| Avsunviroidae | |
|---|---|
 | |
| Viroid of family Avsunviroidae | |
Virus classification  | |
| (unranked): | Virus |
| Family: | Avsunviroidae |
| Genera | |
The Avsunviroidae are a family of viroids. There are four species in three genera ( Avsunviroid , Elaviroid and Pelamoviroid ). [1] They consist of RNA genomes between 246 and 375 nucleotides in length. They are single-stranded covalent circles and have intramolecular base pairing. All members lack a central conserved region. [2]
Replication occurs in the chloroplasts of plant cells. Key features of replication include no helper virus required and no proteins are encoded for. Unlike the other family of viroids, Pospiviroidae , Avsunviroidae are thought to replicate via a symmetrical rolling mechanism. It is thought the positive RNA strand acts as a template to form negative strands with the help of an enzyme thought to be RNA polymerase plus 3 II. The negative RNA strands are then cleaved by ribozyme activity and circularises. A second rolling circle mechanism forms a positive strand which is also cleaved by ribozyme activity and then ligated to become circular. The site of replication is unknown but it is thought to be in the chloroplast and in the presence of Mg2+ ions. [2]
Predictions of structure have suggested that they exist either as rod-shaped molecules with regions of base pairing causing formation of some hairpin loops or have branched configurations. [2] [3]
The family has four stretches of conserved nucleotides, guuuc, uc, ucag, ac from 5' to 3', plus their Watson-Crick pairings on the other end of the loop. This is part of its hammerhead ribozyme. [1] Otherwise there is little structural similarity in the family. [Fl 1] They do not have the conserved CCH, TCR, or TCH motifs, which is one of the features defining their separation from the Pospiviroidae. [Fl 2]
The family has three genera, with a total of five species. [2]
The lack of a long, central conserved region makes Avsunviroidae harder to identify than Pospiviroidae. A method to detect them is to use their circularity: a computer can piece together many overlapping reads that appear to form repeats when placed linearly. [4]
Viroids are small single-stranded, circular RNAs that are infectious pathogens. Unlike viruses, they have no protein coating. All known viroids are inhabitants of angiosperms, and most cause diseases, whose respective economic importance to humans varies widely. A recent metatranscriptomics study suggests that the host diversity of viroids and other viroid-like elements is broader than previously thought and that it would not be limited to plants, encompassing even the prokaryotes.
Virus classification is the process of naming viruses and placing them into a taxonomic system similar to the classification systems used for cellular organisms.
Virusoids are circular single-stranded RNA(s) dependent on viruses for replication and encapsidation. The genome of virusoids consist of several hundred (200–400) nucleotides and does not code for any proteins.
A satellite is a subviral agent that depends on the coinfection of a host cell with a helper virus for its replication. Satellites can be divided into two major classes: satellite viruses and satellite nucleic acids. Satellite viruses, which are most commonly associated with plants, are also found in mammals, arthropods, and bacteria. They encode structural proteins to enclose their genetic material, which are therefore distinct from the structural proteins of their helper viruses. Satellite nucleic acids, in contrast, do not encode their own structural proteins, but instead are encapsulated by proteins encoded by their helper viruses. The genomes of satellites range upward from 359 nucleotides in length for satellite tobacco ringspot virus RNA (STobRV).
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.
The Pospiviroidae are a incertae sedis family of ssRNA viroids with 5 genera and 39 species, including the first viroid to be discovered, PSTVd, which is part of genus Pospiviroid. Their secondary structure is key to their biological activity. The classification of this family is based on differences in the conserved central region sequence. Pospiviroidae replication occurs in an asymmetric fashion via host cell RNA polymerase, RNase, and RNA ligase. its hosts are plants, specifically dicotyledons and some monocotyledons
Rolling circle replication (RCR) is a process of unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular RNA genome of viroids. Some eukaryotic viruses also replicate their DNA or RNA via the rolling circle mechanism.
Potyvirus is a genus of positive-strand RNA viruses in the family Potyviridae. Plants serve as natural hosts. Like begomoviruses, members of this genus may cause significant losses in agricultural, pastoral, horticultural, and ornamental crops. More than 200 species of aphids spread potyviruses, and most are from the subfamily Aphidinae. The genus contains 190 species and potyviruses account for about thirty percent of all currently known plant viruses.
Closterovirus, also known as beet yellows viral group, is a genus of viruses, in the family Closteroviridae. Plants serve as natural hosts. There are 17 species in this genus. Diseases associated with this genus include: yellowing and necrosis, particularly affecting the phloem. This genus has a probably worldwide distribution and includes among other viral species the Beet yellows virus and Citrus tristeza virus, rather economically important plant diseases. At least some species require vectors such as aphids or mealybugs for their transmission from plant to plant.
Cowpea chlorotic mottle virus, known by the abbreviation CCMV, is a virus that specifically infects the cowpea plant, or black-eyed pea. The leaves of infected plants develop yellow spots, hence the name "chlorotic". Similar to its "brother" virus, Cowpea mosaic virus (CPMV), CCMV is produced in high yield in plants. In the natural host, viral particles can be produced at 1–2 mg per gram of infected leaf tissue. Belonging to the bromovirus genus, cowpea chlorotic mottle virus (CCMV) is a small spherical plant virus. Other members of this genus include the brome mosaic virus (BMV) and the broad bean mottle virus (BBMV).
Nepovirus is a genus of viruses in the order Picornavirales, in the family Secoviridae, in the subfamily Comovirinae. Plants serve as natural hosts. There are 40 species in this genus. Nepoviruses, unlike the other two genera in the subfamily Comovirinae, are transmitted by nematodes.
Peach latent mosaic viroid is a species of the genus Pelamoviroid, which belongs to the family Avsunviroidae. This family is characterized as having chloroplastic viroids with hammerhead ribozymes. Peach latent mosaic viroid is a 336-351nt circular RNA which has a branched formation. This branched formation is stabilised by a pseudoknot between two kissing loops. Peach latent mosaic viroid was first described in the 1980s in Spain by a group of scientists.
The hammerhead ribozyme is an RNA motif that catalyzes reversible cleavage and ligation reactions at a specific site within an RNA molecule. It is one of several catalytic RNAs (ribozymes) known to occur in nature. It serves as a model system for research on the structure and properties of RNA, and is used for targeted RNA cleavage experiments, some with proposed therapeutic applications. Named for the resemblance of early secondary structure diagrams to a hammerhead shark, hammerhead ribozymes were originally discovered in two classes of plant virus-like RNAs: satellite RNAs and viroids. They are also known in some classes of retrotransposons, including the retrozymes. The hammerhead ribozyme motif has been ubiquitously reported in lineages across the tree of life.
Machlomovirus is a genus of plant viruses, in the family Tombusviridae. Plants serve as natural hosts. There is only one species in this genus: Maize chlorotic mottle virus (MCMV), which causes significant losses in maize production worldwide. MCMV was first identified in the U.S. state of Kansas causing Maize lethal necrosis disease/MLN/corn lethal necrosis, a severe disease that negatively affects all stages of development for maize plants.
Sobemovirus is a genus of non-enveloped, positive-strand RNA viruses which infect plants.. Plants serve as natural hosts. There are 21 species in this genus. Diseases associated with this genus include: mosaics and mottles.
Trichovirus is a genus of viruses in the order Tymovirales, in the family Betaflexiviridae. Plants, specifically angiosperms such as pome fruits, citrus, and pear, serve as natural hosts for this plant pathogen. There are seven species in this genus.
Emaravirus is a genus of negative-strand RNA viruses which infect plants. The plant virus group is the sole genus in the family Fimoviridae. The genus has 21 species.
Bromovirus is a genus of viruses, in the family Bromoviridae. Plants serve as natural hosts. There are six species in this genus.
Ribozyviria is a realm of satellite nucleic acids — infectious agents that resemble viruses, but cannot replicate without a helper virus. Established in ICTV TaxoProp 2020.012D, the realm is named after the presence of genomic and antigenomic ribozymes of the Deltavirus type. The agents in Ribozyviria are satellite nucleic acids, which are distinct from satellite viruses in that they do not encode all of their own structural proteins but require proteins from their helper viruses in order to assemble. Additional common features include a rod-like structure, an RNA-binding "delta antigen" encoded in the genome, and animal hosts. Furthermore, the size range of the genomes of these viruses is between around 1547–1735nt, they encode a hammerhead ribozyme or a hepatitis delta virus ribozyme, and their coding capacity only involves one conserved protein. Most lineages of this realm are poorly understood, the notable exception being the genus Deltavirus, comprising the causal agents of hepatitis D in humans.
Retrozymes are a family of retrotransposons first discovered in the genomes of plants but now also known in genomes of animals. Retrozymes contain a hammerhead ribozyme (HHR) in their sequences, although they do not possess any coding regions. Retrozymes are nonautonomous retroelements, and so borrow proteins from other elements to move into new regions of a genome. Retrozymes are actively transcribed into covalently closed circular RNAs and are detected in both polarities, which may indicate the use of rolling circle replication in their lifecycle.