Genus: Nucleorhabdovirus


Genus: Nucleorhabdovirus

Distinguishing features

Two of the four genera of plant rhabdovirus (Nucleorhabdovirus and Cytorhabdovirus) were established based on the sites of virus replication and morphogenesis. Nucleorhabdoviruses replicate and mature in the nucleus of infected cells. Based on well-supported Maximum Likelihood trees inferred from complete L sequences, nucleorhabdoviruses cluster with members of the genus Dichorhavirus which also appear to replicate in the nucleus of plant cells. Nucleorhabdoviruses have a non-segmented RNA genome which distinguishes them from dichorhaviruses for which the genome is segmented.

Virion

Morphology

Enveloped virions are bacilliform, 45–100 nm in diameter and 130–300 nm long (Jackson et al., 2005, Goodin and Jackson 2002).

Physicochemical and physical properties

Virus particles sediment at 800–1000 S in sucrose gradients and the buoyant density of virions is 1.18 g cm−3 in isopycnic sucrose gradients (Goodin and Jackson 2002). 

Nucleic acid

The negative-sense, single-stranded RNA genome of 12.0–14.0 kb is unsegmented. Six to seven mRNAs, one for each of the encoded proteins identified in infected plants.

Proteins

N, P, M, G and L represent the five canonical rhabdovirus structural proteins. Sonchus yellow net virus (SYNV) P and rice yellow stunt virus (RYSV) P6 have RNA silencing suppressor activity (Jackson et al., 2005, Guo et al., 2013). The RYSV P3 protein has been shown to have cell-to-cell movement activity in a heterologous virus trans-complementation assay (Huang et al., 2005). The SYNV P3 protein has been shown by reverse genetics to facilitate cell-to-cell movement between plant cells (Wang et al., 2015); the P3 protein of other nucleorhabdoviruses and the Y proteins of potato yellow dwarf virus (PYDV) and eggplant mottled dwarf virus (EMDV) are thought to be movement proteins (Jackson et al., 2005, Bandyopadhyay et al., 2010, Pappi et al., 2013).

SYNV N and P contain nuclear localisation sequences (NLS, or a karyophillic domain) and are independently imported into the nucleus, where they associate and move to a sub-nuclear location (Goodin et al., 2001). A distinct nuclear polymerase complex composed of N, P and L is present in the nuclei of infected cells (Martins et al., 1998, Wagner and Jackson 1997, Wagner et al., 1996). PYDV M can induce the intranuclear accumulation of the inner nuclear membrane in the absence of any other viral protein (Bandyopadhyay et al., 2010). Protein interaction studies for PYDV in live plants have identified binary interactions between N:N, N:P, N:M, M:M, M:Y, M:G, G:G and Y:Y (Bandyopadhyay et al., 2010).

Lipids

The lipoprotein envelope derived from the host plant or insect vector (Jackson et al., 2005). Lipid composition is unknown.

Genome organisation and replication

The PYDV genome (12.9 kb) contains seven genes in the order 3′-N-X-P-Y-M-G-L-5′, which likely encode the nucleocapsid protein (N), phosphoprotein (polymerase cofactor) (P), movement protein (Y), matrix protein (M), glycoprotein (G) and RNA-dependent RNA polymerase (L), respectively (Figure 1.Nucleorhabdovirus). The function of the protein encoded in the X gene has not been determined. The EMDV genome organisation resembles that of PYDV. The PYDV coding sequences are flanked by a 3′-leader RNA of 149 nt and a 5′-trailer RNA of 97 nt, and genes are separated by conserved intergenic “gene junction” regions which are similar in length and have sequence relatedness with those of other rhabdoviruses. 

The SYNV genome (13.7 kb) contains six genes in the order 3′-N-P-sc4-M-G-L-5′, lacking a gene encoding an X protein. The Y gene equivalent (sc4 or P3) has been shown to encode a protein involved in cell-to-cell movement. The 144 nt 3′-leader sequence is transcribed to produce a polyadenylated leader RNA, which localizes in the cytoplasm. The 5′-trailer RNA of 160 nt has extensive terminal complementarity with the leader sequence.

The RYSV genome (14.0 kb) has a gene order similar to that of SYNV, except for the presence of an additional small gene between the G gene and the L gene, which encodes a virion-associated protein. The genomes of maize mosaic virus (MMV), maize Iranian mosaic virus (MIMV) and taro vein chlorosis virus (TaVCV) are approximately 12.0–12.4 kb with a gene order similar to that of SYNV. The maize fine streak virus (MFSV) genome (13.8 kb) has a gene order similar to that of SYNV, but with an additional ORF of unknown function between the P gene and the M gene.

Figure 1.Nucleorhabdovirus. Schematic representation of nucleorhabdovirus genome organisations. N, P, M, G and L represent ORFs encoding the structural proteins. ORFs encoding putative cell-to-cell movement proteins are highlighted (blue).  Other ORFs encode putative accessory proteins of unknown function, including small homologous proteins located between the N gene and P gene of potato yellow dwarf virus and eggplant mottled dwarf virus (orange).

Nucleorhabdoviruses replicate in the nucleus of plant cells, which become greatly enlarged and develop large granular nuclear inclusions that are thought to be sites of virus replication (Jackson et al., 2005). In situ hybridisation analyses have shown that the viral genomic and anti-genomic RNAs of SYNV are highly expressed in subnuclear foci (Jackson et al., 2005, Martins et al., 1998) and immunofluorescence studies have shown that the ribonucleoprotein (RNP) components N, P and L also accumulate in subnuclear foci (Martins et al., 1998, Deng et al., 2007). Viral proteins are synthesised from discrete polyadenylated mRNAs and reporter gene analyses have shown that they accumulate in subnuclear foci (Martins et al., 1998, Wagner and Jackson 1997). Virus morphogenesis occurs at the inner nuclear membrane and enveloped virus particles accumulate in perinuclear spaces (Jackson et al., 2005, Martins et al., 1998). In protoplasts treated with the glycosylation inhibitor tunicamycin, morphogenesis is interrupted and nucleocapsids accumulate in the nucleoplasm (Jones and Jackson 1990). 

Biology

A wide variety of monocot and dicot plant species are susceptible to nucleorhabdoviruses although each virus usually has a restricted host range (Jackson et al., 2005, Goodin and Jackson 2002). Nucleorhabdoviruses are transmitted by leafhoppers (MFSV, RYSV, EMDV, PYDV), planthoppers (MMV, MIMV) or aphids (SYNV, sowthistle yellow vein virus (SYVV)). Some viruses are also transmitted during vegetative propagation, and some can also be transmitted mechanically from infected sap. In all carefully examined cases, viruses replicate in cells of the insect vector as well as in the plant host (Jackson et al., 2005).

Species demarcation criteria

Viruses assigned to different species within the genus Nucleorhabdovirus have several of the following characteristics: A) minimum nucleotide sequence divergence of 50 % in cognate genes; B) occupy different ecological niches as evidenced by differences in hosts and/or arthropod vectors; and C) can be clearly distinguished in serological tests or by nucleic acid hybridisation.

Nucleorhabdovirus species are primarily differentiated by plant host range and vector specificity of the virus. Nucleic acid hybridisation has been used to provide confirmation of identification and serological criteria have enabled verification of common viruses that infect different hosts. However, no virus strains have been defined unambiguously using serology. The complete genome nucleotide sequences are available for 9 of 10 viruses currently assigned to the genus (all except SYVV). RT-PCR-based assays and fluorescent viral protein localisation have proven to be useful tools for species demarcation. Hybridisation using cloned probes and RT-PCR has been used to verify viruses within the genus. 

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus abbreviationIsolate abbreviation
Datura yellow vein nucleorhabdovirusdatura yellow vein virus KM823531NC_028231Complete coding genomeDYVV
Eggplant mottled dwarf nucleorhabdoviruseggplant mottled dwarf virus AgapanthusKJ082087NC_025389Complete coding genomeEMDV
Maize fine streak nucleorhabdovirusmaize fine streak virus AY618417NC_005974Complete genomeMSFV
Maize Iranian mosaic nucleorhabdovirusmaize Iranian mosaic virus FarsMF102281NC_036390Complete coding genomeMIMV
Maize mosaic nucleorhabdovirusmaize mosaic virus AY618418NC_005975Complete coding genomeMMV
Potato yellow dwarf nucleorhabdoviruspotato yellow dwarf virus SYDVGU734660NC_016136Complete genomePYDV
Rice yellow stunt nucleorhabdovirusrice yellow stunt virus AB011257NC_003746Complete genomeRYSV
Sonchus yellow net nucleorhabdovirussonchus yellow net virus L32603NC_001615Complete genomeSYNV
Sowthistle yellow vein nucleorhabdovirussowthistle yellow vein virus No entry in GenbankSYVV
Taro vein chlorosis nucleorhabdovirustaro vein chlorosis virus FijiAY674964NC_006942Complete genomeTaVCV

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.

Derivation of names

Nucleorhabdovirusfrom the nuclear localisation of virus replication complexes (nucleo: from Latin nux,nucis, “nut”).

Related, Unclassified Viruses

Virus name

Accession number

Virus abbreviation

cereal chlorotic mottle virus

not available

CCMoV

cynodon rhabdovirus

EU650683*

CRV

Physostegia chlorotic mottle virus

KX636164

PhCMoV

sorghum stunt mosaic virus

not available

SSMV

wheat yellow striate virus

MG604920

WYSV

* Coding region sequence incomplete
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.