Avsunviroidae

Replication

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.

Structure

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.

The family has four stretches of conserved nucleotides, , , , from 5' to 3', plus their Watson-Crick pairings on the other end of the loop. This is part of its hammerhead ribozyme. They do not have the conserved CCH, TCR, or TCH motifs, which is one of the features defining their separation from the Pospiviroidae.p.118-120, "The other four viroids, Avocado sunblotch viroid (ASBVd) (47), Peach latent mosaic viroid (PLMVd) (45), Chrysanthemum chlorotic mottle viroid (CChMVd) (65), and Eggplant latent viroid (ELVd) (30), do not have the conserved CCR, TCR, and TCH motifs but, remarkably, both their polarity strands self-cleave through hammerhead ribozymes; they form the second family, Avsunviroidae (reviewed in 33), whose type species is ASBVd (formal inclusion of ELVd in this family is pending ICTV approval) (Figure 1b)."

Classification

The family has three genera, with a total of five species.

• Family Avsunviroidae
  • Genus Avsunviroid;p.120, "ASBVd, the only viroid with a high A + U content (62%) (47), forms a monospecific genus"
    • Species: Avocado sunblotch viroid (ASBVd, acc. J02020, gen. len. 247nt)p.119, TABLE 1
  • Genus Elaviroid;p.120, "and ELVd, whose properties fall between those of the members of the other two genera, has been proposed to constitute its own genus (30).
    • Species: Eggplant latent viroid (ELVd, acc. AJ536613, gen. len. 333nt)
  • Genus Pelamoviroid;p.120, "but PLMVd and CChMVd are grouped in one genus because of their branched secondary structure (21, 45, 65), which is stabilized by a pseudoknot (10; S. Gago, M. De la Peňa & R. Flores, unpublished results) (Figure 1b), and their insolubility in2M LiCl (65)."
    • Species: Appler hammerhead viroid, Chrysanthemum chlorotic mottle viroid (CChMVd, acc. Y14700, gen. len. 399nt) and Peach latent mosaic viroid (PLMVd, acc. M83545, gen. len. 337nt)

Detection

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.

References

References

1. (May 2018). "ICTV Virus Taxonomy Profile: Avsunviroidae.". The Journal of General Virology.
2. "ICTV Online Report Avsunviroidae".
3. (October 2014). "Elucidation of the structures of all members of the Avsunviroidae family.". Molecular Plant Pathology.
4. Otherwise there is little structural similarity in the family.p.{{nbs}}120, "Apart from the core nucleotides conserved in their hammerhead structures, no extensive sequence similarities exist between them"
5. (6 March 2012). "Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm.". Proceedings of the National Academy of Sciences of the United States of America.