' end repair and role of polyprotein processing in viral replication.
Public Library of Science (PLoS), 2024Co-Authors: Kunduri Govind, Kristiina Mäkinen, Handanahal S. SavithriAbstract:Sesbania mosaic virus (SeMV) is a positive stranded RNA virus belonging to the genus Sobemovirus. Construction of an infectious clone is an essential step for deciphering the virus gene functions in vivo. Using Agrobacterium based transient expression system we show that SeMV icDNA is infectious on Sesbania grandiflora and Cyamopsis tetragonoloba plants. The efficiency of icDNA infection was found to be significantly high on Cyamopsis plants when compared to that on Sesbania grandiflora. The coat protein could be detected within 6 days post infiltration in the infiltrated leaves. Different species of viral RNA (double stranded and single stranded genomic and subgenomic RNA) could be detected upon northern analysis, suggesting that complete replication had taken place. Based on the analysis of the sequences at the genomic termini of progeny RNA from SeMV icDNA infiltrated leaves and those of its 3' and 5' terminal deletion mutants, we propose a possible mechanism for 3' and 5' end repair in vivo. Mutation of the cleavage sites in the polyproteins encoded by ORF 2 resulted in complete loss of infection by the icDNA, suggesting the importance of correct polyprotein processing at all the four cleavage sites for viral replication. Complementation analysis suggested that ORF 2 gene products can act in trans. However, the trans acting ability of ORF 2 gene products was abolished upon deletion of the N-terminal hydrophobic domain of polyprotein 2a and 2ab, suggesting that these products necessarily function at the replication site, where they are anchored to membranes
Kristiina Mäkinen - One of the best experts on this subject based on the ideXlab platform.
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Sesbania Mosaic Virus (SeMV) Infectious Clone: Possible Mechanism of 39 and 59 End Repair and Role of Polyprotein Processing in Viral Replication
2011Co-Authors: Kunduri Govind, Kristiina Mäkinen, Anahal S. SavithriAbstract:Sesbania mosaic virus (SeMV) is a positive stranded RNA virus belonging to the genus Sobemovirus. Construction of an infectious clone is an essential step for deciphering the virus gene functions in vivo. Using Agrobacterium based transient expression system we show that SeMV icDNA is infectious on Sesbania grandiflora and Cyamopsis tetragonoloba plants. The efficiency of icDNA infection was found to be significantly high on Cyamopsis plants when compared to that on Sesbania grandiflora. The coat protein could be detected within 6 days post infiltration in the infiltrated leaves. Different species of viral RNA (double stranded and single stranded genomic and subgenomic RNA) could be detected upon northern analysis, suggesting that complete replication had taken place. Based on the analysis of the sequences at the genomic termini of progeny RNA from SeMV icDNA infiltrated leaves and those of its 39 and 59 terminal deletion mutants, we propose a possible mechanism for 39 and 59 end repair in vivo. Mutation of the cleavage sites in the polyproteins encoded by ORF 2 resulted in complete loss of infection by the icDNA, suggesting the importance of correct polyprotein processing at all the four cleavage sites for viral replication. Complementation analysis suggested that ORF 2 gene products can act in trans. However, the trans acting ability of ORF 2 gene products was abolished upon deletion of the N-terminal hydrophobic domain of polyprotein 2a and 2ab, suggesting that these products necessarily function at the replication site, where they are anchored to membranes
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Characterization of VPg and the polyprotein processing of cocksfoot mottle virus (genus Sobemovirus).
Journal of General Virology, 2000Co-Authors: Kristiina Mäkinen, Tiina Tamm, Erkki Truve, Katri Mäkeläinen, Natalya Arshava, Andres Merits, Sergei Zavriev, Mart SaarmaAbstract:The polyprotein of Cocksfoot mottle virus (CfMV; genus Sobemovirus) is translated from two overlapping open reading frames (ORFs) 2a and 2b by aN1 ribosomal frameshifting mechanism. In this study, a 12 kDa protein was purified from viral RNA-derived samples that appears to correspond to the CfMV genome-linked protein (VPg). According to the determined N-terminal amino acid sequence, the VPg domain is located between the serine proteinase and replicase motifs and the N terminus of VPg is cleaved from the polyprotein between glutamic acid and asparagine residues. Western blot analysis of infected plant material showed that the polyprotein is processed at several additional sites. An antiserum against the ORF 2a product recognized six distinct proteins, whereas, of these, the VPg antiserum clearly recognized only a 24 kDa protein. This indicates that the fully processed 12 kDa VPg detected in viral RNA-derived samples is a minor product in infected plants. An antiserum against the ORF 2b product recognized a 58 kDa protein, which indicates that the fully processed replicase is entirely or almost entirely encoded by ORF 2b. The origin of the detected cleavage products and a proposed polyprotein processing model are discussed.
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The putative replicase of the cocksfoot mottle Sobemovirus is translated as a part of the polyprotein by -1 ribosomal frameshift.
Virology, 1995Co-Authors: Kristiina Mäkinen, Vigfrid Næss, Tiina Tamm, Erkki Truve, Anu Aaspöllu, Mart SaarmaAbstract:Abstract The polyprotein of cocksfoot mottle Sobemovirus (CfMV) is encoded by two overlapping open reading frames (ORF). The ORF 2a codes for the putative VPg and serine protease and the ORF 2b codes for the putative replicate. The consensus signals for a -1 ribosomal frameshifting event are found at the very beginning of the overlapping region of these ORFs. The shifty heptanucleotide in CfMV is UUUAAAC, and the secondary structure after the shifty sequence is predicted to be a stem-loop. In vitro translation of the CfMV RNA in wheat germ extract produced proteins of several sizes, including one of 100 kDa. According to the nucleotide sequence data, no single ORF is capable of directing the synthesis of a 100-kDa protein. A chimetic β-glucuronidase-CfMV cDNA containing the entire ORF 2a and 2b overlap region including frameshift signals was constructed. A trans-frame protein of 108 kDa was produced from this construct with an efficiency of 26-29% by in vitro translation in wheat germ extract. CfMV is the first Sobemovirus in which the putative replicase is reported to be produced as a part of a polyprotein by a -1 frameshift event. The replicases of the Sobemoviruses are related to the luteovirus subgroup II replicases, which are known to be produced by -1 ribosomal frameshift. The reported amino acid sequences of the putative replicases of sobemo- and subgroup II luteoviruses were compared to that of the putative replicase of CfMV. This comparison revealed more extensive homology between these groups than previously reported.
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Sesbania mosaic virus (SeMV) infectious clone: possible mechanism of 3' and 5' end repair and role of polyprotein processing in viral replication.
Public Library of Science (PLoS), 2024Co-Authors: Kunduri Govind, Kristiina Mäkinen, Handanahal S. SavithriAbstract:Sesbania mosaic virus (SeMV) is a positive stranded RNA virus belonging to the genus Sobemovirus. Construction of an infectious clone is an essential step for deciphering the virus gene functions in vivo. Using Agrobacterium based transient expression system we show that SeMV icDNA is infectious on Sesbania grandiflora and Cyamopsis tetragonoloba plants. The efficiency of icDNA infection was found to be significantly high on Cyamopsis plants when compared to that on Sesbania grandiflora. The coat protein could be detected within 6 days post infiltration in the infiltrated leaves. Different species of viral RNA (double stranded and single stranded genomic and subgenomic RNA) could be detected upon northern analysis, suggesting that complete replication had taken place. Based on the analysis of the sequences at the genomic termini of progeny RNA from SeMV icDNA infiltrated leaves and those of its 3' and 5' terminal deletion mutants, we propose a possible mechanism for 3' and 5' end repair in vivo. Mutation of the cleavage sites in the polyproteins encoded by ORF 2 resulted in complete loss of infection by the icDNA, suggesting the importance of correct polyprotein processing at all the four cleavage sites for viral replication. Complementation analysis suggested that ORF 2 gene products can act in trans. However, the trans acting ability of ORF 2 gene products was abolished upon deletion of the N-terminal hydrophobic domain of polyprotein 2a and 2ab, suggesting that these products necessarily function at the replication site, where they are anchored to membranes
Daniele Giblot Ducraybourdin - One of the best experts on this subject based on the ideXlab platform.
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analysis of a three dimensional structure of potato leafroll virus coat protein obtained by homology modeling
Virology, 2001Co-Authors: Laurent Terradot, Michel Souchet, Vinh Tran, Daniele Giblot DucraybourdinAbstract:Viruses of the family Luteoviridae are ssRNA plant viruses that have particles that exhibit icosahedral symmetry. To identify the residues that might be exposed on the surface of the Potato leafroll virus (PLRV; genus Polerovirus, family Luteoviridae) capsid, and therefore involved in biological interactions, we performed a structural analysis of the PLRV coat protein (CP) on the basis of comparisons with protein sequences and known crystal structures of CPs of other viruses. The CP of PLRV displays 33% sequence similarity with that of Rice yellow mottle virus (genus Sobemovirus) when the sequences were aligned by using the hidden Markov model method. A structure model for PLRV CP was designed by protein homology modeling, using the crystal structure of RYMV as a template. The resulting model is consistent with immunological and site-directed mutagenesis data previously reported. On the basis of this model it is possible to predict some surface properties of the PLRV CP and also speculate about the structural evolution of small icosahedral viruses.
