Editing Plant virus (section)

== Translation of plant viral proteins ==

[[File:Fpls-09-00666-g002.jpg|thumb|Polyprotein processing is used by 45% of plant viruses. Plant virus families that produce [[Protein|polyproteins]], their genomes, and colored triangles indicating [[Proteolysis|self-cleavage]] sites.<ref name=":0"/>]]

75% of plant viruses have genomes that consist of single stranded RNA (ssRNA). 65% of plant viruses have +ssRNA, meaning that they are in the same sense orientation as [[messenger RNA]] but 10% have -ssRNA, meaning they must be converted to +ssRNA before they can be translated. 5% are double stranded RNA and so can be immediately translated as +ssRNA viruses. 3% require a [[reverse transcriptase]] enzyme to convert between RNA and DNA. 17% of plant viruses are ssDNA and very few are dsDNA, in contrast a quarter of animal viruses are dsDNA and three-quarters of [[bacteriophage]] are dsDNA.<ref name="Hull 2001">{{Cite journal |last=Hull |first=Robert |date=November 2001 |title=Classifying reverse transcribing elements: a proposal and a challenge to the ICTV |journal=Archives of Virology |volume=146 |issue=11 |pages=2255–2261 |doi=10.1007/s007050170036 |pmid=11765927 |s2cid=23269106 |doi-access=free}}</ref> Viruses use the plant [[ribosomes]] to produce the 4-10 proteins encoded by their genome. However, since many 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 cell]]s.

=== 5' Cap ===

For [[Translation (biology)|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 <sup>7m</sup>G-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.<ref>{{cite journal |last1=Duijsings |display-authors=etal |year=2001|title=''In vivo'' analysis of the TSWV cap-snatching mechanism: single base complementarity and primer length requirements |journal=The EMBO Journal |volume=20 |issue=10|pages=2545–2552 |doi=10.1093/emboj/20.10.2545 |pmid=11350944 |pmc=125463}}</ref>

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.<ref>{{cite journal |last1=Kneller |first1=Elizabeth L. Pettit |last2=Rakotondrafara |first2=Aurélie M. |last3=Miller |first3=W. Allen |title=Cap-independent translation of plant viral RNAs |journal=Virus Research |date=July 2006 |volume=119 |issue=1 |pages=63–75 |doi=10.1016/j.virusres.2005.10.010 |pmid=16360925 |pmc=1880899}}</ref>

=== Readthrough ===

Some viruses (e.g. [[tobacco mosaic virus]] (TMV)) have RNA sequences that contain a "leaky" stop codon. In TMV 95% of the time the host ribosome will terminate the synthesis of the polypeptide at this codon but the rest of the time it continues past it. This means that 5% of the proteins produced are larger than and different from the others normally produced, which is a form of [[translational regulation]]. In TMV, this extra sequence of polypeptide is an [[RNA polymerase]] that replicates its genome.

=== Production of sub-genomic RNAs ===

Some viruses use the production of [[subgenomic]] RNAs to ensure the translation of all proteins within their genomes. In this process the first protein encoded on the genome, and is the first to be translated, is a [[RNA replicase|replicase]]. This protein will act on 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.

=== Segmented genomes ===

Some viral families, such as the ''[[Bromoviridae]]'' instead opt to have [[multipartite]] 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.

=== Polyprotein processing ===

Polyprotein processing is adopted by 45% of plant viruses, such as the [[Potyviridae]] and [[Tymoviridae]].<ref name=":0">{{Cite journal |last1=Rodamilans |first1=Bernardo |last2=Shan |first2=Hongying |last3=Pasin |first3=Fabio |last4=García |first4=Juan Antonio |date=2018 |title=Plant Viral Proteases: Beyond the Role of Peptide Cutters |journal=Frontiers in Plant Science |volume=9 |page=666 |doi=10.3389/fpls.2018.00666 |pmid=29868107 |pmc=5967125 |doi-access=free}}</ref> The ribosome translates a single protein from the viral genome. Within the polyprotein is an enzyme (or enzymes) with [[proteinase]] function that is able to cleave the polyprotein into the various single proteins or just cleave away the protease, which can then cleave other polypeptides producing the mature proteins.

===Genome packaging===
Besides involvement in the infection process, [[viral replicase]] is a directly necessary part of the [[genome packaging|packaging of RNA viruses' genetic material]]. This was expected due to replicase involvement already being confirmed in various other viruses.<ref name="Rao-2006">{{cite journal |last=Rao |first=A.L.N. |title=Genome Packaging by Spherical Plant RNA Viruses |journal=[[Annual Review of Phytopathology]] |publisher=[[Annual Reviews (publisher)|Annual Reviews]] |volume=44 |issue=1 |year=2006 |doi=10.1146/annurev.phyto.44.070505.143334 |pages=61–87 |pmid=16480335 }}</ref>

The genome of Beet necrotic yellow vein virus (BNYVV) consists of five RNAs, each encapsidated into rod-shaped virus particles. RNA 1, which is 6746 nucleotides long, encodes a single open reading frame (ORF) that produces the 237 kDa protein P237. This protein is cleaved into P150 and P66 by a papain-like proteinase. RNA 2, 4612 nucleotides long, encodes six proteins, including movement proteins (P42, P13, P15), a coat protein (P21), and a regulatory protein (P14). RNA 3, 1775 nucleotides long, encodes P25, which is involved in symptom expression. RNA 4, 1431 nucleotides long, encodes P31, crucial for vector transmission. RNA 5, found in certain isolates, encodes P26 and is associated with more severe symptoms.<ref>{{Cite journal |last=Tamada |first=T. |last2=Abe |first2=H. |date=1989-12-01 |title=Evidence that Beet Necrotic Yellow Vein Virus RNA-4 Is Essential for Efficient Transmission by the Fungus Polymyxa betae |url=https://www.microbiologyresearch.org/content/journal/jgv/10.1099/0022-1317-70-12-3391 |journal=Journal of General Virology |language=en |volume=70 |issue=12 |pages=3391–3398 |doi=10.1099/0022-1317-70-12-3391 |issn=0022-1317}}</ref>