Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus

Fiore, Nicola; Fajardo, T. V. M.; Prodan, Simona; Herranz, Carmen; Aparicio, Frederic; Montealegre, J.; Elena, Santiago F.; Pallás, Vicente; Sánchez‐Navarro, J. A.

doi:10.1007/s00705-008-0066-1

Cited by 31 publications

(21 citation statements)

References 45 publications

(76 reference statements)

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“…In this sense, AMV mutants defective in plasmodesmata localization were also affected in virus transport (Huang et al, 2001). It is worth noting that the C-terminal 32 residues are the most variable part of the PNRSV MP (Aparicio & Pallás, 2002), whereas the region just upstream is highly conserved and contains five sites under negative evolutive selection (V231, D236, R238, T242 and P248), which could be an indication of its importance to maintain the functionality of the protein (Fiore et al, 2008). Our results showed that the small region between residues 242 and 245 (mutant pMPD4-GFP) is critical for both the function of the protein and its subcellular localization.…”

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confidence: 99%

Implication of the C terminus of the Prunus necrotic ringspot virus movement protein in cell-to-cell transport and in its interaction with the coat protein

Aparicio

Pallás

Sánchez‐Navarro

2010

Journal of General Virology

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The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for viral transport. Previous analysis with MPs of other members of the family Bromoviridae has shown that the C-terminal part of these MPs plays a critical role in the interaction with the cognate coat protein (CP) and in cell-to-cell transport. Bimolecular fluorescence complementation and overlay analysis confirm an interaction between the C-terminal 38 aa of PNRSV MP and its cognate CP. Mutational analysis of the C-terminal region of the PNRSV MP revealed that its C-terminal 38 aa are dispensable for virus transport, however, the 4 aa preceding the dispensable C terminus are necessary to target the MP to the plasmodesmata and for the functionality of the protein. The capacity of the PNRSV MP to use either a CP-dependent or a CP-independent cell-to-cell transport is discussed.Prunus necrotic ringspot virus (PNRSV) belongs to the genus Ilarvirus (family Bromoviridae). The PNRSV genome consists of three, single-stranded, plus-sense RNAs. RNAs 1 and 2 encode P1 and P2 polymerase protein subunits, respectively. RNA 3 directly encodes the movement protein (MP), whereas the coat protein (CP) is synthesized via a subgenomic RNA 4 (Sánchez-Navarro & Pallás, 1997).The MP of PNRSV belongs to the 30K superfamily (Melcher, 2000). The C-terminal region of the 30K MPs has a predicted random coiled secondary structure (Melcher, 2000). The alfalfa mosaic virus (AMV) MP specifically interacts with its cognate CP through its Cterminal region and in the cowpea mosaic virus (CPMV) MP this region is the virion-binding domain (Carvalho et al., 2003; Sánchez-Navarro et al., 2006). In the case of the MP of the cauliflower mosaic virus (CaMV), the C terminus interacts indirectly with the cognate CP via the virion-associated protein (Stavolone et al., 2005). The Cterminal region of the corresponding MPs of the cucumber mosaic virus (CMV) and the brome mosaic virus (BMV) controls the requirement of the CP for intercellular movement (Nagano et al., 2001; Sánchez-Navarro & Bol, 2001;Takeda et al., 2004). Deletion of the C-terminal 55 aa of the tobacco mosaic virus (TMV) MP does not affect the cell-to-cell transport of the TMV nor the cell-wall localization of the protein (Berna et al., 1991). In the present study, we have analysed the role of cell-to-cell movement of the PNRSV MP C-terminal region by mutational analysis. We also analysed the putative MP-CP interaction by bimolecular fluorescence complementation (BiFC) and overlay assays, respectively. Finally, we present data indicating that the capacity of the PNRSV MP to mediate virus transport is independent of the MP-CP interaction.Due to the lack of PNRSV infectious clones, a chimera cDNA3 construct between AMV and PNRSV that expresses the green fluorescent protein (GFP), the wild-type (wt) PNRSV MP fused in-frame to the C-terminal 44 aa of AMV MP (A44) and the AMV CP was used (clone pGFP/ MP-A44/CP in Sánchez-Navarro et al., 2006; hereafter pMP P -A44). The A44 is required for a specific interaction wit...

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confidence: 99%

Implication of the C terminus of the Prunus necrotic ringspot virus movement protein in cell-to-cell transport and in its interaction with the coat protein

Aparicio

Pallás

Sánchez‐Navarro

2010

Journal of General Virology

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“…They noted that both of them were phylogenetically closely related to a previously described cherry isolate by Scott et al [52] having the accession number AF013287. Fiore et al [10] recognized that this group was outside of the classical phylogenetic scheme represented by PV96, PV32, and PE5 clusters; but at the same time, they stated that, based on the use of an alternative statistical approach, the four-cluster likelihoodmapping method, these accessions were considered as part of PV96 phylogroup. Gradually, the number of accessions increased including those Indian accessions described by Chandel et al [53][54][55].…”

Section: Discussionmentioning

confidence: 99%

Evidence for Recombination in the Emerged Phylogroup SW6 of Prunus Necrotic Ringspot Virus and Estimate of Selection Pressure Acting on Capsid Protein of Affiliated Members

Boulila¹

2017

JAMB

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Abstract. Recombination plays a key role in virus evolution. Except a limited number of works carried out so far on recombination in Prunus necrotic ringspot virus (PNRSV) genome, knowledge is still poor. Numerous phylogenetic studies particularly those based on capsid (CP) and movement protein (MP) of PNRSV showed that all accessions described so far split into three major phylogroups, i.e., PV96, PV32, and PE5. With the recent characterization of Chilean and Indian isolates which were phylogenetically closely related to the oldest member, i.e., SW6 (AF013287) from USA, a new phylogroup baptized SW6, emerged since it was outside of the evolutionary behavior of the classical PV96, PV32, and PE5 clusters. In order to understand how it evolved, six computerized methods were used to detect potential recombination in the CP sequences of nine components forming SW6 phylogroup. It was clearly demonstrated that various members underwent recombination. Additionally, networked relationships among them proved that numerous incompatibilities occurred in these sequences illustrated by the presence of boxes in the network implying therefore the possibility of recombination. According to inferred network, several sequences contained conflicting signals as illustrated by various splits and edges with special reference to Chilean (EF565255, EF565256), polish (AF332614) and Indian (AM494934) isolates. It is worth noting that the phylogenetic network provided a different clustering compared to the bifurcating tree. In fact, three distinct groups were delineated with SplitsTree4 software instead of a globally homogenous ensemble generated by MEGA7 algorithm. Furthermore, this study pointed out that members of SW6 phylogroup were the only recombinants among 205 tested accessions confirming that SW6 should be considered as the fourth phylogenetic group of PNRSV. On the other hand, CP was predominantly under purifying selection. However, positive selection was evidenced particularly in the C-terminal region of CP comprising part of dimerization region (DR). Such adaptive selection was exerted on a CP segment of AM494934 accession exchanged by recombination.

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“…Located closer to the 5' end of RNA3 is ORF3a, which encodes the movement protein (MP), belongs to the "30K superfamily" (Kasteel et al, 1997;Mekuria et al, 2003;Pallas et al, 2012) and supports the viral cell-to-cell movement The MPs of this family are structurally characterized by the presence of a hydrophobic motif (HR) (Melcher, 2000). This motif is highly conserved in the family Bromoviridae (Codoner et al, 2005, Sanchez-Navarro andPallas, 1997) and is proceeded by a conserved RNA-binding domain (RBD) (Herranz and Pallas, 2004), which is located between 56 to 85 residues (Fiore et al, 2008;Herranz et al, 2005). This domain may support viral RNA transport.…”

Section: Introductionmentioning

confidence: 98%

Phylogenetic Analysis of PDV Movement Protein Compared to Bromoviridae Members as Justification of Possible Intercellular Movement

Kozieł¹,

Otulak²,

Garbaczewska³

2015

Acta Biologica Cracoviensia S. Botanica

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Prune dwarf virus (PDV) is a member of the Ilarvirus genus which is widely spread all over the world and causes considerable economic losses in nurseries and orchards. The virus is transmitted via seeds and pollen and through vegetative reproduction. However, the mechanisms of cell-to-cell and systemic transport of the virus are still not known. For the first time this study presents phylogenetic characterization of the movement protein (MP) of PDV isolates from the GenBank database in the context of geographic origin. The prepared analyses were based on a comparison of the whole amino acid sequence of the MP-PDV, the RNA-binding domain (RBD) in MP of PDV and MPs of four viruses from the Bromoviridae family with known transport mechanisms. Two different bioinformatic programs ClustalW and Jalview were used, and MP sequence variability up to 8% at the amino acid level among PDV isolates was confirmed. In the constructed phylogenetic trees the isolate sequences clustered in three conserved groups. Further analyses revealed similarity of the MP amino acid sequence of PDV and Alfalfa mosaic virus (AMV) of up to 34% and a 40% similarity of RBD between these viruses which suggested that the PDV transport mechanism may be on some level the same as that for AMV.K Ke ey y w wo or rd ds s: : PDV, movement protein, amino acid sequence, phylogenetic analyses

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Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus

Cited by 31 publications

References 45 publications

Implication of the C terminus of the Prunus necrotic ringspot virus movement protein in cell-to-cell transport and in its interaction with the coat protein

Implication of the C terminus of the Prunus necrotic ringspot virus movement protein in cell-to-cell transport and in its interaction with the coat protein

Evidence for Recombination in the Emerged Phylogroup SW6 of Prunus Necrotic Ringspot Virus and Estimate of Selection Pressure Acting on Capsid Protein of Affiliated Members

Phylogenetic Analysis of PDV Movement Protein Compared to Bromoviridae Members as Justification of Possible Intercellular Movement

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