Viroid

Putative secondary structure of the PSTVd viroid. The highlighted nucleotides are found in most other viroids.

As of 2005:[8]

• Family Pospiviroidae
  • Genus Pospiviroid; type species: Potato spindle tuber viroid; 356–361 nucleotides(nt)[18]
    • Tomato chlorotic dwarf viroid; (TCDVd); accession AF162131, genome length 360nt
    • Mexican papita viroid; (MPVd); accession L78454, genome length 360nt
    • Tomato planta macho viroid; (TPMVd); accession K00817, genome length 360nt
    • Citrus exocortis viroid; 368–467 nt[18]
    • Chrysanthemum stunt viroid; (CSVd); accession V01107, genome length 356nt
    • Tomato apical stunt viroid; (TASVd); accession K00818, genome length 360nt
    • Iresine 1 viroid; (IrVd-1); accession X95734, genome length 370nt
    • Columnea latent viroid; (CLVd); accession X15663, genome length 370nt
  • Genus Hostuviroid; type species: Hop stunt viroid; 294–303 nt[18]
  • Genus Cocadviroid; type species: Coconut cadang-cadang viroid; 246–247 nt[18]
    • Coconut tinangaja viroid; (CTiVd); accession M20731, genome length 254nt
    • Hop latent viroid; (HLVd); accession X07397, genome length 256nt
    • Citrus IV viroid; (CVd-IV); accession X14638, genome length 284nt
  • Genus Apscaviroid; type species: Apple scar skin viroid; 329–334 nt[18]
    • Citrus III viroid; (CVd-III); accession AF184147, genome length 294nt
    • Apple dimple fruit viroid; (ADFVd); accession X99487, genome length 306nt
    • Grapevine yellow speckle 1 viroid; (GVYSd-1); accession X06904, genome length 367nt
    • Grapevine yellow speckle 2 viroid; (GVYSd-2); accession J04348, genome length 363nt
    • Citrus bent leaf viroid; (CBLVd); accession M74065, genome length 318nt
    • Pear blister canker viroid; (PBCVd); accession D12823, genome length 315nt
    • Australian grapevine viroid; (AGVd); accession X17101, genome length 369nt
  • Genus Coleviroid; type species: Coleus blumei viroid 1; 248–251 nt[18]
    • Coleus blumei 2 viroid; (CbVd-2); accession X95365, genome length 301nt
    • Coleus blumei 3 viroid; (CbVd-3); accession X95364, genome length 361nt
• Family Avsunviroidae
  • Genus Avsunviroid; type species: Avocado sunblotch viroid; 246–251 nt[18]
  • Genus Pelamoviroid; type species: Peach latent mosaic viroid; 335–351 nt[18]
  • Genus Elaviroid; type species: Eggplant latent viroid; 332–335 nt[18]

The reproduction mechanism of a typical viroid. Leaf contact transmits the viroid. The viroid enters the cell via its plasmodesmata. RNA polymerase II catalyzes rolling-circle synthesis of new viroids.

Viroids only infect plants, and infectious viroids can be transmitted to new plant hosts by aphids, by cross contamination following mechanical damage to plants as a result of horticultural or agricultural practices, or from plant to plant by leaf contact.[18][19] Upon infection, viroids replicate in the nucleus (Pospiviroidae) or chloroplasts (Avsunviroidae) of plant cells in three steps through an RNA-based mechanism. They require RNA polymerase II, a host cell enzyme normally associated with synthesis of messenger RNA from DNA, which instead catalyzes "rolling circle" synthesis of new RNA using the viroid as template.[20]

Unlike plant viruses which produce movement proteins, viroids are entirely passive, relying entirely on the host. This is useful in the study of RNA kinetics in plants.[8]

There has long been uncertainty over how viroids induce symptoms in plants without encoding any protein products within their sequences.[21] Evidence suggests that RNA silencing is involved in the process. First, changes to the viroid genome can dramatically alter its virulence.[22] This reflects the fact that any siRNAs produced would have less complementary base pairing with target messenger RNA. Secondly, siRNAs corresponding to sequences from viroid genomes have been isolated from infected plants. Finally, transgenic expression of the noninfectious hpRNA of potato spindle tuber viroid develops all the corresponding viroid-like symptoms.[23] This indicates that when viroids replicate via a double stranded intermediate RNA, they are targeted by a dicer enzyme and cleaved into siRNAs that are then loaded onto the RNA-induced silencing complex. The viroid siRNAs contain sequences capable of complementary base pairing with the plant's own messenger RNAs, and induction of degradation or inhibition of translation causes the classic viroid symptoms.[24]

Retroviroids and retroviroid-like elements are viroids, which are RNA that have a DNA homologue.[25] These entities are thought to be largely exclusive to the carnation, Dianthus caryophyllus, that are closely related to the family of viruses termed 'carnation small viroid-like RNA' (CarSV RNA).[26][27] These elements may act as a homologous substrate upon which recombination may occur and are linked to double-stranded break repair.[27][28] These elements are dubbed retroviroids as the homologous DNA is generated by reverse transcriptase that is encoded by retroviruses.[29][30]

Diener's 1989 hypothesis[31] had proposed that the unique properties of viroids make them more plausible macromolecules than introns, or other RNAs considered in the past as possible "living relics" of a hypothetical, pre-cellular RNA world. If so, viroids have assumed significance beyond plant virology for evolutionary theory, because their properties make them more plausible candidates than other RNAs to perform crucial steps in the evolution of life from inanimate matter (abiogenesis). Diener's hypothesis was mostly forgotten until 2014, when it was resurrected in a review article by Flores et al.,[29] in which the authors summarized Diener's evidence supporting his hypothesis as:

1. Viroids' small size, imposed by error-prone replication.
2. Their high guanine and cytosine content, which increases stability and replication fidelity.
3. Their circular structure, which assures complete replication without genomic tags.
4. Existence of structural periodicity, which permits modular assembly into enlarged genomes.
5. Their lack of protein-coding ability, consistent with a ribosome-free habitat.
6. Replication mediated in some by ribozymes—the fingerprint of the RNA world.

The presence, in extant cells, of RNAs with molecular properties predicted for RNAs of the RNA world constitutes another powerful argument supporting the RNA world hypothesis. However, the origins of viroids themselves from this RNA world has been cast into doubt by several factors, including the discovery of retrozymes (a family of retrotransposon likely representing their ancestors) and their complete absence from organisms outside of the plants (especially their complete absence from prokaryotes including bacteria and archaea).[14][15][16]

The development of tests based on ELISA, PCR, and nucleic acid hybridization has allowed for rapid and inexpensive detection of known viroids in biosecurity inspections, phytosanitary inspections, and quarantine. However, the ongoing discovery and evolution of new viroids makes such assays always incomplete.[32]

In the 1920s, symptoms of a previously unknown potato disease were noticed in New York and New Jersey fields. Because tubers on affected plants become elongated and misshapen, they named it the potato spindle tuber disease.[33]

The symptoms appeared on plants onto which pieces from affected plants had been budded—indicating that the disease was caused by a transmissible pathogenic agent. A fungus or bacterium could not be found consistently associated with symptom-bearing plants, however, and therefore, it was assumed the disease was caused by a virus. Despite numerous attempts over the years to isolate and purify the assumed virus, using increasingly sophisticated methods, these were unsuccessful when applied to extracts from potato spindle tuber disease-afflicted plants.[7]

In 1971 Theodor O. Diener showed that the agent was not a virus, but a totally unexpected novel type of pathogen, 1/80th the size of typical viruses, for which he proposed the term "viroid".[6] Parallel to agriculture-directed studies, more basic scientific research elucidated many of viroids' physical, chemical, and macromolecular properties. Viroids were shown to consist of short stretches (a few hundred nucleobases) of single-stranded RNA and, unlike viruses, did not have a protein coat. Compared with other infectious plant pathogens, viroids are extremely small in size, ranging from 246 to 467 nucleobases; they thus consist of fewer than 10,000 atoms. In comparison, the genomes of the smallest known viruses capable of causing an infection by themselves are around 2,000 nucleobases long.[34]

In 1976, Sänger et al.[35] presented evidence that potato spindle tuber viroid is a "single-stranded, covalently closed, circular RNA molecule, existing as a highly base-paired rod-like structure"—believed to be the first such molecule described. Circular RNA, unlike linear RNA, forms a covalently closed continuous loop, in which the 3' and 5' ends present in linear RNA molecules have been joined. Sänger et al. also provided evidence for the true circularity of viroids by finding that the RNA could not be phosphorylated at the 5' terminus. In other tests, they failed to find even one free 3' end, which ruled out the possibility of the molecule having two 3' ends. Viroids thus are true circular RNAs.[36]

The single-strandedness and circularity of viroids was confirmed by electron microscopy,[37] The complete nucleotide sequence of potato spindle tuber viroid was determined in 1978.[38] PSTVd was the first pathogen of a eukaryotic organism for which the complete molecular structure has been established. Over thirty plant diseases have since been identified as viroid-, not virus-caused, as had been assumed.[34][39]

Four additional viroids or viroid-like RNA particles were discovered between 2009 and 2015.[32]

In 2014, New York Times science writer Carl Zimmer published a popularized piece that mistakenly credited Flores et al. with the hypothesis' original conception.[40]

• Viroids/ATSU
• ViroidDB, a database of viroids and viroid-like circular RNAs