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Viroid

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Template:Short description Template:For Template:Cs1 config Template:Virusbox

Viroids are small single-stranded, circular RNAs that are infectious pathogens.<ref name="Navarro">Template:Cite journal</ref><ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> Unlike viruses, they have no protein coating. All known viroids are inhabitants of angiosperms (flowering plants),<ref>Template:Cite journal</ref> and most cause diseases, whose respective economic importance to humans varies widely.<ref name="pmid32752288">Template:Cite journal</ref> A recent metatranscriptomics study suggests that the host diversity of viroids and viroid-like elements is broader than previously thought and that it would not be limited to plants, encompassing even the prokaryotes.<ref name=Lee>Template:Cite journal</ref>

The first discoveries of viroids in the 1970s triggered the historically third major extension of the biosphere—to include smaller lifelike entities—after the discoveries in 1675 by Antonie van Leeuwenhoek (of the "subvisible" microorganisms) and in 1892–1898 by Dmitri Iosifovich Ivanovsky and Martinus Beijerinck (of the "submicroscopic" viruses). The unique properties of viroids have been recognized by the International Committee on Taxonomy of Viruses, in creating a new order of subviral agents.<ref>Template:Cite book</ref>

The first recognized viroid, the pathogenic agent of the potato spindle tuber disease, was discovered, initially molecularly characterized, and named by Theodor Otto Diener, plant pathologist at the U.S Department of Agriculture's Research Center in Beltsville, Maryland, in 1971.<ref name="pmid5095900">Template:Cite journal</ref><ref name = "ARS_timeline">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> This viroid is now called potato spindle tuber viroid, abbreviated PSTVd. The Citrus exocortis viroid (CEVd) was discovered soon thereafter, and together understanding of PSTVd and CEVd shaped the concept of the viroid.<ref name="pmid16078879">Template:Cite journal</ref>

Although viroids are composed of nucleic acid, they do not code for any protein.<ref>Template:Cite journal</ref><ref>Template:Cite journal</ref> The viroid's replication mechanism uses 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's RNA as a template. Viroids are often ribozymes, having catalytic properties that allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.<ref name="pmid33800543">Template:Cite journal</ref>

Diener initially hypothesized in 1989 that viroids may represent "living relics" from the widely assumed, ancient, and non-cellular RNA world, and others have followed this conjecture.<ref name="Diener_1989">Template:Cite journal</ref><ref>Template:Cite journal</ref> Following the discovery of retrozymes, it has been proposed that viroids and other viroid-like elements may derive from this newly found class of retrotransposon.<ref name=":3">Template:Cite journal</ref><ref name=":0">Template:Cite journal</ref><ref name=":1">Template:Cite journal</ref>

The human pathogen hepatitis D virus is a subviral agent similar in structure to a viroid, as it is a hybrid particle enclosed by surface proteins from the hepatitis B virus.<ref>Template:Cite journal</ref>

TaxonomyEdit

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

Template:As of:<ref name="pmid16078879"/><ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref>

|CitationClass=web }}</ref>); 356–361 nucleotides(nt)<ref name=nt>Template:Cite book</ref>

|CitationClass=web }}</ref>); (TCDVd); accession AF162131, genome length 360nt

|CitationClass=web }}</ref>); (TPMVd); accession K00817, genome length 360nt

|CitationClass=web }}</ref>); 368–467 nt<ref name=nt />

|CitationClass=web }}</ref>); (CSVd); accession V01107, genome length 356nt

|CitationClass=web }}</ref>); (TASVd); accession K00818, genome length 360nt

|CitationClass=web }}</ref>); (IrVd-1); accession X95734, genome length 370nt

|CitationClass=web }}</ref>); (CLVd); accession X15663, genome length 370nt

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|CitationClass=web }}</ref>); 294–303 nt<ref name=nt/>

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|CitationClass=web }}</ref>); 246–247 nt<ref name=nt/>

|CitationClass=web }}</ref>); (CTiVd); accession M20731, genome length 254nt

|CitationClass=web }}</ref>); (HLVd); accession X07397, genome length 256nt

      • Cocadviroid rimocitri (former names Citrus bark cracking viroid, Citrus IV viroid<ref>{{#invoke:citation/CS1|citation

|CitationClass=web }}</ref>); (CVd-IV); accession X14638, genome length 284nt

|CitationClass=web }}</ref>); 329–334 nt<ref name=nt/>

|CitationClass=web }}</ref>); (ADFVd); accession X99487, genome length 306nt

|CitationClass=web }}</ref>); (GVYSd-1); accession X06904, genome length 367nt

|CitationClass=web }}</ref>); (GVYSd-2); accession J04348, genome length 363nt

|CitationClass=web }}</ref>); (CBLVd); accession M74065, genome length 318nt

|CitationClass=web }}</ref>); (PBCVd); accession D12823, genome length 315nt

|CitationClass=web }}</ref>); (AGVd); accession X17101, genome length 369nt

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|CitationClass=web }}</ref>); (CbVd-1); 248–251 nt<ref name=nt/>

|CitationClass=web }}</ref>); (CbVd-2); accession X95365, genome length 301nt

|CitationClass=web }}</ref>); (CbVd-3); accession X95364, genome length 361nt

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|CitationClass=web }}</ref>); 246–251 nt<ref name=nt/>

|CitationClass=web }}</ref>); 335–351 nt<ref name=nt/>

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|CitationClass=web }}</ref>); 332–335 nt<ref name=nt/>

Transmission and replicationEdit

File:Viroids- how it do.gif
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 are only known to 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.<ref name=nt/><ref>Template:Cite journal</ref> 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.<ref name="pmid22719735">Template:Cite journal</ref>

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.<ref name="pmid16078879"/>

RNA silencingEdit

There has long been uncertainty over how viroids induce symptoms in plants without encoding any protein products within their sequences.<ref name="pmid28738223">Template:Cite journal</ref> Evidence suggests that RNA silencing is involved in the process. First, changes to the viroid genome can dramatically alter its virulence.<ref name="pmid1546460">Template:Cite journal</ref> 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.<ref>Template:Cite journal</ref> 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.<ref>Template:Cite book</ref>

Viroid-like elementsEdit

"Viroid-like elements" refer to pieces of covalently closed circular (ccc) RNA molecules that do not share the viroid's lifecycle. The category encompasses satellite RNAs (including small plant satRNAs "virusoids", fungal "ambivirus", and the much larger HDV-like Ribozyviria) and "retroviroids". Most of them also carry some type of a ribozyme.<ref name=Lee/>

Viroid-like satellite RNAsEdit

Viroid-like satellite RNAs are infectious circular RNA molecules that depend on a carrier virus to reproduce, being carried in their capsids. Like Avsunviroidae, however, they are capable of self-clevage.<ref name=pmid35183574>Template:Cite journal</ref>

AmbivirusesEdit

"Ambiviruses" are mobile genetic elements that were recently (2020s) discovered in fungi. Their RNA genomes are circular, circa 5 kb in length. One of at least two open reading frames encodes a viral RNA-directed RNA polymerase, that firmly places "ambiviruses" into ribovirian kingdom Orthornavirae; a separate phylum Ambiviricota has been established since the 2023 ICTV Virus Taxonomy Release because of the unique features of encoding RNA-directed RNA polymerases but also having divergent ribozymes in various combinations in both sense and antisense orientation – the detection of circular forms in both sense orientations suggest that "ambiviruses" use rolling circle replication for propagation.<ref>Template:Cite journal</ref><ref>Template:Cite journal</ref><ref name=":2">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref>

RetroviroidsEdit

"Retroviroids", more formally "retroviroid-like elements", are viroid-like circular RNA sequences that are also found with homologous copies in the DNA genome of the host.<ref name="daros">Template:Cite journal</ref> The only types found are closely related to the original "carnation small viroid-like RNA" (CarSV).<ref name="pmid11172112">Template:Cite journal</ref><ref name="hegedus">Template:Cite journal</ref> These elements may act as a homologous substrate upon which recombination may occur and are linked to double-stranded break repair.<ref name="hegedus"/><ref name=Truong>Template:Cite journal</ref>

These elements are dubbed retroviroids as the homologous DNA is generated by reverse transcriptase that is encoded by retroviruses.<ref name="Flores-2014"/><ref>Template:Cite book</ref> They are neither true viroids nor viroid-like satellite RNAs: there is no extracellular form of these elements; instead, they are spread only through pollen or egg-cells.<ref name=pmid35183574/> They appear to co-occur with a pararetrovirus.<ref>Template:Cite journal</ref>

ObelisksEdit

{{#invoke:Labelled list hatnote|labelledList|Main article|Main articles|Main page|Main pages}} After applying metatranscriptomics – the computer-aided search for RNA sequences and their analysis – biologists reported in January 2024 the discovery of "obelisks", a new class of viroid-like elements, and "oblins", their related group of proteins, in the human microbiome. Given that the RNA sequences recovered do not have homologies in any other known life form, the researchers suggest that the obelisks are distinct from viruses, viroids and viroid-like entities, and thus form an entirely new class of organisms.<ref name="SA-20240129">Template:Cite journal</ref><ref name="BRX-20240121">Template:Cite Q</ref>

RNA world hypothesisEdit

Diener's 1989 hypothesis<ref>Diener, T O. "Circular RNAs: relics of precellular evolution?."Proc.Natl.Acad.Sci.USA, 1989;86(23):9370-9374</ref> 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.,<ref name="Flores-2014">Template:Cite journal</ref> 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).<ref name=":3" /><ref name=":0" /><ref name=":1" /> However, recent studies suggest that the diversity of viroids and others viroid-like elements is broader than previously thought and that it would not be limited to plants, encompassing even the prokaryotes. Matches between viroid cccRNAs and CRISPR spacers suggest that some of them might replicate in prokaryotes.<ref name=Lee/>

ControlEdit

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.<ref name="pmid26047558"/>

HistoryEdit

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.<ref>Template:Cite journal</ref>

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.<ref name = "ARS_timeline"/>

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".<ref name="pmid5095900"/> 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 nucleotides) of single-stranded RNA and, unlike viruses, did not have a protein coat. Viroids are extremely small, from 246 to 467 nucleotides, smaller than other infectious plant pathogens; 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 nucleotides long.<ref name=Pommerville/>

In 1976, Sanger et al.<ref name="pmid1069269">Template:Cite journal</ref> 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. Sanger 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.<ref name="pmid33460914">Template:Cite journal</ref>

The single-strandedness and circularity of viroids was confirmed by electron microscopy,<ref name="pmid4728831">Template:Cite journal</ref> The complete nucleotide sequence of potato spindle tuber viroid was determined in 1978.<ref>Template:Cite journal</ref> 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.<ref name=Pommerville>Template:Cite book</ref><ref name="Hammond_2006">Template:Cite journal</ref>

Four additional viroids or viroid-like RNA particles were discovered between 2009 and 2015.<ref name="pmid26047558">Template:Cite journal</ref>

In 2014, New York Times science writer Carl Zimmer published a popularized piece that mistakenly credited Flores et al. with the virioid - RNA world hypothesis' original conception.<ref name= Zimmer>Template:Cite news</ref>

In January 2024, biologists reported the discovery of "obelisks", a new class of viroid-like elements, and "oblins", their related group of proteins, in the human microbiome.<ref name="SA-20240129" /><ref name="BRX-20240121" />

See alsoEdit

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ReferencesEdit

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External linksEdit

Template:Self-replicating organic structures Template:Organisms et al. Template:Taxonbar Template:Authority control

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