Viroids are small single-stranded,circular RNAs that are infectious pathogens.[1][2] Unlikeviruses, they have no protein coating. All known viroids are inhabitants ofangiosperms (flowering plants),[3] and most cause diseases whoseeconomic importance to humans varies widely.[4] A recentmetatranscriptomics study suggests that the host diversity of viroids and viroid-like elements is broader than previously thought and may not be limited to plants, encompassing evenprokaryotes.[5]
Although viroids are composed of nucleic acid, they do not code for anyprotein.[7][8] The viroid's replication mechanism usesRNA polymerase II, a host cell enzyme normally associated with synthesis ofmessenger RNA from DNA, which instead catalyzes "rolling circle replication" of new RNA using the viroid's RNA as a template. Viroids are oftenribozymes, havingcatalytic properties that allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.[9]
Diener initially hypothesized in 1989 that viroids may represent "living relics" from the widely assumed, ancient, and non-cellularRNA world, and others have followed this conjecture.[10][11] Following the discovery ofretrozymes, it has been proposed that viroids and other viroid-like elements may derive from this newly found class ofretrotransposon.[12][13][14]
The human pathogenhepatitis D virus is a subviral agent similar in structure to a viroid, as it is a hybrid particle enclosed by surface proteins from thehepatitis B virus.[15]
The reproduction mechanism of a typical viroid. Leaf contact transmits the viroid. The viroid enters the cell via itsplasmodesmata. 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 byaphids, by cross contamination following mechanical damage to plants as a result of horticultural or agricultural practices, or from plant to plant by leaf contact.[19][64] Upon infection, viroids replicate in the nucleus (Pospiviroidae) orchloroplasts (Avsunviroidae) of plant cells in three steps(what are the steps?) through an RNA-based mechanism. They requireRNA polymerase II, a host cell enzyme normally associated with synthesis ofmessenger RNA from DNA, which instead catalyzes "rolling circle" synthesis of new RNA using the viroid as template.[65]
Unlike plant viruses which producemovement proteins, viroids are entirely passive, relying entirely on the host. This is useful in the study of RNA kinetics in plants.[16]
There has long been uncertainty over how viroids inducesymptoms in plants without encoding anyprotein products within their sequences.[66] Evidence suggests thatRNA silencing is involved in the process. First, changes to the viroidgenome can dramatically alter itsvirulence.[67] This reflects the fact that anysiRNAs produced would have less complementarybase pairing with targetmessenger RNA. Secondly,siRNAs corresponding to sequences from viroid genomes have been isolated from infected plants. Finally,transgenic expression of the noninfectioushpRNA ofpotato spindle tuber viroid develops all the corresponding viroid-like symptoms.[68] This indicates that when viroids replicate via a double stranded intermediateRNA, they are targeted by adicer enzyme and cleaved into siRNAs that are then loaded onto theRNA-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.[69]
"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 largerHDV-likeRibozyviria) and "retroviroids". Most of them also carry some type of aribozyme.[5]
Viroid-likesatellite RNAs are infectious circular RNA molecules that depend on a carrier virus to reproduce, being carried in theircapsids. Like Avsunviroidae, however, they are capable of self-clevage.[70]
"Ambiviruses" aremobile genetic elements that were recently (2020s) discovered infungi. Their RNAgenomes are circular, circa 5 kb in length. One of at least two open reading frames encodes a viral RNA-directedRNA polymerase, that firmly places "ambiviruses" intoribovirian kingdomOrthornavirae; a separate phylumAmbiviricota has been established since the 2023 ICTV Virus Taxonomy Release because of the unique features of encoding RNA-directed RNA polymerases but also having divergentribozymes 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.[71][72][73]
"Retroviroids", more formally "retroviroid-like elements", are viroid-like circular RNA sequences that are also found with homologous copies in theDNA genome of the host.[74] The only types found are closely related to the original "carnation small viroid-like RNA" (CarSV).[75][76] These elements may act as ahomologous substrate upon whichrecombination may occur and are linked todouble-stranded break repair.[76][77]
These elements are dubbed retroviroids as the homologous DNA is generated byreverse transcriptase that is encoded byretroviruses.[78][79] They are neither true viroids nor viroid-likesatellite RNAs: there is no extracellular form of these elements; instead, they are spread only through pollen or egg-cells.[70] They appear to co-occur with apararetrovirus.[80]
After applyingmetatranscriptomics – 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 thehuman microbiome. Given that the RNA sequences recovered do not havehomologies 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.[81][82]
Diener's 1989 hypothesis[83] had proposed that the unique properties of viroids make them more plausible macromolecules thanintrons, or other RNAs considered in the past as possible "living relics" of a hypothetical, pre-cellularRNA 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.,[78] in which the authors summarized Diener's evidence supporting his hypothesis as:
Viroids' small size, imposed by error-prone replication.
Their highguanine andcytosine content, which increases stability and replication fidelity.
Their circular structure, which assures complete replication without genomic tags.
Existence of structural periodicity, which permits modular assembly into enlarged genomes.
Their lack of protein-coding ability, consistent with aribosome-free habitat.
Replication mediated in some byribozymes—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 ofretrozymes (a family ofretrotransposon likely representing their ancestors) and their complete absence from organisms outside of theplants (especially their complete absence fromprokaryotes includingbacteria andarchaea).[12][13][14] 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 theprokaryotes. Matches between viroid cccRNAs andCRISPR spacers suggest that some of them might replicate in prokaryotes.[5]
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.[85]
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. Afungus orbacterium 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.[86]
The first recognized viroid, the pathogenic agent of thepotato spindle tuber disease, was discovered, initially molecularly characterized, and named byTheodor Otto Diener, a plant pathologist at theU.S. Department of Agriculture's Research Center in Beltsville, Maryland, in 1971.[87][86] He 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".[87] This agent is now called the potato spindle tuber viroid (PSTVd). TheCitrus exocortis viroid (CEVd) was discovered soon thereafter, and together understanding of PSTVd and CEVd shaped the concept of the viroid.[16]
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.[88]
In 1976, Sanger et al.[89] 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.[90]
The single-strandedness and circularity of viroids was confirmed by electron microscopy,[91] The complete nucleotide sequence of potato spindle tuber viroid was determined in 1978.[92] 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.[88][93]
Four additional viroids or viroid-like RNA particles were discovered between 2009 and 2015.[84]
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.[94]
In January 2024, biologists reported the discovery of "obelisks", a new class of viroid-like elements, and "oblins", their related group of proteins, in thehuman microbiome.[81][82]
^King AM, Adams MJ, Carstens EB, Lefkovitz EJ, et al. (2012).Virus Taxonomy. Ninth Report of the International Committee for Virus Taxonomy. Burlington, Massachusetts, US: Elsevier Academic Press. pp. 1221–1259.ISBN978-0-12-384685-3.
^abcdefghijBrian W. J. Mahy, Marc H. V. Van Regenmortel, ed. (2009-10-29).Desk Encyclopedia of Plant and Fungal Virology. Academic Press. pp. 71–81.ISBN978-0123751485.
^Flores R, Navarro B, Kovalskaya N, Hammond RW, Di Serio F (October 2017). "Engineering resistance against viroids".Current Opinion in Virology.26:1–7.doi:10.1016/j.coviro.2017.07.003.PMID28738223.
^Hammond RW, Owens RA (2006). "Viroids: New and Continuing Risks for Horticultural and Agricultural Crops".APSnet Feature Articles.doi:10.1094/APSnetFeature-2006-1106.
