Genome activation by raspberry bushy dwarf virus coat protein

Genetic Characterization of Raspberry Bushy Dwarf Virus Isolated from Red Raspberry in Kazakhstan

Raspberry bushy dwarf virus (RBDV) is an economically significant pathogen of raspberry and grapevine, and it has also been found in cherry. Most of the currently available RBDV sequences are from European raspberry isolates. This study aimed to sequence genomic RNA2 of both cultivated and wild raspberry in Kazakhstan and compare them to investigate their genetic diversity and phylogenetic relationships, as well as to predict their protein structure. Phylogenetic and population diversity analyses were performed on all available RBDV RNA2, MP and CP sequences. Nine of the isolates investigated in this study formed a new, well-supported clade, while the wild isolates clustered with the European isolates. Predicted protein structure analysis revealed two regions that differed between α- and β-structures among the isolates. For the first time, the genetic composition of Kazakhstani raspberry viruses has been characterized.

The 1b gene of raspberry bushy dwarf virus is a virulence component that facilitates systemic virus infection in plants

A product translated from the 1b gene of raspberry bushy dwarf virus (RBDV) was specifically detected in RBDV-infected Nicotiana benthamiana plants by immunoblot analysis. To analyze the effects of the 1b gene on virus infection in host plants, an RBDV deletion mutant virus (RB∆1bstop), which is unable to express the 1b gene, was constructed and inoculated to N. benthamiana plants. The results showed that accumulation of the virus genomic (g) RNAs 1 and 2 decreased in inoculated leaves, and that systemic virus spread was delayed compared with wild-type RBDV. In contrast, accumulation of the viral gRNAs 1 and 2 was elevated in RB∆1bstop-infected leaf tissues during ectopic expression of the 1b gene. Furthermore, we found that the 1b has weak RNA silencing suppressor activity.

Blackcurrant Leaf Chlorosis Associated Virus: Evidence of the Presence of Circular RNA during Infections

Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next-generation sequencing (NGS) and a new and distinct species in the genus Idaeovirus was proposed. Analysis of NGS-derived paired-end reads revealed the existence of bridge reads encompassing the 3′-terminus and 5′-terminus of RNA-2 or RNA-3 of BCLCaV. The full RNA-2 or RNA-3 could be amplified using outward facing or abutting primers; also, RNA-2/RNA-3 could be detected even after three consecutive RNase R enzyme treatments, with denaturation at 95 °C preceding each digestion. Evidence was obtained indicating that there are circular forms of BCLCaV RNA-2 and RNA-3.

Identification and characterization of privet leaf blotch-associated virus, a novel idaeovirus

A novel virus has been identified by next-generation sequencing (NGS) in privet (Ligustrum japonicum L.) affected by a graft-transmissible disease characterized by leaf blotch symptoms resembling infectious variegation, a virus-like privet disease with an unclear aetiology. This virus, which has been tentatively named 'privet leaf blotch-associated virus' (PrLBaV), was absent in non-symptomatic privet plants, as revealed by NGS and reverse transcription-polymerase chain reaction (RT-PCR). Molecular characterization of PrLBaV showed that it has a segmented genome composed of two positive single-stranded RNAs, one of which (RNA1) is monocistronic and codes for the viral replicase, whereas the other (RNA2) contains two open reading frames (ORFs), ORF2a and ORF2b, coding for the putative movement (p38) and coat (p30) proteins, respectively. ORF2b is very probably expressed through a subgenomic RNA starting with six nucleotides (AUAUCU) that closely resemble those found in the 5'-terminal end of genomic RNA1 and RNA2 (AUAUUU and AUAUAU, respectively). The molecular signatures identified in the PrLBaV RNAs and proteins resemble those of Raspberry bushy dwarf virus (RBDV), currently the only member of the genus Idaeovirus. These data, together with phylogenetic analyses, are consistent with the proposal of considering PrLBaV as a representative of the second species in the genus Idaeovirus. Transient expression of a recombinant PrLBaV p38 fused to green fluorescent protein in leaves of Nicotiana benthamiana, coupled with confocal laser scanning microscopy assays, showed that it localizes at cell plasmodesmata, strongly supporting its involvement in viral movement/trafficking and providing the first functional characterization of an idaeovirus encoded protein.

Genetic characterization of Blueberry necrotic ring blotch virus, a novel RNA virus with unique genetic features

A new disorder was observed on southern highbush blueberries in several south-eastern states in the USA. Symptoms included irregularly shaped circular spots or blotches with green centres on the upper and lower surfaces of leaves. Double-stranded RNA was extracted from symptomatic leaves suggesting the presence of virus(es) possibly involved in the disease. Sequencing revealed the presence of a novel RNA virus with a ~14 kb genome divided into four RNA segments. Sequence analyses showed that the virus, for which we propose the name Blueberry necrotic ring blotch virus (BNRBV), possesses protein domains conserved across RNA viruses in the alpha-virus-like supergroup. Phylogenetic inferences using different genes placed BNRBV in a clade that includes the Bromoviridae, the genus Cilevirus (CiLV) and the recently characterized Hibiscus green spot virus (HGSV). Despite the strong genetic relationships found among BNRBV, Cilevirus and HGSV, the genome of BNRBV contains three features that distinguish it significantly from its closest relatives: (i) the presence of two helicase domains with different evolutionary pathways, (ii) the existence of three conserved nucleotide stretches located at the 3' non-coding regions of each RNA segment and (iii) the conservation of terminal nucleotide motifs across each segment. Furthermore, CiLV and HGSV possess poly(A)-tailed bipartite and tripartite genomes, respectively, whereas BNRBV has a quadra-partite genome lacking a poly(A) tail. Based on these genetic features a new genus is proposed for the classification of BNRBV.

The molecular biology of ilarviruses

Ilarviruses were among the first 16 groups of plant viruses approved by ICTV. Like Alfalfa mosaic virus (AMV), bromoviruses, and cucumoviruses they are isometric viruses and possess a single-stranded, tripartite RNA genome. However, unlike these other three groups, ilarviruses were recognized as being recalcitrant subjects for research (their ready lability is reflected in the sigla used to create the group name) and were renowned as unpromising subjects for the production of antisera. However, it was recognized that they shared properties with AMV when the phenomenon of genome activation, in which the coat protein (CP) of the virus is required to be present to initiate infection, was demonstrated to cross group boundaries. The CP of AMV could activate the genome of an ilarvirus and vice versa. Development of the molecular information for ilarviruses lagged behind the knowledge available for the more extensively studied AMV, bromoviruses, and cucumoviruses. In the past 20 years, genomic data for most known ilarviruses have been developed facilitating their detection and allowing the factors involved in the molecular biology of the genus to be investigated. Much information has been obtained using Prunus necrotic ringspot virus and the more extensively studied AMV. A relationship between some ilarviruses and the cucumoviruses has been defined with the recognition that members of both genera encode a 2b protein involved in RNA silencing and long distance viral movement. Here, we present a review of the current knowledge of both the taxonomy and the molecular biology of this genus of agronomically and horticulturally important viruses.