PLANT VIRUSES

PLANT VIRUSES IN THE ICTV Xth report (2016)

• 21 families of plant viruses
• 10 of these common with other hosts
• 9 genera of plant viruses not assigned to any family
Among the 21 families,
• 11 has (+) ssRNA genome
• 7 genera (unassigned to any family) has (+) ssRNA genome
• 2 families (Ophioviridae, Rhabdoviridae) & 1 genus (Emaravirus-family
unassigned) has exclusively (-) ssRNA genome
• 2 families (Metaviridae, Pseudoviridae) have (+)ssRNA-RT
• 2 families (Partiviridae, Reoviridae) have ds RNA genome
• 1 family (Bunyaviridae) & 1 genus (Tenuivirus-family unassigned) each
has (+/-) ssRNA – ambisense genome.
Only 3 families have DNA genome:
• 1 family (Nanoviridae) has (+) ssDNA genome
• 1 family (Geminiviridae) has (+/-) ssDNA – ambisense
• 1 family (Caulimoviridae) has dsDNA-RT genome
 PLANT VIRUSES -- FEATURES
• Plant viruses number ~1000 today (out of 4000 recognized viruses).
• Known for a long time to infect plants and plant viral diseases cause
considerable economic loss.
• Many natural infections are not detrimental, some even beneficial.
• Plants deploy a battery of antiviral defense responses that viruses must
counteract or evade. These include: i) RNA silencing; ii) salicylic acid
mediated responses directed by dominant resistant genes.
• In fact science of virology started with knowledge of TMV, their RNA
genome and their purification into paracrystalline bodies.
• Some plant viruses like TMV can be grown in isolated protoplasts, just as
phages and some animal viruses cultivated in cell suspensions; some of
course need whole plant/tissue preparations for growth.
• Many plant viruses need insect vectors for transmission; some of them can
grow in monolayers of cell cultures derived from aphids, leaf-hoppers or
other insects.
• Recent metagenomic studies reveal the large diversity of virus found in
wild plants.
 PLANT VIRUSES – FEATURES (contd)
VIRION MORPHOLOGY:
 Many with rigid/flexible helical capsid, rod-shaped, filamentous/flexuous/bacilliform.
 Others icosahedra, which may be modified by acquisition of extra capsomeres, e.g.
turnip yellow mosaic virus (TYMV) – an RNA virus.
 Capsids mostly of one type of protein
 No specialized attachment proteins detected
ASSEMBLY OF COAT PROTEIN(CP):
 The CP mRNA of TMV has the same sequence as in the 3′-end of its RNA genome.
 The CP of TMV grows by addition of protomers, in the form of disks, to the ends of
the rods.
 As the rods lengthen, the RNA passes through a channel at its centre and forms a loop
at its growing end.
 In this way, the RNA can easily fit as a spiral into the interior of the helical capsid.
 Length of helical capsid determined by length of nucleic acid, but their width
determined by size, shape & packaging of protein subunits.
 One face of icosahedron can accommodate 3 protomers and hence 20 faces x 3 = 60
protomers
 PLANT VIRUSES – FEATURES (contd).
GENOME
 Normally small with limited coding capacity (usually 4-20 kb encoding 5-10 proteins).

 However, the small genomes are complex and many proteins encoded are multifunctional – e.g. Potyvirus
HC-Pro (protease, aphid transmission factor, suppressor of RNA silencing), Caulimovirus P6 (translational
trans-activator, silencing suppressor, & a facilitator of cell-to-cell movement), Cucumovirus 2b (silencing
suppressor, manipulates jasmonate defense pathway & volatile emissions to render plants more attractive to
insects & also represses ABA-mediated pathway to enhance drought tolerance, Tombusvirus p33 proteins that
regulates various steps of viral RNA replication, acts as an RNA chaperone & remodels intracellular
membranes to form replication complexes. Actuallyp33 protein is known to interact with a minimum of 100
host proteins, with plant lipids and with intracellular membranes).

 Most plant viruses have RNA genomes, though many with DNA genomes are also known, such as the

Caulimoviruses, Geminiviruses.
 Again, the RNA viruses can be single-stranded or double-stranded, (+) or (-) or (+/-) or (+) ssRNA – RT.
 The majority are with (+) ss RNA genome.
 The DNA plant viruses can also have (+) ssDNA, (+/-) ssDNA or dsDNA – RT genome.
 Most plants contain RNA dependent RNA polymerase (RdRp) which helps the viruses to replicate.
 However, some RNA viruses encode their own RNA replicase as in TurnipYellowVirus, Comovirus , TMV etc.
 PLANT VIRUSES – FEATURES – contd.
ENTRY & PROPAGATION INSIDE THE HOST:
 Plant viruses usually gains entry through natural wounds, or through incisions made by insects
(aphids, leaf-hoppers) when they feed on the cell sap.
 Some viruses are transmitted by seeds, tubers, pollen.
 Soil-nematodes also transmit the disease, e.g., Tobacco Ringspot Virus.
 Parasitic fungi can also spread the viruses, e.g. Tobacco Necrosis Virus
 Viruses can remain in the foregut of aphids, infecting plants while they regurgitate during
feeding.
 Several plant viruses such as the wound tumour virus – can multiply in leaf-hopper tissues
before reaching the salivary glands and being inoculated into plants, i.e., it uses both insects
and plants as hosts.
 Once a plant virus gains entry into a host cell, it uncoats its capsid by interacting with
cytoplasmic proteins, possibly aided by divalent cations like Calcium.
 Plant virus infection often produce microscopic inclusions, usually comprising virion
aggregates. [Hexagonal crystalline mass of almost pure TMV virion found in host cells].
 Host cell chloroplasts become abnormal (chlorotic) & degenerate, while new chloroplast
synthesis is inhibited.
 Plant viruses spread inside the host usually through the vascular system.
 They typically form movement proteins (MP), which forms channels through plasmodesmata.
 TMV spreads ~ 1 mm per day in the plant.
Figure 1.Tobamovirus. (Left) Model of particle of tobacco mosaic virus (TMV). Also shown is
the RNA as it is thought to participate in the assembly process.
(Right) Negative contrast electron micrograph of TMV particle stained with uranyl acetate.
[The bar represents 100 nm].
Realm: Riboviria.
Family – Virgaviridae (unassigned to any order)
Genus: Tobamovirus
No. of species: 37 – excepting three, complete genome sequence known for all species
including Tobacco Mosaic Virus
 GENUS TOBAMOVIRUS
DISTINGUISHING FEATURES
• Tobamoviruses are the only members of the family to have a non-segmented genome.
They have a “30K”-like cell-to-cell movement protein, are not vector-transmissible and
when seed transmitted, the embryo is not affected. It is the largest genus in the family
and the literature is extensive. For reviews of diversity and evolution within the genus
see (Gibbs et al., 2015, Lartey et al., 1996, Stobbe et al., 2012).
VIRION
• Morphology
Virions are 18 nm in diameter and have a predominant length of 300–310 nm (Fig
1.Tobamovirus). Structure and assembly of the particles have been reviewed by (
Klug 1999). Shorter virions produced by the encapsidation of subgenome-sized RNA
are usually a minor component of the virion population, although virions of two
species produce an abundant short virion of 32–34 nm. Virions often form large
crystalline arrays visible by light microscopy.
• Physicochemical and physical properties
Virion weighs ~ 39mDa, Mr is 40×10 6. Buoyant density in CsCl is 1.325 g cm −3. S20,w is
194S. Tobamoviruses have thermal inactivation points (10 min) of 90 °C and survive in
plant sap for many years.
 Tobamovirus nucleic acid
 The genome is 6.3–6.6 kb in size wound in a spiral inside the capsid on a
groove formed by protomers.
 An approximately 70 nt long 5′-NTR contains many AAC repeats and few
or no G nucleotides.
 The 0.2–0.4 kb 3′-NTR contains sequences that can be folded into
pseudoknots followed by 3′-terminal sequences that can be folded into a
tRNA-like, amino acid-accepting structure.
 The subgenomic mRNAs transcribed in infected cells also have a 5′-
terminal cap and 3′-tRNA-like structure.
 The encapsidation signal is usually located within the ORF encoding the
MP (Wilson and McNicol 1995) or within the ORF encoding the CP in the
studied isolates of Cucumber green mottle mosaic virus and Sun hemp
mosaic virus.
 Often code for polypeptides with domains essential for insect transmission.
 Mutation rates in RNA plant viruses very high (10⁻⁴ /nt/replication cycle),
due to lack of proof-reading of RdRp, and are also prone to insertions &
deletions.
 However, viral genomes are highly evolved and cannot support many
mutational changes.
 Genome organization and replication
 The single genomic RNA encodes at least FOUR proteins – CP, two replication
proteins and one MP.
 The 124–132 kDa and 181–189 kDa replication proteins are translated directly from
the 5' proximal ORF of the genomic RNA.
 The 124–132 kDa replication protein contains the Mtr and Hel domains.
 The 181–189 kDa replication protein additionally contains the Polymerase domain,
synthesized by occasional readthrough of the leaky termination codon of the 124 –
132 kDa protein encoding ORF.
 The 181–189 kDa replication protein is the only protein required for replication in
single cells, although the 124–132 kDa replication protein is also required for
efficient replication.
 The  downstream ORFs encode the 28–31 kDa MP and 17–18 kDa CP, which are
translated from their respective 3′ co-terminal sgRNAs, both of which contain a 5′
cap (Fig.2. Tobamovirus).
 In the members of some species, the MP ORF overlaps both the 181–189 kDa
protein and the CP ORFs, whereas in other species it does not overlap either ORF or
overlaps one of the ORFs.
 An ORF  that encodes a cysteine-rich protein is located between the 181-189 kDa
and MP ORFs in passion fruit mosaic virus. a tobamovirus isolated from maypop, a
plant classified in the order Malpighiales (Stobbe et al., 2012).
 TOBAMOVIRUS PROTEINS
 Virions contain a single structural protein (17–18 kDa).
 Two nonstructural proteins are expressed directly from the genomic RNA:
• a 124–132 kDa protein terminated by an amber (UAG) stop codon and
• 181–189 kDa protein produced by readthrough of this stop codon, both of which are
required for efficient replication.
• third nonstructural protein (28–31 kDa) is required for cell-to-cell and long-distance
movement and belongs to the “30K”-like cell-to-cell movement proteins.
 The MP is associated with plasmodesmata and has ss nucleic acid binding activity in
vitro.
 The CP is not required for cell-to-cell movement, but has a role in vascular tissue
dependent virus accumulation.
 The replication proteins have also been implicated in virus movement.
 The MP and CP are expressed from individual 3′-co-terminal subgenomic mRNAs.
 The MP is expressed early during infection, whereas the CP is expressed later, and at
higher levels.
 The MP and CP are not required for replication in single cells.
 The N-terminal one-third of the 124–132 kDa protein has similarity with
methyltransferase/guanylyl transferases whereas the C-terminal one-third of the
124–132 kDa protein has similarity with RNA helicases (including an NTP-binding
motif).
 The readthrough domain of the 181–189 kDa protein has motifs common to RdRPs.
MOVEMENT OF TMV THROUGH PLASMODESMATA
Tobamovirus. Genome organization of tobacco mosaic virus (TMV).
Genomic RNA is capped and is template for expression of the 126 and 183 kDa
proteins, the latter derived by a readthrough (RT) of the stop signal for replication.
The 3′ distal movement protein (MP) and capsid protein (CP) ORFs are expressed
from separate 3′ co-terminal subgenomic RNAs. The tRNA structure motif at the
3′-end of the RNA is represented by a dark square.
The MP is 30kDa and CP the smallest, 17.6 kDa. [ICTV X report, 2016]
 RNA replication

RNA replication occurs via several steps:

• (a) synthesis of viral replication proteins by translation of the genomic RNA;
• (b) translation-coupled binding of the replication proteins to a 5'-terminal
region of the genomic RNA;
• (c) recruitment of the genomic RNA by replication proteins onto membranes
and formation of a complex with host proteins TOM1 and ARL8;
• (d) synthesis of complementary (negative-strand) RNA in the complex; and

• (e) synthesis of progeny genomic RNA (Ishibashi and Ishikawa 2016).

 ANTIGENICITY, BIOLOGY & SPECIES DEMARCATION CRITERIA

Antigenicity
• The virions act as strong immunogens and members of different species are serologically
distinct.
Biology
• Most species have moderate to wide host ranges under experimental conditions, although in
nature host ranges are usually quite narrow.
• The viruses are found in all parts of host plants.
• Transmission occurs without the help of vectors by contact between plants and sometimes
by seed, although this occurs in the absence of infection of the embryo. 
Species demarcation criteria
Many tobamoviruses that were historically designated as strains of tobacco mosaic virus are
now defined as separate species based on nucleotide sequence data.
The criteria demarcating species in the genus are:
• Sequence similarity: >90% whole genome nt sequence identity is considered to characterize
strains of the same species.
Most of the sequenced tobamoviruses of different species have considerably less than 90%
sequence identity.
• Host range: however many of these viruses have wider and more overlapping host ranges in
experimental rather than natural situations
• Antigenic relationships between the CPs 
TOBAMOVIRUSES HAVE PROBABLY CO-
DIVERGED WITH THEIR
EUDICOTYLEDONOUS HOSTS FOR AT
LEAST 110 MILLION YEARS.
[Gibbs AJ et al, Virus Evol. 2015 Dec 16;1(1)]

TOBAMOVIRUSES SERVE AS MODELS

FOR THE STUDY OF VIRUS EVOLUTION.
[Fraile A, García-Arenal F. Adv Virus Res. 2018;102:89-117].
 Abbreviations
AIDS : Acquired Immune Deficiency Syndrome
CP : capsid/coat protein (unless otherwise defined)
CPE : cytopathic effect
DI : defective interfering
gRNA: genomic RNA
HE: hemagglutinin-esterase
HI: hemagglutination inhibition
IRES: internal ribosome entry site
MP: movement protein
N: nucleoprotein
NC: nucleocapsid
Rep: replication associated protein
RF: replicative form
RI: replicative intermediate
RNP: ribonucleoprotein
RT: reverse transcriptase
sgRNA: subgenomic RNA
(+) strand RNA: positive strand RNA (mRNA sense)
(-) strand RNA: negative strand RNA (non-mRNA sense)
T (e.g. T3): triangulation number
VPg: genome-linked protein