Вироидтар: Өсімдіктердегі және басқа да организмдердегі патогендік шеңберлі РНҚ

Pathogenic small single stranded circular RNA

a variant of it which is dependent on viruses

Viroids are small single stranded, circular RNAs that are infectious pathogens. Unlike viruses, they have no protein coating. All known viroids are inhabitants of angiosperms (flowering plants), and most cause diseases, whose respective economic importance to humans varies widely. A recent metatranscriptomics study suggests that the host diversity of viroids and other viroid like elements is broader than previously thought and that it would not be limited to plants, encompassing even the prokaryotes. 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. 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. 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. Although viroids are composed of nucleic acid, they do not code for any protein. 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. 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. 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. 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.

"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.

"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.

"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. The only types found are closely related to the original "carnation small viroid like RNA" (CarSV). These elements may act as a homologous substrate upon which recombination may occur and are linked to double stranded break repair. These elements are dubbed retroviroids as the homologous DNA is generated by reverse transcriptase that is encoded by retroviruses. 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.

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.

Diener's 1989 hypothesis 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., 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 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). 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. 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. The single strandedness and circularity of viroids was confirmed by electron microscopy, The complete nucleotide sequence of potato spindle tuber viroid was determined in 1978. 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. Four additional viroids or viroid like RNA particles were discovered between 2009 and 2015. In 2014, New York Times science writer Carl Zimmer published a popularized piece that mistakenly credited Flores et al. with the hypothesis' original conception. 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.