| Lily virus X | |
|---|---|
Virus classification  | |
| (unranked): | Virus |
| Realm: | Riboviria |
| Kingdom: | Orthornavirae |
| Phylum: | Kitrinoviricota |
| Class: | Alsuviricetes |
| Order: | Tymovirales |
| Family: | Alphaflexiviridae |
| Genus: | Potexvirus |
| Species: | Lily virus X |
Lily virus X (LVX) is a pathogenic ssRNA(+) plant virus of the family Alphaflexiviridae and the order Tymovirales .
LVX is described in the 4th report of the ICTV (1982). It is found primarily in lilies, although more plants are susceptible, and the virus is thought to be only transmitted mechanically. There are no known vectors; however, the application of insecticides effectively reduced the spread of LVX, from which it may be gathered that the virus’ transmission is insect-mediated. [1] Symptoms of this virus are as of yet unknown, obfuscating the capability to examine the extent of natural infection and spread.
LVX is a non-enveloped virus with helical symmetry. All potexviruses, including LVX are believed to have slightly less than 9 protein subunits per helical turn. [3] This pattern of nucleocapsid formation causes the nucleocapsid to be an elongated, flexible, filamentous virus like most plant viruses. Unlike other potexviruses (average length of 550 nm), LVX has a length of 470 nm and a width of 13 nm. [4] LVX is distinguishable from lily symptomless carlavirus (LSV) by serological tests, such as immunogold labeling tests. [5]
The LVX genome consists of one single stranded (+)RNA sequence of 5.9-7 kilobases in size. The genome contains only three Open Reading Frames (ORFs), coding for five proteins (RdRp, TGBp1, TGBp2, TGBp3, CP). [6] The 5’ end is capped and the 3’ terminus is polyadenylated.
These proteins are 24 kilodaltons (kDa), 12 kDa, and 22 kDa, with the third being the coat protein, while also encoding for RNA-dependent RNA polymerase (RdRp). [7] The stop codon of the 24 kDa ORF and the start codon of the 12 kDa ORF overlap one another. While many potexvirus genomes contain a small ORF that is immediately 5’ of this coat protein ORF, this is not found in the LVX genome. This difference is surprising as this ORF has been identified in at least six other potexvirus genomes. However, when looking at the proteins encoded by LVX and other potexviruses, there were significant similarities between the amino acid sequences. At the 5’ end of LVX, there is a truncated ORF, which encodes for a polypeptide which contains a GDD motif. This motif is also found in the C-terminal end of proteins encoded by other potexviruses. Examination of the 24 kDa protein of LVX reveals that it contains a nucleoside triphosphate binding motif (GXXGXGKS/T). This motif also found in the lily symptomless virus 25 kDa protein, as well as the 25-26 kDa proteins of other potexviruses, such as potato virus X and potato virus S.
LVX also contains a supposed potexvirus subgenomic promoter sequence (GGTTAAGTT---GAA) upstream (5’) of the 24 kDa protein. This sequence is also found upstream of initiation codons of coat proteins in similar viruses, most notably lily symptomless virus. Researchers looked at LVX-infected lily leaves and found the presence of subgenomic RNAs. These RNAs were about 2000 and 850 nucleotides in length, which matched up with the presumed subgenomic promoters. From this, it was determined that they likely function as messengers for both the 24 kDa and 22 kDa proteins (coat protein). In the LVX sequence, there is a region between the 12 kDa ORF and the 22 kDa (coat protein) ORF that is not translated. In other potexvirus sequences, this region contains respective 7 kDa and 11 kDa ORFs; however, in this region of the LVX sequence, there is an uninterrupted reading frame. This reading frame begins at nucleotide position 1236 and ends at position 1646. If this region were to be translated, the protein encoded would be similar to the 7 kDa and 11 kDa proteins mentioned above, ending 18 nucleotides inside of LVX's coat protein ORF. Translation of this LVX ORF does not get translated because the genome is missing an initiation codon.
Triple Gene Block 1 (TGBp1) is a multifunctional protein. It acts to promote translation of viral RNAs by acting as an RNA helicase, separating double-stranded RNA for RdRp functions. Moreover, it can act as a suppressor of RNA interference, which is an immune defense against the accumulation of viral RNAs. [8] TGBp1 transports the viral genome to adjacent plant cells directly through plasmosdesmata, allowing for efficient propagation by circumventing the host's cell wall barrier. [9] TGBp1 also increases plasmodesmal size exclusion limits, allowing the viral genome to pass more easily from one cell to another. Finally, it suppresses RNA silencing, preventing the host from disabling the RNA genome.
TGBp2 and TGBp3 are membrane binding proteins involved in attachment and entry. TGBp3 is expressed through leaky scanning of the TGBp2 subgenomic mRNA. The TGBp2 ORF has a weak initiation codon that is sometimes skipped by the ribosome in translation initiation. In this instance, the 40S ribosomal subunit continues to scan until it encounters the initiation codon of TGBp3 and begins translation.
CP is the coat protein of LVX that forms ribonucleoprotein complexes along with TGBp1 and viral mRNA.
“The nucleotide sequence of LVX appears to be unique among potexviruses inasmuch as it apparently lacks the small open reading frame, 5’ to the coat protein cistron, common to all other potexvirus.” [10] In addition, the TGBp3 region of the genome lacked a normal start codon. [11] The 5′-non-coding region begins with GGAAAA, whereas those of other sequenced potexviruses probably all begin with GAAAA. [12] Phylogenetic analysis of the LVX coding sequence revealed that LVX was most closely related to Strawberry mild yellow-edge virus. [13]
LVX does not have a known vector, but it most likely spreads and enters the cell through mechanical inoculation by insects. The replication of LVX, like other ssRNA(+) viruses, occurs in the cytoplasm of cells. Once the virus enters into the host cell, the virus is uncoated and releases the viral genome RNA into the cytoplasm. The viral monocistronic RNA is then translated into RNA-dependent RNA polymerase, encoded by the 5’-proximal ORF. The replication of LVX occurs in viral factories which are organized by the protein TGBp1. [15] TGBp1 works to rearrange the actin and endomembranes of the host and creates an assembly of helical arrangements. These helical structures are surrounded by the host endomembranes, which create a region where the virus can replicate more efficiently. [16]
The replication of the ssRNA(+) virus generates a dsRNA(+) virus, which is then further transcribed and replicated to create more LVX mRNAs and ssRNA(+) genomes, respectively. Subgenomic promoters on the virus lead to translation of sgRNAs, which results in the formation of capsid and movement proteins. These are used to arrange the virion structure and organize the viral genomes. New virus particles are then able to be produced and assembled. With the help of LVX's triple gene block proteins, these completed particles can traverse long distances among plasmodesmata and shorter, intercellular spaces in order to infect other host cells. [17]
LVX has no known associated diseases.
There are no known outstanding symptoms that arise in LVX's natural host range of Lilium formosanum; however, Yang (1997) found that LVX-infected lilies grow more slowly and tend to be smaller than uninfected specimens. Mechanical inoculation of other susceptible plant species, such as Tetragonia tetragonioides and Chenopodium murale, result in chlorotic local lesions. [18]
Although not seen in nature, lab tests have shown that LVX is able to infect several other plants beyond Lilium formosanum. [19] Other species that have been shown to be susceptible are: [20]
LVX is able to infect all tissues of the lily plant. Virions have been cytopathologically detected in all parts of the host plants and contain approximately 5% nucleic acid and 95% protein, with no lipid contents. [21] The mode of transmission is expected to be that of mechanical inoculation through insect vectors, since the spread of the virus was inhibited by insecticides but not mineral-oil sprays. [22]
Tobacco mosaic virus (TMV) is a positive-sense single-stranded RNA virus species in the genus Tobamovirus that infects a wide range of plants, especially tobacco and other members of the family Solanaceae. The infection causes characteristic patterns, such as "mosaic"-like mottling and discoloration on the leaves. TMV was the first virus to be discovered. Although it was known from the late 19th century that a non-bacterial infectious disease was damaging tobacco crops, it was not until 1930 that the infectious agent was determined to be a virus. It is the first pathogen identified as a virus. The virus was crystallised by W.M. Stanley. It has a similar size to the largest synthetic molecule, known as PG5.
Rubella virus (RuV) is the pathogenic agent of the disease rubella, transmitted only between humans via the respiratory route, and is the main cause of congenital rubella syndrome when infection occurs during the first weeks of pregnancy.
Plant viruses are viruses that affect plants. Like all other viruses, plant viruses are obligate intracellular parasites that do not have the molecular machinery to replicate without a host. Plant viruses can be pathogenic to vascular plants.
Potyviridae is a family of positive-strand RNA viruses that encompasses more than 30% of known plant viruses, many of which are of great agricultural significance. The family has 12 genera and 235 species, three of which are unassigned to a genus.
Tombusviridae is a family of single-stranded positive sense RNA plant viruses. There are three subfamilies, 17 genera, and 95 species in this family. The name is derived from Tomato bushy stunt virus (TBSV).
Nidovirales is an order of enveloped, positive-strand RNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, molluscs, and helminths. The order includes the families Coronaviridae, Arteriviridae, Roniviridae, and Mesoniviridae.
Ribosome shunting is a mechanism of translation initiation in which ribosomes bypass, or "shunt over", parts of the 5' untranslated region to reach the start codon. However, a benefit of ribosomal shunting is that it can translate backwards allowing more information to be stored than usual in an mRNA molecule. Some viral RNAs have been shown to use ribosome shunting as a more efficient form of translation during certain stages of viral life cycle or when translation initiation factors are scarce. Some viruses known to use this mechanism include adenovirus, Sendai virus, human papillomavirus, duck hepatitis B pararetrovirus, rice tungro bacilliform viruses, and cauliflower mosaic virus. In these viruses the ribosome is directly translocated from the upstream initiation complex to the start codon (AUG) without the need to unwind RNA secondary structures.
Tomato bushy stunt virus (TBSV) is a virus of the tombusvirus family. It was first reported in tomatoes in 1935 and primarily affects vegetable crops, though it is not generally considered an economically significant plant pathogen. Depending upon the host, TBSV causes stunting of growth, leaf mottling, and deformed or absent fruit. The virus is likely to be soil-borne in the natural setting, but can also transmitted mechanically, for example through contaminated cutting tools. TBSV has been used as a model system in virology research on the life cycle of plant viruses, particularly in experimental infections of the model host plant Nicotiana benthamiana.
Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group. Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, and whether the sense of a single-stranded RNA genome is positive or negative.
Drosophila X virus (DXV) belongs to the Birnaviridae family of viruses. Birnaviridae currently consists of three genera. The first genus is Entomobirnavirus, which contains DXV. The next genus is Aquabirnavirus, containing infectious pancreatic necrosis virus (IPNV). The last genus is Avibirnavirus, which contains infectious bursal disease virus (IBDV). All of these genera contain homology in three specific areas of their transcripts. The homology comes from the amino and carboxyl regions of preVP2, a small 21-residue-long domain near the carboxyl terminal of VP3, and similar small ORFs sequences.
Deformed wing virus (DWV) is an RNA virus, one of 22 known viruses affecting honey bees. While most commonly infecting the honey bee, Apis mellifera, it has also been documented in other bee species, like Bombus terrestris, thus, indicating it may have a wider host specificity than previously anticipated. The virus was first isolated from a sample of symptomatic honeybees from Japan in the early 1980s and is currently distributed worldwide. It is found also in pollen baskets and commercially reared bumblebees. Its main vector in A. mellifera is the Varroa mite. It is named after what is usually the most obvious deformity it induces in the development of a honeybee pupa, which is shrunken and deformed wings, but other developmental deformities are often present.
Partitiviridae is a family of double-stranded RNA viruses. Plants, fungi, and protozoa serve as natural hosts. It has been suggested that they can also infect bacteria. The name comes from the Latin partitius, which means divided, and refers to the segmented genome of partitiviruses. There are five genera and 60 species in the family, 15 of which are unassigned to a genus.
Alfalfa mosaic virus (AMV), also known as Lucerne mosaic virus or Potato calico virus, is a worldwide distributed phytopathogen that can lead to necrosis and yellow mosaics on a large variety of plant species, including commercially important crops. It is the only Alfamovirus of the family Bromoviridae. In 1931 Weimer J.L. was the first to report AMV in alfalfa. Transmission of the virus occurs mainly by some aphids, by seeds or by pollen to the seed.
Idaeovirus is a genus of positive-sense ssRNA viruses that contains two species: Raspberry bushy dwarf virus (RBDV) and Privet idaeovirus. RBDV has two host-dependent clades: one for raspberries; the other for grapevines. Infections are a significant agricultural burden, resulting in decreased yield and quality of crops. RBDV has a synergistic relation with Raspberry leaf mottle virus, with co-infection greatly amplifying the concentration of virions in infected plants. The virus is transmitted via pollination with RBDV-infected pollen grains that first infect the stigma before causing systemic infection.
Potexvirus is a genus of pathogenic viruses in the order Tymovirales, in the family Alphaflexiviridae. Plants serve as natural hosts. There are 48 species in this genus, three of which are assigned to a subgenus. Diseases associated with this genus include: mosaic and ringspot symptoms. The genus name comes from POTato virus X).
Carlavirus, formerly known as the "Carnation latent virus group", is a genus of viruses in the order Tymovirales, in the family Betaflexiviridae. Plants serve as natural hosts. There are 53 species in this genus. Diseases associated with this genus include: mosaic and ringspot symptoms.
Donkey orchid symptomless virus (DOSV) was first discovered in Perth, Australia which is located on the Western side of Australia. The Southwest Australian Floristic Region is very biodiverse and secluded with deserts on the east and northeast side along with the ocean on the south side. It is home to approximately 8,000 indigenous plant species that are accustomed to living in a Mediterranean climate. This type of climate means that the plants have adapted to living in unfertile soil, dryness, and can withstand frequent fires in the area. Out of 394 terrestrial orchid species, 76 of these species are threatened. Reasons contributing to plants being threatened in this area could be due to the rate at which they reproduce fruit, pollinate, or human contact.
ORF3b is a gene found in coronaviruses of the subgenus Sarbecovirus, encoding a short non-structural protein. It is present in both SARS-CoV and SARS-CoV-2, though the protein product has very different lengths in the two viruses. The encoded protein is significantly shorter in SARS-CoV-2, at only 22 amino acid residues compared to 153-155 in SARS-CoV. Both the longer SARS-CoV and shorter SARS-CoV-2 proteins have been reported as interferon antagonists. It is unclear whether the SARS-CoV-2 gene expresses a functional protein.
ORF1ab refers collectively to two open reading frames (ORFs), ORF1a and ORF1b, that are conserved in the genomes of nidoviruses, a group of viruses that includes coronaviruses. The genes express large polyproteins that undergo proteolysis to form several nonstructural proteins with various functions in the viral life cycle, including proteases and the components of the replicase-transcriptase complex (RTC). Together the two ORFs are sometimes referred to as the replicase gene. They are related by a programmed ribosomal frameshift that allows the ribosome to continue translating past the stop codon at the end of ORF1a, in a -1 reading frame. The resulting polyproteins are known as pp1a and pp1ab.