Mapping of the P1 proteinase cleavage site in the polyprotein of Wheat streak mosaic virus (genus Tritimovirus)

Plant Viral Synergism: Co-expression of P1 and NIaPro Cistrons of Wheat Streak Mosaic Virus and Triticum Mosaic Virus Is Required for Synergistic Interaction in Wheat

Synergistic interactions among unrelated viruses in mixed infections can cause significant yield losses, and viral determinants of these interactions are poorly understood. Wheat (Triticum aestivum L.) co-infection with wheat curl mite-transmitted wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) results in disease synergism with a drastically increased symptom phenotype of stunted growth, leaf bleaching, and enhanced titers of both viruses compared with individual virus infections. In this study, we examined the viral determinants responsible for WSMV-TriMV disease synergism through transient expression of select cistrons of WSMV in wheat through TriMV and vice-versa. We found that expression of WSMV P1, NIa, or NIaPro in wheat through TriMV or vice-versa elicited moderate to severe symptoms with a moderate or no increase in virus titer. However, co-expression of P1 and NIaPro of WSMV in wheat through TriMV or vice-versa exhibited a WSMV-TriMV disease synergism-like phenotype with enhanced accumulation of genomic RNA copies and coat protein. Additionally, we found that the P3 of both viruses is dispensable for synergism. HCPro and NIaVPg of WSMV and TriMV are not the primary determinants but might have a minor role in efficient synergism. In co-infected wheat, the accumulation of virus-specific small interfering RNAs (vsiRNAs) was increased, similar to viral genomic RNA copies, despite the presence of two viral RNA-silencing suppressors (VRSS), which function through sequestration of vsiRNAs. Our findings revealed that WSMV-TriMV disease synergism is not caused by the suppression of host posttranscriptional gene silencing by two VRSS proteins in co-infected wheat, and the P1 and NIaPro of both viruses collectively drive synergistic interactions between WSMV and TriMV in wheat. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.

Distribution of Wheat-Infecting Viruses and Genetic Variability of Wheat Streak Mosaic Virus and Barley Stripe Mosaic Virus in Kazakhstan

Wheat is an essential cereal crop for the economy and food safety of Kazakhstan. In the present work, a screening of wheat and barley from different regions of Kazakhstan was conducted using newly developed specific primers for reverse transcription PCR and loop-mediated isothermal amplification (LAMP) assays. In total, 82 and 19 of 256 samples of wheat and barley tested positive for wheat streak mosaic virus (WSMV) and barley stripe mosaic virus (BSMV), respectively. A phylogenetic analysis using two independent methods revealed that most of the analyzed isolates had a European origin. Molecular data on the distribution and diversity of cereal viruses in Kazakhstan were obtained for the first time and will help lay a foundation for the implementation of genetics and genomics in wheat phyto-epidemiology in the country.

Occurrence and Characterization of Wheat Streak Mosaic Virus Found in Mono- and Mixed Infection with High Plains Wheat Mosaic Virus in Winter Wheat in Ukraine

Although wheat streak mosaic virus (WSMV) is a well-known pathogen inducing significant crop losses and endangering wheat production worldwide, the recent discovery of High Plains wheat mosaic virus (HPWMoV) in Ukraine raises questions on the co-existence of these two viruses having a similar host range and the same mite vector. Here we report on the screening of winter wheat industrial plantings in several important regions of Ukraine for WSMV and HPWMoV. WSMV was identified in an extremely high number of symptomatic plants (>85%) as compared to HPWMoV detected in 40% of wheat samples. Importantly, the preferred mode of HPWMoV circulation in Ukraine was mixed infection with WSMV (>30%) as opposed to WSMV, which was typically found in monoinfection (60%). Screening wheat varieties for possible virus resistance indicated that all but one were susceptible to WSMV, whereas over 50% of the same varieties were not naturally infected with HPWMoV. Overall, phylogenetic analysis of the collected WSMV and HPWMoV isolates indicated their high identity and similarity to other known isolates of the respective viruses. Here we first characterize WSMV isolates found in winter wheat plants in mono- or mixed infection with HPWMoV, which was recently reported as a typical wheat pathogen in Ukraine.

OUP accepted manuscript

Potyviridae, the largest family of known RNA viruses (realm Riboviria), belongs to the picorna-like supergroup and has important agricultural and ecological impacts. Potyvirid genomes are translated into polyproteins, which are in turn hydrolyzed to release mature products. Recent sequencing efforts revealed an unprecedented number of potyvirids with a rich variability in gene content and genomic layouts. Here, we review the heterogeneity of non-core modules that expand the structural and functional diversity of the potyvirid proteomes. We provide a family-wide classification of P1 proteinases into the functional Types A and B, and discuss pretty interesting sweet potato potyviral ORF (PISPO), putative zinc fingers, and alkylation B (AlkB)—non-core modules found within P1 cistrons. The atypical inosine triphosphate pyrophosphatase (ITPase/HAM1), as well as the pseudo tobacco mosaic virus-like coat protein (TMV-like CP) are discussed alongside homologs of unrelated virus taxa. Family-wide abundance of the multitasking helper component proteinase (HC-pro) is revised. Functional connections between non-core modules are highlighted to support host niche adaptation and immune evasion as main drivers of the Potyviridae evolutionary radiation. Potential biotechnological and synthetic biology applications of potyvirid leader proteinases and non-core modules are finally explored.

Translation of Plant RNA Viruses

Plant RNA viruses encode essential viral proteins that depend on the host translation machinery for their expression. However, genomic RNAs of most plant RNA viruses lack the classical characteristics of eukaryotic cellular mRNAs, such as mono-cistron, 5′ cap structure, and 3′ polyadenylation. To adapt and utilize the eukaryotic translation machinery, plant RNA viruses have evolved a variety of translation strategies such as cap-independent translation, translation recoding on initiation and termination sites, and post-translation processes. This review focuses on advances in cap-independent translation and translation recoding in plant viruses.

Full Genome Evolutionary Studies of Wheat Streak Mosaic-Associated Viruses Using High-Throughput Sequencing

Wheat streak mosaic (WSM), a viral disease affecting cereals and grasses, causes substantial losses in crop yields. Wheat streak mosaic virus (WSMV) is the main causal agent of the complex, but mixed infections with Triticum mosaic virus (TriMV) and High plains wheat mosaic emaravirus (HPWMoV) were reported as well. Although resistant varieties are effective for the disease control, a WSMV resistance-breaking isolate and several potential resistance-breaking isolates have been reported, suggesting that viral populations are genetically diverse. Previous phylogenetic studies of WSMV were conducted by focusing only on the virus coat protein (CP) sequence, while there is no such study for either TriMV or HPWMoV. Here, we studied the genetic variation and evolutionary mechanisms of natural populations of WSM-associated viruses mainly in Kansas fields and fields in some other parts of the Great Plains using high-throughput RNA sequencing. In total, 28 historic and field samples were used for total RNA sequencing to obtain full genome sequences of WSM-associated viruses. Field survey results showed WSMV as the predominant virus followed by mixed infections of WSMV + TriMV. Phylogenetic analyses of the full genome sequences demonstrated that WSMV Kansas isolates are widely distributed in sub-clades. In contrast, phylogenetic analyses for TriMV isolates showed no significant diversity. Recombination was identified as the major evolutionary force of WSMV and TriMV variation in KS fields, and positive selection was detected in some encoding genomic regions in the genome of both viruses. Furthermore, the full genome sequence of a second Kansas HPWMoV isolate was reported. Here, we also identified previously unknown WSMV isolates in the Great Plains sharing clades and high nucleotide sequence similarities with Central Europe isolates. The findings of this study will provide more insights into the genetic structure of WSM-associated viruses and, in turn, help in improving strategies for disease management.

Simultaneous gene expression and multi-gene silencing in Zea mays using maize dwarf mosaic virus

BACKGROUND

Maize dwarf mosaic virus (MDMV), a member of the genus Potyvirus, infects maize and is non-persistently transmitted by aphids. Several plant viruses have been developed as tools for gene expression and gene silencing in plants. The capacity of MDMV for both gene expression and gene silencing were examined.

RESULTS

Infectious clones of an Ohio isolate of MDMV, MDMV OH5, were obtained, and engineered for gene expression only, and for simultaneous marker gene expression and virus-induced gene silencing (VIGS) of three endogenous maize target genes. Single gene expression in single insertion constructs and simultaneous expression of green fluorescent protein (GFP) and silencing of three maize genes in a double insertion construct was demonstrated. Constructs with GFP inserted in the N-terminus of HCPro were more stable than those with insertion at the N-terminus of CP in our study. Unexpectedly, the construct with two insertion sites also retained insertions at a higher rate than single-insertion constructs. Engineered MDMV expression and VIGS constructs were transmissible by aphids (Rhopalosiphum padi).

CONCLUSIONS

These results demonstrate that MDMV-based vector can be used as a tool for simultaneous gene expression and multi-gene silencing in maize.

Wheat streak mosaic virus alters the transcriptome of its vector, wheat curl mite (Aceria tosichella Keifer), to enhance mite development and population expansion

Wheat streak mosaic virus (WSMV; genus Tritimovirus; family Potyviridae) is an economically important wheat virus that is transmitted by the wheat curl mite (WCM; Aceria tosichella Keifer) in a persistent manner. Virus-vector coevolution may potentially influence vector gene expression to prolong viral association and thus increase virus transmission efficiency and spread. To understand the transcriptomic responses of WCM to WSMV, RNA sequencing was performed to assemble and analyse transcriptomes of WSMV viruliferous and aviruliferous mites. Among 7291 de novo-assembled unigenes, 1020 were differentially expressed between viruliferous and aviruliferous WCMs using edgeR at a false discovery rate ≤0.05. Differentially expressed unigenes were enriched for 108 gene ontology terms, with the majority of the unigenes showing downregulation in viruliferous mites in comparison to only a few unigenes that were upregulated. Protein family and metabolic pathway enrichment analyses revealed that most downregulated unigenes encoded enzymes and proteins linked to stress response, immunity and development. Mechanistically, these predicted changes in mite physiology induced by viral association could be suggestive of pathways needed for promoting virus-vector interactions. Overall, our data suggest that transcriptional changes in viruliferous mites facilitate prolonged viral association and alter WCM development to expedite population expansion, both of which could enhance viral transmission.

Wheat streak mosaic virus: a century old virus with rising importance worldwide

Wheat streak mosaic virus (WSMV) causes wheat streak mosaic, a disease of cereals and grasses that threatens wheat production worldwide. It is a monopartite, positive-sense, single-stranded RNA virus and the type member of the genus Tritimovirus in the family Potyviridae. The only known vector is the wheat curl mite (WCM, Aceria tosichella), recently identified as a species complex of biotypes differing in virus transmission. Low rates of seed transmission have been reported. Infected plants are stunted and have a yellow mosaic of parallel discontinuous streaks on the leaves. In the autumn, WCMs move from WSMV-infected volunteer wheat and other grass hosts to newly emerged wheat and transmit the virus which survives the winter within the plant, and the mites survive as eggs, larvae, nymphs or adults in the crown and leaf sheaths. In the spring/summer, the mites move from the maturing wheat crop to volunteer wheat and other grass hosts and transmit WSMV, and onto newly emerged wheat in the fall to which they transmit the virus, completing the disease cycle. WSMV detection is by enzyme-linked immunosorbent assay (ELISA), reverse transcription-polymerase chain reaction (RT-PCR) or quantitative RT-PCR (RT-qPCR). Three types of WSMV are recognized: A (Mexico), B (Europe, Russia, Asia) and D (USA, Argentina, Brazil, Australia, Turkey, Canada). Resistance genes Wsm1, Wsm2 and Wsm3 have been identified. The most effective, Wsm2, has been introduced into several wheat cultivars. Mitigation of losses caused by WSMV will require enhanced knowledge of the biology of WCM biotypes and WSMV, new or improved virus detection techniques, the development of resistance through traditional and molecular breeding, and the adaptation of cultural management tactics to account for climate change.

Genome sequence of two isolates of Yellow oatgrass mosaic virus, a new grass-infecting Tritimovirus

Complete genome sequences of two Yellow oatgrass mosaic virus (YOgMV) isolates have been determined to be 9,292 nucleotides excluding the 3' polyadenylated tail. The viral RNA encodes a large putative open reading frame (ORF) of a single polyprotein consisting of 3,002 amino acids with typical genome organization of monopartite potyvirids. A small overlapping ORF encoding a pretty interesting Potyviridae ORF of 122 amino acids is found in the P3 cistron of both YOgMV isolates. The nucleotide and amino acid identities between the two YOgMV isolates are 90 and 97 %, respectively. Pairwise comparison of YOgMV putative mature proteins and proteinase cleavage sites with those of representative members of the family Potyviridae indicated that YOgMV is more closely related to members of the genus Tritimovirus. In phylogenetic trees constructed with sequences of putative polyprotein, YOgMV consistently groups with members of the genus Tritimovirus. These results suggest that YOgMV should be classified as a distinct species in the genus Tritimovirus in the family Potyviridae.

Tall oatgrass mosaic virus (TOgMV): a novel member of the genus Tritimovirus infecting Arrhenatherum elatius

A novel tritimovirus of the family Potyviridae was isolated from tall oatgrass, Arrhenatherum elatius, exhibiting mosaic symptoms. The virus, for which the name tall oatgrass mosaic virus (TOgMV) is coined, has a filamentous particle of 720 nm and is associated with pinwheel inclusion bodies characteristic of members of the family Potyviridae. The virus was mechanically transmitted to tall oatgrass seedlings, which subsequently exhibited mosaic symptoms. The experimental host range was limited to a few monocot species. The complete genome sequence of TOgMV was determined to be 9359 nucleotides, excluding the 3' polyadenylated tail. The viral RNA encodes one large putative open reading frame of 3029 amino acids with a genome organization typical of monopartite potyvirids. Pairwise comparison of putative mature proteins and proteinase cleavage sites indicated that TOgMV is most closely related to members of the genus Tritimovirus. Phylogenetic analysis of the complete polyprotein and CP sequences of representative members of the family Potyviridae indicate that TOgMV is a distinct tritimovirus naturally infecting tall oatgrass.

Tritimovirus P1 functions as a suppressor of RNA silencing and an enhancer of disease symptoms

Wheat streak mosaic virus (WSMV) is an eriophyid mite-transmitted virus of the genus Tritimovirus, family Potyviridae. Complete deletion of helper component-proteinase (HC-Pro) has no effect on WSMV virulence or disease synergism, suggesting that a different viral protein suppresses RNA silencing. RNA silencing suppression assays using Nicotiana benthamiana 16C plants expressing GFP were conducted with each WSMV protein; only P1 suppressed RNA silencing. Accumulation of GFP siRNAs was markedly reduced in leaves infiltrated with WSMV P1 at both 3 and 6 days post infiltration relative to WSMV HC-Pro and the empty vector control. On the other hand, helper component-proteinase (HC-Pro) of two species in the mite-transmitted genus Rymovirus, family Potyviridae was demonstrated to be a suppressor of RNA silencing. Symptom enhancement assays were conducted by inoculating Potato virus X (PVX) onto transgenic N. benthamiana. Symptoms produced by PVX were more severe on transgenic plants expressing WSMV P1 or potyvirus HC-Pro compared to transgenic plants expressing GFP or WSMV HC-Pro.

Efficient and stable expression of GFP through Wheat streak mosaic virus-based vectors in cereal hosts using a range of cleavage sites: formation of dense fluorescent aggregates for sensitive virus tracking

A series of Wheat streak mosaic virus (WSMV)-based expression vectors were developed by engineering a cycle 3 GFP (GFP) cistron between P1 and HC-Pro cistrons with several catalytic/cleavage peptides at the C-terminus of GFP. WSMV-GFP vectors with the Foot-and-mouth disease virus 1D/2A or 2A catalytic peptides cleaved GFP from HC-Pro but expressed GFP inefficiently. WSMV-GFP vectors with homologous NIa-Pro heptapeptide cleavage sites did not release GFP from HC-Pro, but efficiently expressed GFP as dense fluorescent aggregates. However, insertion of one or two spacer amino acids on either side of NIb/CP heptapeptide cleavage site or deletion in HC-Pro cistron improved processing by NIa-Pro. WSMV-GFP vectors were remarkably stable in wheat for seven serial passages and for 120 days postinoculation. Mite transmission efficiencies of WSMV-GFP vectors correlated with the amount of free GFP produced. WSMV-GFP vectors infected the same range of cereal hosts as wild-type virus, and GFP fluorescence was detected in most wheat tissues.

An Amino Acid Deletion in Wheat streak mosaic virus Capsid Protein Distinguishes a Homogeneous Group of European Isolates and Facilitates Their Specific Detection

The tritimovirus Wheat streak mosaic virus (WSMV) is widespread throughout the world and represents a severe threat to cereal crop production. To increase knowledge of genetic diversity of WSMV in Europe, until now scarce, capsid protein (CP) sequences of several Czech, French, Italian, Slovak, and Turkish isolates have been determined. A multiple alignment of CP nucleotide sequences using available WSMV sequences revealed only limited sequence variation among 3 previously sequenced European isolates and the 14 European isolates sequenced in this study. Moreover, these isolates were characterized by an identical 3-nucleotide deletion, resulting in the lack of the Gly₂₇₆₁ codon within the CP region of the polyprotein. The results indicate that this monophyletic group of isolates (designated as WSMV-ΔE) is common and widely dispersed throughout the European continent. The close relationship of WSMV-ΔE isolates implies a single common ancestor and, presumably, subsequent dispersal throughout Europe from a single focus. We developed two simple assays for specific and accurate detection of WSMV-ΔE isolates. First, a conserved ClaI restriction site in the core CP gene sequence unique to WSMV-ΔE isolates was used for restriction fragment length polymorphism analysis of amplified polymerase chain reaction (PCR) products. Second, the conserved and specific codon gap in WSMV-ΔE sequences was used as a target to design specific primers functional in one-step reverse-transcription PCR detection of WSMV-ΔE isolates.

Random mutagenesis of wheat streak mosaic virus HC-Pro: non-infectious interfering mutations in a gene dispensable for systemic infection of plants

Mutations within the HC-Pro coding region of Wheat streak mosaic virus (WSMV) were introduced by misincorporation during PCR and evaluated for phenotype within the context of an infectious clone. Nine synonymous substitutions and 15 of 25 non-synonymous substitutions had no phenotypic effect. Four non-synonymous substitutions, including one that reverted consistently to wild type, resulted in attenuated systemic infection. Six non-synonymous substitutions and one nonsense substitution abolished systemic infectivity. Mutants bearing the GUS reporter gene were evaluated for the ability to establish primary infection foci. All attenuated mutants and two systemic infection-deficient mutants produced localized regions of GUS expression on inoculated leaves 3 days post-inoculation. In vitro assays revealed that mutants able to establish infection foci retained HC-Pro proteinase activity. Among mutants unable to establish infection foci, HC-Pro proteinase activity was retained, reduced or absent. As a complete HC-Pro deletion mutant can infect plants systemically, certain substitutions in this dispensable gene probably prevented infection of WSMV via interference.

Nested deletion analysis of Wheat streak mosaic virus HC-Pro: Mapping of domains affecting polyprotein processing and eriophyid mite transmission

A series of in-frame and nested deletion mutations which progressively removed 5'-proximal sequences of the Wheat streak mosaic virus (WSMV) HC-Pro coding region (1152 nucleotides) was constructed and evaluated for pathogenicity to wheat. WSMV HC-Pro mutants with 5'-proximal deletions of 12 to 720 nucleotides systemically infected wheat. Boundary sequences flanking the deletions were stable and unaltered by passage through plants for all deletion mutants except HCD12 (lacking HC-Pro codons 3-6) that exhibited strong bias for G to A substitution at nucleotide 1190 in HC-Pro codon 2 (aspartic acid to asparagine). HC-Pro mutants with 5'-proximal deletions of up to 720 nucleotides retained autoproteolytic activity in vitro. In contrast, 5'-proximal deletion of 852 nucleotides of the HC-Pro coding region (HCD852) abolished both infectivity and in vitro proteolytic activity, confirming that the proteolytic domain of WSMV HC-Pro resides within the carboxy-terminal third of the protein and includes the cysteine proteinase motif (GYCY) conserved among four genera of the family Potyviridae. Inoculation of wheat with HC-Pro deletion mutants also bearing the GUS reporter gene revealed that HCD852 was unable to establish primary infection foci in inoculated leaves, indicating that processing of the P3 amino-terminus was essential. Deletion of as few as 24 nucleotides of HC-Pro (codons 3-10) eliminated transmission by the eriophyid mite vector Aceria tosichella Keifer. Collectively, these results demonstrated similar organization of proteinase and vector transmission functional domains among divergent HC-Pro homologues encoded by potyviruses and tritimoviruses.

Complete deletion of Wheat streak mosaic virus HC-Pro: a null mutant is viable for systemic infection

A Wheat streak mosaic virus (WSMV) genome lacking HC-Pro was constructed and confirmed by reverse transcription-PCR to systemically infect wheat, oat, and corn. Coupled in vitro transcription/translation reactions indicated that WSMV P1 proteinase cleaved the polyprotein at the P1/P3 junction of the HC-Pro null mutant. The WSMV HC-Pro null mutant was competent for virion formation, but the virus titer was reduced 4.5-fold relative to that of the wild type. Collectively, these results indicate that WSMV HC-Pro is dispensable for replication and movement, two essential processes that are disrupted by point and small-insertion mutations introduced into potyvirus HC-Pro.

An internal RNA element in the P3 cistron of Wheat streak mosaic virus revealed by synonymous mutations that affect both movement and replication

Multiple synonymous substitution mutations in the Wheat streak mosaic virus P3 cistron did not affect translation in vitro but rendered the virus incapable of systemic infection. Multiple synonymous substitutions in the cylindrical inclusion cistron did not alter infectivity or in vitro translation. To assess replication and movement phenotypes, P3 mutations were placed in context with a GUS reporter gene. GUS activity measured in barley protoplasts 36 h post-transfection indicated that mutants with synonymous substitutions in P3 retained the ability to replicate at 22–80 % of wild-type levels. Almost no GUS activity was detected in protoplasts transfected with a P3 frame-shift mutant. Histochemical GUS assays conducted 3 days post-inoculation (p.i.) revealed genomes with multiple synonymous substitutions in P3, which were able to establish infection foci limited to small clusters of cells that increased in size only slightly by 5 days p.i. Infection foci produced by wild-type Wheat streak mosaic virus-expressing GUS were much larger at 3 days p.i. and had coalesced by 5 days p.i. No GUS activity was detected in plants inoculated with the frame-shift mutant bearing GUS. Three of four mutants, each with a single synonymous substitution in the 3′-proximal half of the P3 cistron, were wild-type with respect to systemic infectivity. A model RNA secondary structure obtained for the region was disrupted by the debilitating single mutation but not by the other three single mutations. Collectively, these results identify an internal RNA sequence element in the P3 cistron that affects both replication and movement of the viral genome.

Overview and analysis of the polyprotein cleavage sites in the family Potyviridae

SUMMARY The genomes of plant viruses in the family Potyviridae encode large polyproteins that are cut by virus-encoded proteases into ten mature proteins. Three different types of protease have been identified, each of which cuts at sites with a distinctive sequence pattern. The experimental evidence for this specificity is reviewed and the cleavage site patterns are compiled for all sequenced species within the family. Seven of the nine cleavage sites in each species are cut by the viral NIa-Pro and patterns around these sites are related where possible to the active site-substrate interactions recently deduced following the resolution of the crystal structure of Tobacco etch virus (TEV) NIa-Pro (Phan et al., 2002. J. Biol. Chem. 277, 50564-50572). In particular, a revised series of cleavage sites for Sweet potato mild mottle virus (genus Ipomovirus) is proposed with a conserved His at the P1 position. This is supported by homology modelling studies using the TEV structure as a template. The data also provide a standard to correct the annotation of some other published sequences and to help predict these sites in further virus sequences as they become available. Comprehensive data for all sequences of each virus in the family, together with some summaries, have been made available at http://www.rothamsted.bbsrc.ac.uk/ppi/links/pplinks/potycleavage/index.html.

Plant virus HC-Pro is a determinant of eriophyid mite transmission

The eriophyid mite transmitted Wheat streak mosaic virus (WSMV; genus Tritimovirus, family Potyviridae) shares a common genome organization with aphid transmitted species of the genus Potyvirus. Although both tritimoviruses and potyviruses encode helper component-proteinase (HC-Pro) homologues (required for nonpersistent aphid transmission of potyviruses), sequence conservation is low (amino acid identity, approximately 16%), and a role for HC-Pro in semipersistent transmission of WSMV by the wheat curl mite (Aceria tosichella [Keifer]) has not been investigated. Wheat curl mite transmissibility was abolished by replacement of WSMV HC-Pro with homologues of an aphid transmitted potyvirus (Turnip mosaic virus), a rymovirus (Agropyron mosaic virus) vectored by a different eriophyid mite, or a closely related tritimovirus (Oat necrotic mottle virus; ONMV) with no known vector. In contrast, both WSMV-Sidney 81 and a chimeric WSMV genome bearing HC-Pro of a divergent strain (WSMV-El Batán 3; 86% amino acid sequence identity) were efficiently transmitted by A. tosichella. Replacing portions of WSMV-Sidney 81 HC-Pro with the corresponding regions from ONMV showed that determinants of wheat curl mite transmission map to the 5'-proximal half of HC-Pro. WSMV genomes bearing HC-Pro of heterologous species retained the ability to form virions, indicating that loss of vector transmissibility was not a result of failure to encapsidate. Although titer in systemically infected leaves was reduced for all chimeric genomes relative to WSMV-Sidney 81, titer was not correlated with loss of vector transmissibility. Collectively, these results demonstrate for the first time that HC-Pro is required for virus transmission by a vector other than aphids.

Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Eurasia

The genetic structure of populations of Turnip mosaic virus in Eurasia was assessed by making host range and gene sequence comparisons of 142 isolates. Most isolates collected in West Eurasia infected Brassica plants whereas those from East Eurasia infected both Brassica and Raphanus plants. Analyses of recombination sites (RSs) in five regions of the genome (one third of the full sequence) showed that the protein 1 (P1 gene) had recombined more frequently than the other gene regions in both subpopulations, but that the RSs were located in different parts of the genomes of the subpopulations. Estimates of nucleotide diversity showed that the West Eurasian subpopulation was more diverse than the East Eurasian subpopulation, but the Asian-BR group of the genes from the latter subpopulation had a greater nonsynonymous/synonymous substitution ratio, especially in the P1, viral genome-linked protein (VPg) and nuclear inclusion a proteinase (NIa-Pro) genes. These subpopulations seem to have evolved independently from the ancestral European population, and their genetic structure probably reflects founder effects.

Inter- and intralineage recombinants are common in natural populations of Turnip mosaic virus

A recombination map of the genome of Turnip mosaic virus (TuMV) was assembled using data from 19 complete genomic sequences, previously reported, and a composite sample of three regions of the genome, one-third in total, of a representative Asia-wide collection of 70 isolates. Thus, a total of 89 isolates of worldwide origin was analysed for recombinants. Eighteen recombination sites were found spaced throughout the 5′ two-thirds of the genome, but there were only two in the 3′ one-third; thus, 24 and 35 % of the P1 and NIa-VPg gene sequences examined were recombinants, whereas only 1 % of the corresponding NIa-Pro and CP gene sequences were recombinants. Recombinants with parents from the same or from different lineages were found, and some recombination sites characterized particular lineages. Most of the strain BR recombinants belonged to the Asian-BR group, as defined previously, and it was concluded that this lineage resulted from a recent migration, whereas many of the strain B recombinants from Asia fell into the world-B group. Again, a large proportion of isolates in this group were recombinants. Some recombination sites were found only in particular lineages, and hence seemed more likely to be the surviving progeny from single recombinational events, rather than the progeny of multiple events occurring at recombination hotspots. It seems that the presence of recombination sites, as well as sequence similarities, may be used to trace the migration and evolution of TuMV.

Functional replacement of Wheat streak mosaic virus HC-Pro with the corresponding cistron from a diverse array of viruses in the family Potyviridae

Helper component-proteinase (HC-Pro) of Wheat streak mosaic virus strain Sidney 81 (WSMV-Sidney 81) was systematically replaced with the corresponding cistron derived from four strains of WSMV (Type, TK1, CZ, and El Batán 3), the tritimovirus Oat necrotic mottle virus (ONMV), the rymoviruses Agropyron mosaic virus (AgMV) and Hordeum mosaic virus (HoMV), or the potyviruses Tobacco etch virus (TEV) and Turnip mosaic virus (TuMV). These HC-Pro proteins varied in amino acid sequence identity shared with HC-Pro of WSMV-Sidney 81 from high (strains of WSMV at approximately 86-99%) to moderate (ONMV at 70%) to low (rymoviruses and potyviruses at approximately 15-17%). Surprisingly, all chimeric viral genomes examined were capable of systemic infection of wheat upon inoculation with RNA transcripts produced in vitro. HC-Pro replacements derived from tritimoviruses did not alter host range relative to WSMV-Sidney 81, as each of these chimeric viruses was able to systemically infect wheat, oat, and corn line SDp2. These results indicate that differences in host range among tritimoviruses, including the inability of ONMV to infect wheat or the inability of WSMV strains Type and El Batán 3 to infect SDp2 corn, are not determined by HC-Pro. In contrast, all chimeric viruses bearing HC-Pro replacements derived from rymoviruses or potyviruses were unable to infect SDp2 corn and oat. Collectively, these results indicate that HC-Pro from distantly related virus species of the family Potyviridae are competent to provide WSMV-Sidney 81 with all functions necessary for infection of a permissive host (wheat) and that virus-host interactions required for systemic infection of oat and SDp2 corn are more stringent. Changes in symptom severity or mechanical transmission efficiency observed for some chimeric viruses further suggest that HC-Pro affects virulence in WSMV.

Evolution of Wheat streak mosaic virus: dynamics of population growth within plants may explain limited variation

Like many other plant RNA viruses, Wheat streak mosaic virus (WSMV) sequence diversity within and among infected plants is low given the large number of virions produced. This may be explained by considering aspects of plant virus life history. Intracellular replication of RNA viruses is predominately linear, not exponential, which means that the rate at which mutations accumulate also is linear. Bottlenecks during systemic movement further limit diversity. Analysis of mixed infections with two WSMV isolates suggests that about four viral genomes participate in systemic invasion of each tiller. Low effective population size increases the role of stochastic processes on dynamics of plant virus population genetics and evolution. Despite low pair-wise diversity among isolates, the number of polymorphic sites within the U.S. population is about the same as between divergent strains or a sister species. Characteristics of polymorphism in the WSMV coat protein gene suggest that most variation appears neutral.

Patterns of polymorphism in wheat streak mosaic virus: sequence space explored by a clade of closely related viral genotypes rivals that between the most divergent strains

Nucleotide (nt) sequence polymorphism within a collection of Wheat streak mosaic virus (WSMV) isolates was examined. An approximately 1267-nt region encompassing the coat protein (CP) cistron and flanking sequences was amplified by reverse transcription-polymerase chain reaction (RT-PCR) for each of 49 isolates not previously sequenced. Consensus sequences were compiled for each isolate based on sequences derived from three clones per RT-PCR product. Among 59 consensus sequences examined, only two were identical. Clades A-C contained divergent isolates from Mexico (Clade A); the Czech Republic, Hungary, and Russia (Clade B); and Iran (Clade C). Fifty-four closely related consensus sequences of isolates from the U.S. (51 sequences), Canada (1 sequence), and Turkey (2 sequences) comprised Clade D. Pair-wise nt divergence between two of the most distantly related sequences (Sidney 81 of Clade D and El Batán 3 of Clade A) was 20%, representing over half of the variable sites (34.1%) in the entire WSMV data set. Maximum pairwise nt divergence within Clade D was 3.6%, yet the proportion of all variable sites within Clade D (21.4%) was similar to that of the Sidney 81-El Batán 3 pair. Patterns of polymorphism within Clade D and the Sidney 81-El Batán 3 pair were remarkably similar with respect to synonymous, nonsynonymous, and noncoding substitutions, as were the proportions of substitutions as a function of nt position within codons. The majority of substitutions within Clade D were synonymous and randomly distributed throughout the coding region examined, whereas nonsynonymous substitutions exhibited a clumped distribution and mostly occurred within the 5'-proximal portion of the CP cistron. Because over half of the polymorphic sites within Clade D were of allele size class 1, the isolates appear to be evolving independently and in a nondeterministic manner, within the constraints of selection. These results indicate that Clade D has undergone substantial and, most likely, recent divergence with the majority of consensus sequence substitutions potentially neutral with respect to fitness. An estimate of evolution rate suggests that the present diversity within the U.S. population arose in about a century, a timeframe corresponding to the establishment of wheat monoculture in the Great Plains.