User:Ryan (Wiki Ed)/virusoid

Virusoids are circular single-stranded RNA(s) dependent on viruses for replication and encapsidation. The genome of virusoids consist of several hundred nucleotides and does not code for any proteins. In humans, the hepatitis D virus is a virusoid capable of causing pathology when in the presence of the hepatitis B virus.

Virusoids are essentially viroids that have been encapsulated by a helper virus coat protein. They are thus similar to viroids in their means of replication (rolling circle replication) and due to the lack of genes, but they differ in that viroids do not possess a protein coat.

Virusoids, while being studied in virology, are subviral particles rather than viruses. Since they depend on helper viruses, they are classified as satellites. In the virological taxonomy they appear as Satellites/Satellite nucleic acids/Subgroup 3: Circular satellite RNA(s).

Viroids, satellite RNA, and virusoids
Virusoids are categorized as sub-viral particles, along with viroids and satellite RNAs.

Viroids are comprised of a few hundred nucleotides of highly complementary, circular, single-stranded RNA that does not contain an open reading frame, is not encapsidated by a coat protein, yet can infect plants. Viroids do not require the presence of a helper virus.

Satellite RNAs are small RNA molecules which are encapsidated inside the coat protein of the helper virus particle. Satellite RNAs contain open reading frames and encode proteins.

Virusoids are a special class of satellite RNA, only 200-400 nt in size, that are circular, single stranded and contain ribozymes structures. Virusoids are encapsidated by a helper virus and require the helper virus for replication, but contain no open reading frames. Two examples of virusoids are Lucerne transient streak virus satellite RNA (LTSV) and Subterranean clover mottle virus satellite RNA (SCMV) Replication takes place using a rolling circle strategy with cleavage of multimeric copies of the genome taking place using the ribozyme activity.

History
The first virusoid was discovered in Nicotiana velutina plants infected with Velvet tobacco mottle virus R2 (VTMOV). These RNAs have also been referred to as viroid-like RNAs that can infect commercially important agricultural crops and are non–self-replicating single stranded RNAs. RNA replication of virusoids is similar to that of viroids but, unlike viroids, virusoids require specific “helper” viruses.

Replication
The circular structure of virusoid RNA molecules is ideal for rolling circle replication, in which multiple copies of the genome are generated in an efficient manner from a single replication initiation event. Another advantage to circular RNAs as replication intermediates is that they are inaccessible and resistant to exonucleases. Additionally, their high GC content and high degree of self-complementarity make them very stable against endonucleases. Circular RNAs impose constraints on RNA folding by which secondary structures that are favored for replication differ from those assumed during ribozyme-mediated self-cleavage.

Plant satellite RNAs and virusoids depend on their respective helper viruses for replication, while the helper viruses themselves are dependent upon plants to provide some of the components required for replication. Therefore, a complex interaction involving all three major players including satellites, helper viruses and host plants is essential for satellite / virusoid replication.

satLTSV replication has been shown to occur through the symmetric rolling circle mechanism, wherein the satLTSV self-cleaves both (+) and (-) strands. Both the (+) and (-) strands of satLTSV were found to be equally infectious. Nevertheless, since only the (+) strand is packaged in the LTSV particles, the origin of assembly sequence (OAS) / secondary structure is assumed to be present on the (+) strand only.

Gellatly et al., 2011 demonstrated that the entire satLTSV molecule possesses sequence and structural significance wherein any mutations (insertions / deletions) causing disruption in the overall rod-like structure of the virusoid molecule are lethal to its infectivity. Foreign nucleotides introduced into the molecule will only be tolerated if they preserve the overall cruciform structure of the satLTSV. Furthermore, the introduced foreign sequences are eliminated in successive generations to ultimately reproduce the wild-type satLTSV.

Therefore, in satLTSV RNA, the entire sequence seems to be essential for replication. This contrasts with satRNA of TBSV or the defective-interfering RNAs, in which only a small portion of their respective sequences / secondary structures were found to be sufficient for replication.

Role of ribozyme structures in the self-cleavage and replication of virusoids
Virusoids structurally resemble the viroids as they possess native secondary structures that form double-stranded rod-like molecules with short terminal branches. They also contain hammerhead ribozymes that are involved in autocatalytic cleavage of satRNA multimers during rolling circle replication. It was proposed that the hammerhead ribozyme structure of satLTSV is formed only transiently, similar to that observed by Song & Miller (2004) with satRPV (Cereal yellow dwarf polerovirus serotype RPV) RNA. This hammerhead structure contains a short stem III that is stabilized by only two base-paired nucleotides. This unstable conformation thus suggests that a double hammerhead mode of cleavage takes place. These structures are similar to those reported for CarSV and newt ribozymes, which implies an ancient relationship between these divergent RNAs. The observation by Collins et al., 1998 that the dimer of the satRYMV RNA is more efficiently self-cleaved than the monomer is consistent with the double hammerhead mode of cleavage. The self-cleavage of the satRYMV in the (+) strand and not in the (-) strand implies that the satRYMV replicates through an asymmetric mode of rolling circle replication, similar to other sobemoviral satellites with the exception of satLTSV.

Hepatitis D virus
Hepatitis delta virus (HDV) is also a circular, single-stranded virusoid that is supported by Hepatitis B helper virus (HBV) and packaged into HBV virions, where it is coinfected along with HBV. HDV encodes a single open reading frame. Similar to viroids, HDV RNA requires the host DNA-dependent RNA polymerase to initiate rolling circle replication through which linear concatemers are produced in a fashion similar to virusoids, which in turn are processed into monomers by enzyme or ribozyme cleavage. This leaves 5′ -hydroxyl and 2′,3′ -cyclic phosphate termini, following which the 5’ and 3’ ends of these monomers are ligated to generate (-) strand circular RNAs. These (-) strand circles then serve as templates for rolling circle replication in which (+) strand multimers are produced followed by their processing, leading to the formation of a large number of (+) strand monomeric genomes. These go on to propagate further infection. The ligation could take place by a reversal of the ribozyme cleavage reaction or by a host encoded cellular ligase that links the 5’ and 3’ ends of the RNA.

Evolutionary origin
Considering properties such as their diminutive size, circular structure and the presence of hammerhead ribozymes, viroids may have had an ancient evolutionary origin distinct from that of the viruses. Likewise, the lack of any sequence similarity between the satellite RNAs and their host viruses, host plants and insect vectors implies that these satellite RNAs have had a spontaneous origin. Alternatively, the siRNAs and microRNAs generated during viral infections may have been amplified by helper virus replicases, whereby these molecules assembled to form satellite RNAs.

Virusoids and viroids have been compared to circular introns due to their size similarity. It has been proposed that virusoids and viroids originated from introns. Comparisons have been made between the (-) strand of viroids and the U1 small nuclear ribonucleoprotein particle (snRNPs), implicating that viroids could be escaped introns. Dickson (1981) also observed such homologies within both the (+) and (-) strands of viroids and virusoids. In particular, virusoids and viroids exhibit several structural and sequence homologies to the group I introns such as the self-splicing intron of Tetrahymena thermophila.

Virusoids and other circular RNAs are ancient molecules that are being explored with renewed interest. Circular RNAs have been shown to possess a number of functions, ranging from modulation of gene expression, interactions with RNA binding proteins (RBPs) acting as miRNA sponges and have been linked to a number of human diseases, including aging and cancer.

Developments
Abouhaidar et al., 2014 demonstrated the only example of protein translation and messenger RNA activity in the Rice yellow mottle virus small circular satellite RNA (scRYMV). This group suggested that the scRYMV be designated as a virusoid satelliteRNA that could serve as a model system for both translation and replication. The most promising application of these subviral agents is to make specific vectors that can be used for the future development of biological control agents for plant viral diseases. The vector system could be applied for the overexpression and silencing of foreign genes. The unique example of a foreign expression vector is Bamboo mosaic virus satellite RNA (satBaMV),, which possesses an open reading frame that encodes a 20-kDa P20 protein. It was observed that when this nonessential ORF region was replaced with a foreign gene, expression of the foreign gene was enhanced or overexpressed. In the case of gene silencing, various satellite RNA-based vectors can be used for sequence-specific inactivation. Satellite Tobacco Mosaic Virus (STMV) was the first subviral agent to be developed as a satellite virus-induced silencing system (SVISS).