Viroid

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Viroid
PSTviroid.png
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Informal group: Subviral agents
(unranked):Viroid
Families

Pospiviroidae
Avsunviroidae

Viroids are small single-stranded, circular RNAs that are infectious pathogens. [1] [2] Unlike viruses, they have no protein coating. All known viroids are inhabitants of angiosperms (flowering plants), [3] and most cause diseases, whose respective economic importance to humans varies widely. [4] 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. [5]

Contents

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. [6]

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 protein. [10] [11] 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. [12]

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 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. [18]

Taxonomy

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

As of 2005: [9]

Transmission and replication

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- 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. [19] [20] 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. [21]

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. [9]

RNA silencing

There has long been uncertainty over how viroids induce symptoms in plants without encoding any protein products within their sequences. [22] Evidence suggests that RNA silencing is involved in the process. First, changes to the viroid genome can dramatically alter its virulence. [23] 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. [24] 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. [25]

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 "virusoids", fungal "ambivirus", and the much larger HDV-like Ribozyviria ) and "retroviroids". Most of them also carry some type of a ribozyme. [5]

Viroid-like satellite RNAs

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. [26]

Ambiviruses

"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. [27] [28] [29]

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. [30] The only types found are closely related to the original "carnation small viroid-like RNA" (CarSV). [31] [32] These elements may act as a homologous substrate upon which recombination may occur and are linked to double-stranded break repair. [32] [33]

These elements are dubbed retroviroids as the homologous DNA is generated by reverse transcriptase that is encoded by retroviruses. [34] [35] 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. [26] They appear to co-occur with a pararetrovirus. [36]

Obelisks

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. [37] [38]

RNA world hypothesis

Diener's 1989 hypothesis [39] 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., [34] 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). [15] [16] [17] 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. [5]

Control

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. [40]

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. [41]

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. [42]

In 1976, Sanger et al. [43] 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. [44]

The single-strandedness and circularity of viroids was confirmed by electron microscopy, [45] The complete nucleotide sequence of potato spindle tuber viroid was determined in 1978. [46] 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. [42] [47]

Four additional viroids or viroid-like RNA particles were discovered between 2009 and 2015. [40]

In 2014, New York Times science writer Carl Zimmer published a popularized piece that mistakenly credited Flores et al. with the hypothesis' original conception. [48]

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. [37] [38]

See also

Related Research Articles

<span class="mw-page-title-main">RNA world</span> Hypothetical stage in the early evolutionary history of life on Earth

The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence of this stage.

Virus classification is the process of naming viruses and placing them into a taxonomic system similar to the classification systems used for cellular organisms.

Hepatitis D is a type of viral hepatitis caused by the hepatitis delta virus (HDV). HDV is one of five known hepatitis viruses: A, B, C, D, and E. HDV is considered to be a satellite because it can propagate only in the presence of the hepatitis B virus (HBV). Transmission of HDV can occur either via simultaneous infection with HBV (coinfection) or superimposed on chronic hepatitis B or hepatitis B carrier state (superinfection).

<span class="mw-page-title-main">Ribozyme</span> Type of RNA molecules

Ribozymes are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material and a biological catalyst, and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems.

Virusoids are circular single-stranded RNA(s) dependent on viruses for replication and encapsidation. The genome of virusoids consists of several hundred (200–400) nucleotides and does not code for any proteins.

<span class="mw-page-title-main">Satellite (biology)</span> Subviral agent which depends on a helper virus for its replication

A satellite is a subviral agent that depends on the coinfection of a host cell with a helper virus for its replication. Satellites can be divided into two major classes: satellite viruses and satellite nucleic acids. Satellite viruses, which are most commonly associated with plants, are also found in mammals, arthropods, and bacteria. They encode structural proteins to enclose their genetic material, which are therefore distinct from the structural proteins of their helper viruses. Satellite nucleic acids, in contrast, do not encode their own structural proteins, but instead are encapsulated by proteins encoded by their helper viruses. The genomes of satellites range upward from 359 nucleotides in length for satellite tobacco ringspot virus RNA (STobRV).

<span class="mw-page-title-main">Theodor Otto Diener</span> American plant pathologist (1921–2023)

Theodor Otto Diener was a Swiss-American plant pathologist. In 1971, he discovered that the causative agent of the potato spindle tuber disease is not a virus, but a novel agent, which consists solely of a short strand of single-stranded RNA without a protein capsid, eighty times smaller than the smallest viruses. He proposed to name it, and similar agents yet to be discovered, viroids. Viroids displaced viruses as the smallest known infectious agents.

The potato spindle tuber viroid (PSTVd) was the first viroid to be identified. PSTVd is a small, single stranded circular RNA molecule closely related to the chrysanthemum stunt viroid. Present within the viroidal RNA is the Pospiviroid RY motif stem loop common to its genus. The natural hosts are potatoes and tomatoes. All potatoes and tomatoes are susceptible to PSTVd and there is no form of natural resistance. Natural infections have also been seen in avocados and infections in other solanaceous crops have been induced in the laboratory. Until 2017 PSTVd was thought to be unable to infect Solanum sisymbriifolium. Then in May seeds exported by a Dutch company were noticed to be infected. These seeds were shipped from the company, but had been originally bred to their specifications in two Asian countries. Pstv also causes Tomato bunchy top and is seed transmitted in tomato.

The Pospiviroidae are a incertae sedis family of ssRNA viroids with 5 genera and 39 species, including the first viroid to be discovered, PSTVd, which is part of genus Pospiviroid. Their secondary structure is key to their biological activity. The classification of this family is based on differences in the conserved central region sequence. Pospiviroidae replication occurs in an asymmetric fashion via host cell RNA polymerase, RNase, and RNA ligase. Its hosts are plants, specifically dicotyledons and some monocotyledons.

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Peach latent mosaic viroid is a species of the genus Pelamoviroid, which belongs to the family Avsunviroidae. This family is characterized as having chloroplastic viroids with hammerhead ribozymes. Peach latent mosaic viroid is a 336-351nt circular RNA which has a branched formation. This branched formation is stabilised by a pseudoknot between two kissing loops. Peach latent mosaic viroid was first described in the 1980s in Spain by a group of scientists.

<i>Avsunviroidae</i> Family of viruses

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<span class="mw-page-title-main">Hammerhead ribozyme</span>

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<span class="mw-page-title-main">Hairpin ribozyme</span> Enzymatic section of RNA

The hairpin ribozyme is a small section of RNA that can act as a ribozyme. Like the hammerhead ribozyme it is found in RNA satellites of plant viruses. It was first identified in the minus strand of the tobacco ringspot virus (TRSV) satellite RNA where it catalyzes self-cleavage and joining (ligation) reactions to process the products of rolling circle virus replication into linear and circular satellite RNA molecules. The hairpin ribozyme is similar to the hammerhead ribozyme in that it does not require a metal ion for the reaction.

<span class="mw-page-title-main">Hepatitis delta virus ribozyme</span>

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<span class="mw-page-title-main">Ribozyviria</span> Realm of viruses

Ribozyviria is a realm of satellite nucleic acids — infectious agents that resemble viruses, but cannot replicate without a helper virus. Established in ICTV TaxoProp 2020.012D, the realm is named after the presence of genomic and antigenomic ribozymes of the Deltavirus type. The agents in Ribozyviria are satellite nucleic acids, which are distinct from satellite viruses in that they do not encode all of their own structural proteins but require proteins from their helper viruses in order to assemble. Additional common features include a rod-like structure, an RNA-binding "delta antigen" encoded in the genome, and animal hosts. Furthermore, the size range of the genomes of these viruses is between around 1547–1735nt, they encode a hammerhead ribozyme or a hepatitis delta virus ribozyme, and their coding capacity only involves one conserved protein. Most lineages of this realm are poorly understood, the notable exception being the genus Deltavirus, comprising the causal agents of hepatitis D in humans.

Retrozymes are a family of retrotransposons first discovered in the genomes of plants but now also known in genomes of animals. Retrozymes contain a hammerhead ribozyme (HHR) in their sequences, although they do not possess any coding regions. Retrozymes are nonautonomous retroelements, and so borrow proteins from other elements to move into new regions of a genome. Retrozymes are actively transcribed into covalently closed circular RNAs and are detected in both polarities, which may indicate the use of rolling circle replication in their lifecycle.

References

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