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Genome organization of potato leafroll virus (PLRV) and description of the CP mutants. The wild-type amino acid sequence of the two domains of the acidic patch are provided in the single-letter code. The domains are separated by 55 amino acids. Bold letters indicate residues that are conserved among all poleroviruses whose sequence is known. The five acidic amino acids (D or E) are in italics. The 11 single and multiple amino acid mutants are defined under the wild-type sequence. The amino acid changes (all alanine substitutions except one) are underlined and are shown in the center of the threeor four-letter mutant designations. The numbers indicate the amino acid residue position within the PLRV CP. Note that the upstream domain overlaps the virus movement protein (P17) encoded by ORF 4, whereas the downstream domain does not.
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Two acidic domains of the Potato leafroll virus (PLRV) coat protein, separated by 55 amino acids and predicted to be adjacent surface features on the virion, were the focus of a mutational analysis. Eleven site-directed mutants were generated from a cloned infectious cDNA of PLRV and delivered to plants by Agrobacterium-mediated mechanical inoculat...
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... to PLRV nucleotides 4382 to 4402) as the external primers. The sequences of the partially overlapping forward and reverse mutagenic primers are available on request. The resulting PCR fragments were inserted into linearized pBPY by homologous recombination in S. cerevisiae (15). The 11 mutants constructed for this study are shown in Fig. 1. The CP of the various mutants was sequenced to verify that each contained only the desired changes. The resulting plasmids were introduced into Agrobacterium tumefaciens strain LBA4404 and used for plant ...
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... in the PLRV acidic patch domains. Eleven site- directed mutants were generated (Fig. 1), and with one excep- tion, all were alanine substitutions. V169 was substituted with K because an alanine substitution would have been a conser- vative replacement and K is present in other luteoviruses at this position. The E-to-A substitution at position 109 resulted in an amino acid substitution (S to L) in the P17 movement protein ...
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... tion, all were alanine substitutions. V169 was substituted with K because an alanine substitution would have been a conser- vative replacement and K is present in other luteoviruses at this position. The E-to-A substitution at position 109 resulted in an amino acid substitution (S to L) in the P17 movement protein encoded by the overlapping ORF 4 (Fig. 1). The P17 coding sequence terminates prior to the downstream domain of the acid patch, and therefore the 10 downstream acidic patch domain mutants express wild-type P17. In addition, two other previously described mutants (15) were used as controls. The mutant CPRD translated only a full-length RT and not the 22-kDa CP. This mutant does ...
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... also resulted in a reduction of protected RNA. CPRD was a negative control in this RNase protection assay. CPRD was not able to assemble virions and the viral RNA was not protected (Fig. 2B, lane 2). The wild-type and RTD viruses served as positive controls. RTD could assemble sta- ble particles and did protect the RNA, similar to the wild type (Fig. 2B, lane 3 versus lane ...
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... The rate for CBSV is indicated with an asterisk. domain located in the surface loop of potato leafroll virus established the role of CP in virion assembly, systematic movement and aphid transmission (Lee et al., 2005). The CP gene of vectored plant viruses, which interact with both host and vector, are under more pressure to be unchanging, as evidenced by very low ratios of the rate of non-synonymous changes to the rate of synonymous changes (dN/dS) (Chare and Holmes, 2004;Jenkins et al., 2002). ...
The ipomoviruses (family Potyviridae) that cause cassava brown streak disease (cassava brown streak virus [CBSV] and Uganda cassava brown streak virus [UCBSV]) are damaging plant pathogens that affect the sustainability of cassava production in East and Central Africa. However, little is known about the rate at which the viruses evolve and when they emerged in Africa – which inform how easily these viruses can host shift and resist RNAi approaches for control. We present here the rates of evolution determined from the coat protein gene (CP) of CBSV (Temporal signal in a UCBSV dataset was not sufficient for comparable analysis). Our BEAST analysis estimated the CBSV CP evolves at a mean rate of 1.43 × 10⁻³ nucleotide substitutions per site per year, with the most recent common ancestor of sampled CBSV isolates existing in 1944 (95% HPD, between years 1922 – 1963). We compared the published measured and estimated rates of evolution of CPs from ten families of plant viruses and showed that CBSV is an average-evolving potyvirid, but that members of Potyviridae evolve more quickly than members of Virgaviridae and the single representatives of Betaflexiviridae, Bunyaviridae, Caulimoviridae and Closteroviridae.
... The rate for CBSV is indicated with an asterisk. domain located in the surface loop of potato leafroll virus established the role of CP in virion assembly, systematic movement and aphid transmission (Lee et al., 2005). The CP gene of vectored plant viruses, which interact with both host and vector, are under more pressure to be unchanging, as evidenced by very low ratios of the rate of non-synonymous changes to the rate of synonymous changes (dN/dS) (Chare and Holmes, 2004;Jenkins et al., 2002). ...
... Polerovirus particles are composed of the major coat protein (CP) and a few copies of a minor readthrough protein (RTP) which is a fusion protein with the CP at its N-terminus and the readthrough domain (RTD) at its C-terminus. It has been reported that mutations in the CP or RTP of potato leaf roll virus (PLRV) can seriously affect the transmission efficiency of aphids, virus movement, and virus accumulation [15,16]. For circulative phytoviruses, when they move through the insect vector, the interaction between the virus and vector proteins would have occurred to overcome gut and salivary gland barriers to achieve successful transmission. ...
Viruses in the genus Polerovirus infect a wide range of crop plants and cause severe economic crop losses. BrYV belongs to the genus Polerovirus and is transmitted by Myzus persicae. However, the changes in transcriptome and proteome profiles of M. persicae during viral infection are unclear. Here, RNA-Seq and TMT-based quantitative proteomic analysis were performed to compare the differences between viruliferous and nonviruliferous aphids. In total, 1266 DEGs were identified at the level of transcription with 980 DEGs being upregulated and 286 downregulated in viruliferous aphids. At the protein level, among the 18 DEPs identified, the number of upregulated proteins in viruliferous aphids was twice that of the downregulated DEPs. Enrichment analysis indicated that these DEGs and DEPs were mainly involved in epidermal protein synthesis, phosphorylation, and various metabolic processes. Interestingly, the expressions of a number of cuticle proteins and tubulins were upregulated in viruliferous aphids. Taken together, our study revealed the complex regulatory network between BrYV and its vector M. persicae from the perspective of omics. These findings should be of great benefit to screening key factors involved in the process of virus circulation in aphids and provide new insights for BrYV prevention via vector control in the field.
... The mutations in the CP clearly affect the long-distance movement of PEMV-1 and PEMV-2 (Doumayrou et al. 2016). The CP and RTP also affect systemic infection of PLRV (Lee et al. 2005;Xu et al. 2018). In this study, based on the amino acid sequence analysis, PEMV-1 has the CP and RTP domains that are highly conserved in PLRV. ...
The pea enation mosaic disease (PEMD) causes significant yield losses worldwide. PEMD is caused by two taxonomically unrelated but symbiotic viruses, pea enation mosaic virus 1 (PEMV-1) and pea enation mosaic virus 2 (PEMV-2). In this study, the complete genomes of four isolates of PEMV-1 and PEMV-2 from Yunnan Province of China were determined and analyzed. The four isolates of PEMV-1 or PEMV-2 shared ≥ 98.7% nucleotide sequence identities at whole genome level. The four Chinese PEMV-1 isolates were most closely related to PEMV-1-Ramsey-1 with nucleotide sequence identities of 97.8–98.0%, while the four Chinese PEMV-2 isolates were most closely related to PEMV-2-DSMZ PV-0088, with nucleotide sequence identities of 94.3–94.5%. The two full-length infectious cDNA clones of the Yunnan-Dali isolates of the two viruses (PEMV-1-YDL and PEMV-2-YDL) were constructed. Co-inoculation of PEMV-1-YDL and PEMV-2-YDL in pea seedlings caused systemic infection, with typical enation and mosaic symptoms on new leaves after inoculation, while the inoculated Nicotiana benthamiana plants showed curling symptoms. Inoculation of pea seedlings with either PEMV-1-YDL or PEMV-2-YDL did not cause obvious symptoms on the new leaves. It has been known that PEMV-2 helps the systemic infection of PEMV-1. However, our results showed that PEMV-1-YDL alone could cause a systemic infection. The pathogenicity of the two infectious clones was tested on different pea cultivars, and some cultivars were PEMD-tolerant. This is the first report of the infectious clones constructed from the Chinese isolates of PEMV-1 and PEMV-2. The current approach will facilitate determination of the synergistic relationship between PEMV-1 and PEMV-2 and their interactions with the host plant by reverse genetic analysis.
... Stochastic ribosomal readthrough of the CP stop codon generates a second minor capsid component termed the readthrough protein (RTP), which contains an additional readthrough domain (RTD) encoded by ORF5 that is fused to the CP C-terminus [6][7][8][9] . The leakiness of the CP stop codon has been maintained throughout evolution and ensures that the RTP is incorporated into the capsid substoichiometrically 10 : mutant viruses that lack the stop codon and make only the full-length RTP cannot assemble proper virions, infect plants, or be transmitted by aphid vectors [11][12][13] . A soluble form of the RTP that is not associated with the capsid plays a role in phloem limitation and movement within the plant host 13,14 . ...
Poleroviruses, enamoviruses, and luteoviruses are icosahedral, positive sense RNA viruses that cause economically important diseases in food and fiber crops. They are transmitted by phloem-feeding aphids in a circulative manner that involves the movement across and within insect tissues. The N-terminal portion of the viral readthrough domain (NRTD) has been implicated as a key determinant of aphid transmission in each of these genera. Here, we report crystal structures of the NRTDs from the poleroviruses turnip yellow virus (TuYV) and potato leafroll virus (PLRV) at 1.53-Å and 2.22-Å resolution, respectively. These adopt a two-domain arrangement with a unique interdigitated topology and form highly conserved dimers that are stabilized by a C-terminal peptide that is critical for proper folding. We demonstrate that the PLRV NRTD can act as an inhibitor of virus transmission and identify NRTD mutant variants that are lethal to aphids. Sequence conservation argues that enamovirus and luteovirus NRTDs will follow the same structural blueprint, which affords a biological approach to block the spread of these agricultural pathogens in a generalizable manner.
... On the other hand, P3 has a biologically active region that plays a vital role in CP subunit interactions, plant-virus interactions and aphid-virus recognition. Furthermore, the viral particle's assembly is required for vector transmission and determines which insect vectors can transmit the virus [97][98][99]. Thus, recombination and mutation might affect critical biological functions governed by the P3 gene. ...
The genus Polerovirus contains positive-sense, single-stranded RNA plant viruses that cause significant disease in many agricultural crops, including vegetable legumes. This study aimed to identify and determine the abundance of Polerovirus species present within Tasmanian pea crops and surrounding weeds that may act as virus reservoirs. We further sought to examine the genetic diversity of TuYV, the most commonly occurring polerovirus identified. Pea and weed samples were collected during 2019–2020 between October and January from thirty-four sites across three different regions (far northwest, north, and midlands) of Tasmania and tested by RT-PCR assay, with selected samples subject to next-generation sequencing. Results revealed that the presence of polerovirus infection and the prevalence of TuYV in both weeds and pea crops varied across the three Tasmanian cropping regions, with TuYV infection levels in pea crops ranging between 0 and 27.5% of tested plants. Overall, two species members from each genus, Polerovirus and Potyvirus, one member from each of Luteovirus, Potexvirus, and Carlavirus, and an unclassified virus from the family Partitiviridae were also found as a result of NGS data analysis. Analysis of gene sequences of the P0 and P3 genes of Tasmanian TuYV isolates revealed substantial genetic diversity within the collection, with a few isolates appearing more closely aligned with BrYV isolates. Questions remain around the differentiation of TuYV and BrYV species. Phylogenetic inconsistency in the P0 and P3 ORFs supports the concept that recombination may have played a role in TuYV evolution in Tasmania. Results of the evolutionary analysis showed that the selection pressure was higher in the P0 gene than in the P3 gene, and the majority of the codons for each gene are evolving under purifying selection. Future full genome-based analyses of the genetic variations will expand our understanding of the evolutionary patterns existing among TuYV populations in Tasmania.
... In addition, ORF1 could be expressed with ORF2 in a −1 ribosomal frameshift manner as a viral RNA-dependent RNA polymerase (RdRp) [5]. ORF3 and ORF4 are expressed by translation from subgenomic RNAs to encode coat protein (CP) [6,7] and movement protein (MP), respectively [8]. ORF5 is expressed via translational readthrough of the leaky stop codon of ORF3 to produce the putative P3-P5 fusion protein, which is necessary for vector transmission of the viral component [9]. ...
Poleroviruses are positive-sense, single-stranded viruses. In this study, we describe the identification of a novel polerovirus isolated from soybean displaying curled leaves. The complete viral genome sequence was identified using high-throughput sequencing and confirmed using rapid amplification of cDNA ends (RACE), RT-PCR and Sanger sequencing. Its genome organization is typical of the members of genus Polerovirus, containing seven putative open reading frames (ORFs). The full genome is composed of single-stranded RNA of 5822 nucleotides in length, with the highest nucleotide sequence identity (79.07% with 63% coverage) for cowpea polerovirus 2 (CPPV2). Amino acid sequence identities of the protein products between the virus and its relatives are below the threshold determined by the International Committee of Taxonomy of Viruses (ICTV) for species demarcation, and this strongly supports this virus’ status as a novel species, for which the name soybean chlorotic leafroll virus (SbCLRV) is proposed. Recombination analysis identified a recombination event in the ORF5 of the 3’ portion in the genome. Phylogenetic analyses of the genome and encoded protein sequences revealed that the new virus is closely related to phasey bean mild yellows virus, CPPV2 and siratro latent polerovirus. Subsequently, we demonstrated the infectivity of SbCLRV in Nicotiana benthamiana via infectious cDNA clone generation and agroinoculation.
... The virus is the type species of genus Polerovirus; it belongs to family Solemoviridae and was first identified by Somera et al. in 2021 [5]. It is efficiently transmitted by aphid species, particularly the green peach aphid M. persicae, in a circulative non-propagative manner and is restricted to the phloem tissues of infected plants [6]. The pathogen is responsible for 50% yield reduction in individual plants and over 20 million tons yield losses all over the world [7]. ...
The potato leaf roll virus (PLRV) disease is a serious threat to successful potato production and is mainly controlled by integrated disease management; however, the use of chemicals is excessive and non-judicious, and it could be rationalized using a predictive model based on meteorological variables. The goal of the present investigation was to develop a disease predictive model based on environmental responses viz. minimum and maximum temperature, rainfall and relative humidity. The relationship between epidemiological variables and PLRV disease incidence was determined by correlation analysis, and a stepwise multiple regression was used to develop a model. For this purpose, five years (2010–2015) of data regarding disease incidence and epidemiological variables collected from the Plant Virology Section Ayub Agriculture Research Institute (AARI) Faisalabad were used. The model exhibited 94% variability in disease development. The predictions of the model were evaluated based on two statistical indices, residual (%) and root mean square error (RMSE), which were ≤±20, indicating that the model was able to predict disease development. The model was validated by a two-year (2015–2017) data set of epidemiological variables and disease incidence collected in Faisalabad, Pakistan. The homogeneity of the regression equations of the two models, five years (Y = −47.61 − 0.572x1 + 0.218x2 + 3.78x3 + 1.073x4) and two years (Y = −28.93 − 0.148x1 + 0.510x2 + 0.83x3 + 0.569x4), demonstrated that they validated each other. Scatter plots indicated that minimum temperature (5–18.5 °C), maximum temperature (19.1–34.4 °C), rainfall (3–5 mm) and relative humidity (35–85%) contributed significantly to disease development. The foliar application of salicylic acid alone and in combination with other treatments significantly reduced the PLRV disease incidence and its vector population over control. The salicylic acid together with acetamiprid proved the most effective treatment against PLRV disease incidence and its vector M. persicae.
... The virus is the type species of genus Polerovirus; it belongs to family Solemoviridae and was first identified by Somera et al. in 2021 [5]. It is efficiently transmitted by aphid species, particularly the green peach aphid M. persicae, in a circulative non-propagative manner and is restricted to the phloem tissues of infected plants [6]. The pathogen is responsible for 50% yield reduction in individual plants and over 20 million tons yield losses all over the world [7]. ...
Citation: Ali, Y.; Raza, A.; Aatif, H.M.; Ijaz, M.; Ul-Allah, S.; Rehman, S.u.; Mahmoud, S.Y.M.; Farrag, E.S.H.; Amer, M.A.; Moustafa, M. Regression Modeling Strategies to Predict and Manage Potato Leaf Roll Virus Disease Incidence and Its Vector. Agriculture 2022, 12, 550.
... For systemic infection and symptom expression of poleroviruses, the P3a, CP and C-terminal region in RTP are reported to be important [29][30][31][32]. According to other research, the PLRV mutant, which does not translate the P17 (MP), can still spread systemically from inoculated leaves in Nicotiana spp., showing that P17 is not necessary for the movement of PLRV in Nicotiana spp. ...
P0 proteins encoded by poleroviruses Brassica yellows virus (BrYV) and Potato leafroll virus (PLRV) are viral suppressors of RNA silencing (VSR) involved in abolishing host RNA silencing to assist viral infection. However, other roles that P0 proteins play in virus infection remain unclear. Here, we found that C-terminal truncation of P0 resulted in compromised systemic infection of BrYV and PLRV. C-terminal truncation affected systemic but not local VSR activities of P0 proteins, but neither transient nor ectopic stably expressed VSR proteins could rescue the systemic infection of BrYV and PLRV mutants. Moreover, BrYV mutant failed to establish systemic infection in DCL2/4 RNAi or RDR6 RNAi plants, indicating that systemic infection might be independent of the VSR activity of P0. Partially rescued infection of BrYV mutant by the co-infected PLRV implied the functional conservation of P0 proteins within genus. However, although C-terminal truncation mutant of BrYV P0 showed weaker interaction with its movement protein (MP) when compared to wild-type P0, wild-type and mutant PLRV P0 showed similar interaction with its MP. In sum, our findings revealed the role of P0 in virus systemic infection and the requirement of P0 carboxyl terminal region for the infection.
