Plant viruses, like all other viruses, are obligate intracellular parasites that do not have the molecular machinery to replicate without the host. The plant viruses are defined as viruses pathogenic to higher plants. While this article does not intend to list all plant viruses, it discusses some important viruses as well as their uses in plant molecular biology.
After the initial discovery of the ‘viral concept’ there was need to classify any other known viral diseases based on the mode of transmission even though microscopic observation proved fruitless. In 1939 Holmes published a classification list of 129 plant viruses. This was expanded and in 1999 there were 977 officially recognized, and some provisional, plant virus species.
The purification (crystallization) of the TMV was first performed by Wendell Stanley, who published his findings in 1935, although he did not determine that the RNA was the infectious material. However, he received the Nobel Prize in Chemistry in 1946. In the 1950s a discovery by two labs simultaneously proved that the purified RNA of the TMV was infectious which reinforced the argument. The RNA was carrying genetic information to code for the production of new infectious particles.
More recently virus research has been focused on understanding the genetics and molecular biology of plant virus genomes, with a particular interest in determining how the virus can replicate, move, and infect plants. Understanding the virus genetics and protein functions has been used to explore the potential for commercial use by biotechnology companies. In particular, viral-derived sequences have been used to provide an understanding of novel forms of resistance. The recent boom in technology allowing humans to manipulate plant viruses may provide new strategies for production of value-added proteins in plants.
Viruses are very small and can only be observed with an electron microscope. The structure of a virus is given by its coat of proteins, which surround the viral genome. Assembly of viral particles takes place spontaneously.
Over 50% of known plant viruses are rod shaped (flexuous or rigid). The length of the particle is normally dependent on the genome but it is usually between 300–500 nm with a diameter of 15–20 nm. Protein subunits can be placed around the circumference of a circle to form a disc. In the presence of the viral genome, the discs are stacked, then a tube is created with room for the nucleic acid genome in the middle.
The second most common structure amongst plant viruses are isometric particles. They are 40–50 nm in diameter. In cases when there is only a single coat protein, the basic structure consists of 60 T subunits, where T is an integer. Some viruses may have 2 coat proteins are the formation of the particle is analogous to a football.
It implies direct transfer of sap by contact of and wounded plant with a healthy one. Such process occurs during agricultural practices by tools, hands, or by animal feeding on the plant. Generally TMV, potato viruses and cucumber mosaic viruses are transmitted via sap.
Plant viruses need to be transmitted by a vector, most often insects such as leafhoppers. One class of viruses, the Rhabdoviridae, have been proposed to actually be insect viruses that have evolved to replicate in plants. The chosen insect vector of a plant virus will often be the determining factor in that virus' host range: it can only infect plants that the insect vector feeds upon. This was shown in part when the old world white fly made it to the USA, where it transferred many plant viruses onto new hosts.
Depending on the way they are transmitted, plant viruses are classified as non-persistent, semi-persistent and persistent. In non-persistent transmission, viruses become attached to the distal tip of the stylet of the insect and on the next plant it feeds on, it inoculates it with the virus. Semi-persistent viral transmission involves the virus entering the foregut of the insect.
Those viruses that manage to pass through the gut into the haemolymph and then to the salivary glands are known as persistent. There are two sub-classes of persistent viruses: propergative and circulative. Propergative viruses are able to replicate in both the plant and the insect (and may have originally been insect viruses), whereas circulative can not.
Many plant viruses encode within their genome polypeptides with domains essential for transmission by insects. In non-persistent and semi-persistent viruses, these domains are in the coat protein and another protein known as the helper component. A bridging hypothesis has been proposed to explain how these proteins aid in insect-mediated viral transmission. The helper component will bind to the specific domain of the coat protein, and then the insect mouthparts — creating a bridge.
In persistent propagative viruses, such as tomato spotted wilt virus (TSWV), there is often a lipid coat surrounding the proteins that is not seen in the other classes of plant viruses. In the case of TSWV, 2 viral proteins are expressed in this lipid envelope. It has been proposed that the viruses bind via these proteins and are then taken into the insect cell by receptor-mediated endocytosis.
Soil-borne nematodes also have been shown to transmit viruses. They acquire and transmit them by feeding on infected roots. Viruses can be transmitted by non-persistently and persistently, but there is no evidence of viruses being able to replicate in nematodes.
A number of viral genera are transmitted, both persistently and non-persistently, by soil borne zoosporic protozoa. These protozoa are not phytopathogenic themselves, but parasitic. Transmission of the virus takes place when they become associated with the plant roots.
An example is Polymyxa graminis, which has been shown to transmit a plant viral diseases in ceral crops.
Plant virus transmission from generation to generation occurs in about 20% of plant viruses. When viruses are transmitted by seeds, the seed is infected in the generative cells and the virus is maintained in the germ cells and sometimes, but less often, in the seed coat. When the growth and development of plants is delayed because of situations like unfavourable weather, there is an increase in the amount of virus infections in seeds. There does not seem to be a correlation between the location of the seed on the plant and its chances of being infected.  Little is known about the mechanisms involved in the transmission of plant viruses via seeds, although it is known that it is environmentally influenced and that seed transmission occurs because of a direct invasion of the embryo via the ovule or by an indirect route with an attack on the embryo mediated by infected gametes.   These processes can occur concurrently or separately depending on the host plant. It is unknown how the virus is able to directly invade and cross the embryo and boundary between the parental and progeny generations in the ovule.  Many plants species can be infected through seeds including but not limited to the families Leguminoseae, Solanacease, Compositae, Rosaceae, Curcurbitaceae, Gramineae. 
As mentioned above, 90% of plant viruses have genomes that consist of single stranded RNA, meaning that they are in the same sense orientation as messenger RNA. Viruses use the plant ribosomes to produce the 4-10 proteins encoded by their genome. However, since all of the proteins are encoded on a single strand (that is, they are polycistronic) this will mean that the ribosome will either only produce one protein, as it will terminate translation at the first stop codon or that a polyprotein will be produced. Plant viruses have had to evolve special techniques to allow the production of viral proteins by plant cells.
In order for translation to occur eukaryotic mRNAs require a 5' Cap structure. This means that viruses must also have one. This normally consists of 7MeGpppN where N is normally adenine or guanine. The viruses encode a protein, normally a replicase, with a methyltransferase activity to allow this.
Some viruses are cap-snatchers. During this process, a 7mG-capped host mRNA is recruited by the viral transcriptase complex and subsequently cleaved by a virally encoded endonuclease. The resulting capped leader RNA is used to prime transcription on the viral genome.
However some plant viruses do not use cap, yet translate efficiently due to cap-independent translation enhancers present in 5' and 3' untranslated regions of viral mRNA
Some viruses use the production of sub-genomic RNAs to ensure the translation of all proteins within their genomes. In this process the first protein encoded on the genome, and this the first to be translated, is a replicase. This protein will act of the rest of the genome producing negative strand sub-genomic RNAs then act upon these to form positive strand sub-genomic RNAs that are essentially mRNAs ready for translation.
Some viral families, such as the Bromoviridae instead opt to have multi-partite genomes, genomes split between multiple viral particles. For infection to occur, the plant must be infected with all particles across the genome. For instance Brome mosaic virus has a genome split between 3 viral particles, and all 3 particles with the different RNAs are required for infection to take place.
This stratergy is adopted by viral genra such as the Potyviridae and Tymovirus. The ribosome translates a single protein from the viral genome. Within the polyprotein is an ezyme with proteinase function that is able cleave the polyprotein into the various single proteins or just cleave away the replicase, which can then produce sub-genomic RNAs.
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