Viroid
Viroid | |
---|---|
Virus classification | |
Informal group: | Subviral agents
|
(unranked): | Viroid |
Families | |
Viroids are small single-stranded,
The first discoveries of viroids in the 1970s triggered the historically third major extension of the
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.[7][8] 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.[9]
Although viroids are composed of nucleic acid, they do not code for any
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.[13][14] 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.[15][16][17]
The human pathogen
Taxonomy
- Family Pospiviroidae: relies on host Rnase III[5]
- Genus Pospiviroid; type species: Potato spindle tuber viroid; 356–361 nucleotides(nt)[19]
- 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[19]
- 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[19]
- Genus Coconut cadang-cadang viroid; 246–247 nt[19]
- 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[19]
- 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[19]
- Coleus blumei 2 viroid; (CbVd-2); accession X95365, genome length 301nt
- Coleus blumei 3 viroid; (CbVd-3); accession X95364, genome length 361nt
- Genus Pospiviroid; type species: Potato spindle tuber viroid; 356–361 nucleotides(nt)[19]
- Family Avsunviroidae: autocatalytic clevage[5]
- Genus Avsunviroid; type species: Avocado sunblotch viroid; 246–251 nt[19]
- Genus Pelamoviroid; type species: Peach latent mosaic viroid; 335–351 nt[19]
- Genus Elaviroid; type species: Eggplant latent viroid; 332–335 nt[19]
- Genus
Transmission and replication
Viroids are only known to infect plants, and infectious viroids can be transmitted to new plant hosts by
Unlike plant viruses which produce
RNA silencing
There has long been uncertainty over how viroids induce
Viroid-like elements
"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 "
Viroid-like satellite RNAs
Viroid-like
Retroviroids
"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.[27] The only types found are closely related to the original "carnation small viroid-like RNA" (CarSV).[28][29] These elements may act as a homologous substrate upon which recombination may occur and are linked to double-stranded break repair.[29][30]
These elements are dubbed retroviroids as the homologous DNA is generated by
Obelisks
After applying
RNA world hypothesis
Diener's 1989 hypothesis[36] 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.,[31] in which the authors summarized Diener's evidence supporting his hypothesis as:
- Viroids' small size, imposed by error-prone replication.
- Their high guanine and cytosine 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 a ribosome-free habitat.
- 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
Control
The development of tests based on
History
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.[38]
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.[8]
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".[7] 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.[39]
In 1976, Sanger et al.[40] 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.[41]
The single-strandedness and circularity of viroids was confirmed by electron microscopy,[42] The complete nucleotide sequence of potato spindle tuber viroid was determined in 1978.[43] 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.[39][44]
Four additional viroids or viroid-like RNA particles were discovered between 2009 and 2015.[37]
In 2014,
In January 2024, biologists reported the discovery of "
See also
- Circular RNA
- Microparasite
- Non-cellular life
- Obelisk (life form)
- Plant pathology
- Plasmid
- Prion
- RNA world hypothesis
- Satellite (biology)
- Virus
- Virus classification
- Virusoid
References
- ^ Di Serio F, Owens RA, Li SF, Matoušek J, Pallás V, Randles JW, Sano T, Verhoeven JT, Vidalakis G, Flores R (November 2020). Zerbini FM, Sabanadzovic S (eds.). "Viroids". Archived from the original on December 2, 2020. Retrieved February 3, 2021.
- PMID 30699972.
- PMID 32752288.
- ^ PMID 36696902.
- ISBN 978-0-12-384685-3.
- ^ PMID 5095900.
- ^ a b "ARS Research Timeline – Tracking the Elusive Viroid". 2006-03-02. Retrieved 2007-07-18.
- ^ PMID 16078879.
- S2CID 221581424.
- .
- PMID 33800543.
- PMID 2480600.
- PMID 33800543.
- ^ PMID 27339130.
- ^ PMID 28448743.
- ^ PMID 35054497.
- PMID 24198831.
- ^ ISBN 978-0123751485.
- S2CID 44660564.
- PMID 22719735.
- PMID 28738223.
- PMID 1546460.
- PMID 14978267.
- PMID 22678590.
- ^ S2CID 246987005.
- PMID 7542779.
- PMID 11172112.
- ^ PMID 15246267.
- PMID 23610439.
- ^ PMID 25002087.
- ISBN 978-0-12-384872-7.
- PMID 36840552.
- ^ a b Koumoundouros T (29 January 2024). "'Obelisks': Entirely New Class of Life Has Been Found in The Human Digestive System". ScienceAlert. Archived from the original on 29 January 2024. Retrieved 29 January 2024.
- ^ from the original on 29 January 2024. Retrieved 29 January 2024.
- ^ Diener, T O. "Circular RNAs: relics of precellular evolution?."Proc.Natl.Acad.Sci.USA, 1989;86(23):9370-9374
- ^ PMID 26047558.
- .
- ^ ISBN 978-1-284-03968-9.
- PMID 1069269.
- PMID 33460914.
- PMID 4728831.
- S2CID 19398777.
- .
- New York Times. Retrieved November 22, 2014.
External links
- Viroids/ATSU
- ViroidDB, a database of viroids and viroid-like circular RNAs