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Do DNA viroids exist?

Do DNA viroids exist?


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Viroids are described as short circular ssRNA with no protein coating.

Are there any analogous infectious particles that contain DNA instead of RNA?

If DNA viroids do not exist, is there an obvious reason for this?


The definition on the Wikipedia page you recite uses the language 'no protein coating' as opposed to 'protein coating'.

A protein coating would make it a virus.

No protein-coating would make it a Viroid.

As far as we know DNA Viroids do not exist. But this is an advancing field of research and it depends on what structure of genetic material you are referring too.

The general different types of genetic material include - but are not limited to: Single-stranded DNA (ssDNA), Double-stranded DNA (dsDNA), Single-stranded RNA (ssRNA), and double-stranded RNA (dsRNA).

There is more information on Classes I and II DNA viruses here: https://www.ncbi.nlm.nih.gov/books/NBK21523/

If there were no DNA viruses without a protein coating - what is the reason? Viroids only infect plant cells. It may be that Viroids route of entry via microscopic junctions between plant cells (Plasmodesmata) are only large enough to fit single stranded genetic material. Therefore allowing ssDNA and ssRNA, but not dsDNA and dsRNA to act as plant cell infectious agents.


Difference between Viroids and Lichens

It has been discovered a new infectious agent that was smaller than viruses and caused potato spindle tuber disease. It was found to be a free RNA it lacked the protein coat that is found in viruses, hence the name viroid. The RNA of the viroid was of low molecular weight.

Viroids are a group of pathogens comprising the smallest known agents of infectious disease. They are un-encapsulated and are capable of replicating autonomously in susceptible cells. Positively identified viroids composed of single-stranded RNA have been isolated from higher plants, but the existence of DNA viroids pathogenic to animals is suspected.

Lichens:

Lichens are symbiotic associations i.e. mutually useful associations, between algae and fungi as shown in coloured image 11.7. Algae prepare food for fungi and fungi provide shelter and absorb mineral nutrients and water for its partner. Lichens are very good pollution indicators – they do not grow in polluted areas.

It has been discovered that lichens are two organisms namely an alga and a fungus which living together as one. Mushrooms are perhaps the most familiar. Only certain species of fungi combine with algae to form lichens. The fungus acts as the house for the alga, giving it shelter from the weather.

The fungus makes up 90 percent of the whole lichen. In lichens, the alga makes food energy that is carbohydrates. Because the fungus cannot make its own food, it harvests energy from the alga. Symbiosis occurs when two organisms benefit by living together.

The symbiotic relationship of fungus and alga helps lichens adapt to life in all kinds of places. Some lichens grow on dead wood, on tree bark, or on the ground, such as reindeer lichen and some grow on rocks. All lichens need some water to grow, but they can exist in a dry state for a long time. Lichens need water and sunlight to grow.

Lichens do most of their growing in spring and fall when rainfall adds moisture to the air. A lichens cross-section is shown in colored image 11.8. When the weather is dry, lichens may go dormant.

New lichens form in three basic ways:

(1) Small pieces of lichen may break off and grow.

(2) Lichen may shoot out little packets of alga cells surrounded by fungal threads and each packet can grow into lichen.

(3) Fungus in lichen may release dust like spores and if spores land on an alga, a new fungus develops and lives with the alga, forming new lichen.

Lichens thrive in clean, moist air. Fewer lichens live in cities because they have trouble surviving in polluted air. Because lichens take in water and air, they also absorb pollutants such as sulfur dioxide. This gas is released into the air by burning coal and oil. By measuring the amount of sulfur in lichens, scientists can determine how much sulfur dioxide has entered the air. In heavily polluted places,

Lichens cannot grow because sulfur dioxide harms the algae’s chlorophyll, the essential ingredient for producing the lichen’s food energy. American Indians found many uses for lichens. They used lichens to dye fabric such as yarn to weave rugs, brew medicinal teas, and to make poultices to soothe skin irritations.

They discovered that super-absorbent lichens also made fine baby diapers. Rich in carbohydrates, lichens provide energy for animals that eat them. Squirrels, chipmunks, deer, and spruce grouse all nibble on lichens.

Lichens are a large group of symbiotic associations between fungi and green and occasionally blue green algae. Several genera of algae and of fungi are involved and the associations are so stable and of such varied but distinct types that the lichens have been classified into genera and species. A variety of incompatibility phenomena are often manifesting between individual lichens. Confined to terrestrial habitats and often used as indicators of pollution status of the environment.


Prions

Prions , so-called because they are proteinaceous, are infectious particles&mdashsmaller than viruses&mdashthat contain no nucleic acids (neither DNA nor RNA). Historically, the idea of an infectious agent that did not use nucleic acids was considered impossible, but pioneering work by Nobel Prize-winning biologist Stanley Prusiner has convinced the majority of biologists that such agents do indeed exist.

Fatal neurodegenerative diseases, such as kuru in humans and bovine spongiform encephalopathy (BSE) in cattle (commonly known as &ldquomad cow disease&rdquo) were shown to be transmitted by prions. The disease was spread by the consumption of meat, nervous tissue, or internal organs between members of the same species. Kuru, native to humans in Papua New Guinea, was spread from human to human via ritualistic cannibalism. BSE, originally detected in the United Kingdom, was spread between cattle by the practice of including cattle nervous tissue in feed for other cattle. Individuals with kuru and BSE show symptoms of loss of motor control and unusual behaviors, such as uncontrolled bursts of laughter with kuru, followed by death. Kuru was controlled by inducing the population to abandon its ritualistic cannibalism.

On the other hand, BSE was initially thought to only affect cattle. Cattle dying of the disease were shown to have developed lesions or &ldquoholes&rdquo in the brain, causing the brain tissue to resemble a sponge. Later on in the outbreak, however, it was shown that a similar encephalopathy in humans known as variant Creutzfeldt-Jakob disease (CJD) could be acquired from eating beef from animals with BSE, sparking bans by various countries on the importation of British beef and causing considerable economic damage to the British beef industry (FIgure (PageIndex<1>)). BSE still exists in various areas, and although a rare disease, individuals that acquire CJD are difficult to treat. The disease can be spread from human to human by blood, so many countries have banned blood donation from regions associated with BSE.

The cause of spongiform encephalopathies, such as kuru and BSE, is an infectious structural variant of a normal cellular protein called PrP (prion protein). It is this variant that constitutes the prion particle. PrP exists in two forms, PrP c , the normal form of the protein, and PrP sc , the infectious form. Once introduced into the body, the PrP sc contained within the prion binds to PrP c and converts it to PrP sc . This leads to an exponential increase of the PrP sc protein, which aggregates. PrP sc is folded abnormally, and the resulting conformation (shape) is directly responsible for the lesions seen in the brains of infected cattle. Thus, although not without some detractors among scientists, the prion seems likely to be an entirely new form of infectious agent, the first one found whose transmission is not reliant upon genes made of DNA or RNA.

Figure (PageIndex<1>): (a) Endogenous normal prion protein (PrP c ) is converted into the disease-causing form (PrP sc ) when it encounters this variant form of the protein. PrP sc may arise spontaneously in brain tissue, especially if a mutant form of the protein is present, or it may occur via the spread of misfolded prions consumed in food into brain tissue. (b) This prion-infected brain tissue, visualized using light microscopy, shows the vacuoles that give it a spongy texture, typical of transmissible spongiform encephalopathies. (credit b: modification of work by Dr. Al Jenny, USDA APHIS scale-bar data from Matt Russell)


Here, I report how the biological community reacted to my hypothesis and by what means scientists suggested to test its plausibility.

While my hypothesis was frequently cited in the biological literature with little or no comment, it was first critically examined in 1994 by Cheles-Flores [12], who pointed out that “a difficulty may be raised against the Diener hypothesis that viroids may be interpreted as molecular fossils of the RNA world,” in that viroids are known to exist only in angiosperms, whose first appearance was in the Cretaceous period. The author presented a scheme, based on cyanobacteria, which, after “extensive additional work by plant pathologists”, if successful, would “remove the importance, in the preservation of the relics of the RNA world, of the time of the first appearance of angiosperms” and thus show that “viroids could have been present during the major part of the duration of life on Earth.”

In a second 1994 paper [13], Chela-Flores expanded on these thoughts, but again asked the question whether it is possible to envisage a possible evolutionary pathway of the early replicators spanning the vast time span separating the first appearance of the angiosperms, late in the Mesozoic era (the Lower Cretaceous) from the most likely sub-eras in which the RNA world may have occurred, namely the Hadean/Early Archean. The author suggested that “through horizontal gene transfer, as well as through a series of symbioses in the precursor cells of the land plants, the genes of the replicases associated with RNA plasmids and other putative DNA-independent RNA replicators may have been transferred vertically, eventually becoming specific to the angiosperms.” However, no further report from Cheles-Flores has appeared apparently, the proposed experimental work has not been performed or it was not successful.

In 1998, Jeffares. et al. [14] reported results of a theoretical study, in which the authors estimated—based on what they considered to be plausible parameters—which of many individual, extant RNAs may be relics of the RNA World and which are probably of more recent provenance. While the authors cited my 1989 hypothesis (as described in a 1993 book chapter [15]), they do not discuss it, or its relevance to their work.

Given the strong trend RNA --- > RNP --- > protein, Jeffares et al. examined the phylogenetic distribution of RNA in modern organisms for relics and thus developed a model for complexity in the RNA world. Candidates were RNAs which fit at least one of their criteria: “catalytic, ubiquitous (or at least conserved within the eukaryotic lineage…), or central to some aspect of metabolism.”

Most importantly, in the context of the present assessment, is Jeffares et al.’s conclusion that viroids, plant satellite RNAs, and “hammer heads” are, indeed, ancient relics of the RNA world. It is not clear, however, on which of the parameters this conclusion is based. Viroids are listed confusingly (together with “hammer heads”) at the bottom of table 2—titled “RNA functions in modern cells”— under the rubric “Function,“ as “Various,” under the rubric “Distribution” as “Plant satellite RNA,“ and under the rubric “In the RNA world?” as “In RNA world (see text)” but this referral in a footnote is not illuminating.

By the authors’ parameters, many, if not most, extant RNAs (or their precursors) were also already present in the RNA world, including precursors of the three major cellular RNAs: rRNA, mRNA, and tRNA.

A distinction must be made, however, between Jeffares et al.’s chosen criteria for relics and those chosen in my 1989 publication. Whereas Jeffares et al. developed their “model for the final complexity of the RNA World,”— just prior to the evolution of translation and proteins—it was actual properties of viroids, listed in 1989, which I considered to suit them for survival in a prebiotic “soup” far less hospitable than that envisioned by Jeffares et al., i.e., for an earlier stage in the RNA World.

Therefore, if correct, Jeffares et al.‘s results would not only be in accord with the relic hypothesis, but more accurately define the stage of the RNA World, in which viroids (or their precursors) could presumably have prospered. However, Jeffares et al.’s choice of parameters is, by necessity, subjective and any substitutions would likely alter the conclusions. Even given the existence of an ancient RNA World, there are problems with understanding how, without DNA or proteins, cellular life could have evolved. One of the major problems is the question as to how one and the same kind of RNA molecule could serve simultaneously as both information carrier and biocatalyst, which would require a combination of features: good “templating” ability (for replication) and stable folding (for ribozymes). This poses a paradox, because well folded sequences are poor templates for copying, but poorly folded sequences are unlikely to be good ribozymes [16].

In 2013, Ivica et al. [16] described a novel strategy to overcome this dilemma it is based on G:U wobble pairing in RNA: Unlike Watson-Crick base pairs, wobble pairs contribute highly to the energetic stability of the folded structure of their sequence, but only slightly, if at all, to the stability of the folded reverse complement. Sequences in the RNA World might therefore combine stable folding of the ribozyme with an unstructured, reverse-complementary genome, resulting in a ‘division of labor’ between the strands.

The investigators demonstrated this strategy by use of computational simulations of RNA sequences (including 40 viroid sequences) and their folding as experimental models of early replication, “involving non-enzymatic, template-directed, RNA primer extension.” The investigators recognized the fact that “interestingly, viroid RNA sequences…show significant asymmetry in folding energy between the infectious (+) and template (-) strands due to G: U pairing, suggesting that this strategy may even be used by replicators in the present day world,” as well, as postulated, in the RNA world. If so, this viroid-suggested process should be amenable—beyond computer simulation—by experimentation with actual RNA molecules.

Also in 2013, Ma et al. [17] cited my 1989 paper and—“inspired by features of viroids,”—studied their properties in mathematical simulations. Ma et al. were particularly interested in determining whether the known structure of viroids, “their circularity and small, self-splicing ribozymes (e.g., the hammerhead ribozymes), could have been instrumental in helping them overcome problems in replication and stability.” Their study indicated “that an RNA chromosome can spread (increase in quantity and be sustained) in the system, if it is a circular one and its linear ‘transcripts’ are readily broken at the sites between genes the chromosome works as genetic material and ribozymes ‘coded’ by it serve as functional molecules.” Ma et al. concluded that circularity and self-cleavage are important for the spread of the chromosome.” The authors concluded that “in the RNA world, circularity and self-cleavage may have been adopted as a strategy to overcome the immediate difficulties for the emergence of a chromosome (with linked genes).” While Ma et al. thus seemed to provide important evidence for the possible ancient nature of viroids, their conclusions are placed in doubt by the unknown significance of mathematical simulations to real-world evolutionary situations.

Forterre’s revolutionary proposal [18] to divide the biosphere according to organisms’ fundamental properties into two parts: capsid-encoding organisms (i.e., viruses) and ribosome-encoding cellular organisms. The author’s proposal is compatible with my 1989 hypothesis, except that viroids and other subviral agents belong to neither part, but must be accorded a new, third part, consisting of non-capsid, non-cellular life forms.

Theoretical studies [19] indicate that “selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators.” Indeed, genetic parasites seem to be truly ubiquitous: some such elements apparently are associated with all cellular life forms and mathematical models of the evolution of replicator systems—aimed at the reconstruction of the first stages in the history of life—invariably reveal partitioning into hosts and parasites [19]. It is therefore not surprising, that viroids, if viewed as survivors of the RNA World, would not be self-replicating, but would, like viruses, depend on host enzymes for their (autonomous) replication.

Koonin and Dolja [20] studied “the evolutionary relationships between typical viruses with different replication-expression strategies and capsidless genetic elements,” on the basis of which they proposed a paradigm of virus-world evolution that is in accord with Forterre’s model. The authors stated that “host-parasite arms races are a major formative factor in all evolution of life” and that “the simplest genomic parasites might be small RNA molecules that encoded no proteins and consisted primarily of cis signals for replication.” Koonin and Dolja [20] also described features of hepatitis delta virus (HDV), which “appears to be a derivative of a viroid that encodes a protein required for replication and virion formation, and is encapsidated into particles that consist of the capsid protein of the helper Hepatitis B virus” and that “most likely HDV evolved from a viroid-like ancestor by acquiring a protein-encoding gene from a still unknown source and adapting to use the capsid protein of the helper virus.”

Koonin and Dolja [21] concluded from a landmark, comprehensive review of all virus groups, that “among the parasites of modern organisms, viroids that cause many diseases of plants and satellites of plant RNA viruses show a striking resemblance to the putative primordial parasites.” However, “given that viroids so far have been identified only in plants,” the authors considered it “unlikely that viroids are direct descendants of the primordial parasites.” But then, the authors stated again: “Nevertheless, viroids seem to recapitulate the principle features of the selfish elements from the ancient RNA world”—thus leading to an internal contradiction, in that by one criterion (molecular properties), viroids “strikingly” appear to be descendants of primordial RNAs, whereas by another criterion (apparent evolutionary age), they clearly are not. Which is correct?


Viruses, Viroids, and Prions

David P. Clark , . Michelle R. McGehee , in Molecular Biology (Third Edition) , 2019

7.2 Viroids Are Naked Molecules of Infectious RNA

Viroids are infectious agents that consist only of naked RNA without any protective layer such as a protein coat. Viroids infect plants (but no other forms of life) and are replicated at the expense of the host cell. Viroid genomes are small single-stranded circles of RNA that are only 250–400 bases long. For example, the coconut cadang-cadang viroid has only 246 bases of RNA ( Fig. 24.34 ).

Figure 24.34 . Coconut Cadang-Cadang Viroid, Variant CCCVd.1

Complete sequence (246 bases) of coconut cadang-cadang viroid.

Viroids have no protective coat, just single-stranded RNA.

Although viroid RNA is single-stranded, base pairing occurs between bases on opposite halves of the circle to produce a rod-like structure ( Fig. 24.35 ). Because viroids have no protein coat, they lack attachment proteins and cannot recognize and penetrate healthy cells as can a true virus. Viroids can infiltrate a plant cell only when its surrounding membrane is already damaged. They often take advantage of damage done to plant tissue by insects. Once inside, viroids may be passed from one plant cell to another via cellular junctions.

Figure 24.35 . Viroid RNA Forms a Rod-Like Structure

Viroids are naked pieces of RNA, which can only infiltrate an already-damaged plant cell. The viroid is a single-stranded piece of circular RNA that has an unusual structure due to complementary base pairing. Some form a simple rod-like structure, whereas other viroids have a complex branched structure.

Viruses all encode at least one protein needed for replication of the virus genome. However, viroid RNA does not contain any genes that encode proteins it merely carries signals for its own replication by the host machinery. Although the viroid encodes no protein enzymes, the viroid RNA itself acts as a ribozyme that is, the RNA catalyzes an enzymatic reaction. Whether or not a viroid has any genes depends on whether we count the sequence of RNA that possesses ribozyme activity as a gene.

Viroids have no protein coding genes, but the viroid RNA itself acts as a ribozyme.

Viroids replicate by a rolling circle mechanism ( Fig. 24.36 ). The viroids own ribozyme activity is used for self-cleavage of the multimeric RNA generated during replication. Host enzymes provide all other functions. First, host RNA polymerase copies the circular plus strand to form a multimeric minus strand. Site-specific cleavage of this strand by the viroid ribozyme gives monomers that are circularized by a host RNA ligase. The minus-stranded circles are the templates for a second round of rolling circle replication by RNA polymerase. The resulting multimeric plus strand undergoes ribozyme cleavage to create monomers. These are circularized to produce the progeny viroids (circular, positive single-stranded RNA).

Figure 24.36 . Viroids Replicate by a Rolling Circle Mechanism

Two rounds of rolling circle replication are used by viroids to replicate themselves. Upon entry into a plant cell, the circular, positive single-stranded RNA uses the plant RNA polymerase to make a minus strand. The polymerase continues to make multiple copies using the rolling circle mechanism. The linear, negative single-stranded RNA uses its own catalytic activity to cut itself into genome-sized units that are circularized. The circular, negative single-stranded RNA then undergoes another round of rolling circle replication and self-cleavage to produce multiple copies of the linear plus strand. Finally, these are circularized to give the infectious circular, positive single-stranded RNA form.

Most viroids replicate in the plant cell nucleus and rely on RNA polymerase II for RNA synthesis. A smaller group of viroids (e.g., chrysanthemum chlorotic mottle viroid) have a highly branched structure, rather than a rod with bulges, and replicate in the chloroplast.

Some viroids cause no detectable symptoms in their host plants, whereas others cause massive damage. How viroids damage plants is still rather mysterious. However, it appears that the viroid and/or its replicative intermediates trigger RNA interference (see Chapter 20 : Genome Defense). This results in the production of short single-stranded RNA molecules (known as vsRNA—viroid short RNA) of the same size as the microRNAs widely used by plant cells to regulate genes ( Fig. 24.37 ). This decreases expression of multiple plant genes, hence causing disease.

Figure 24.37 . Viroids Cause Disease by Making vsRNA

Cutting of precursor microRNA (pre-miRNA) by the nucleases Dicer or Drosha releases the small regulatory RNAs—miRNA. Cutting of viroid RNA by the same nucleases releases small RNA molecules—vsRNA. These mimic the action of miRNA. The RISC complex helps both vsRNA and miRNA to bind to complementary sequences on target messenger RNAs. This alters the expression of the mRNA. In the case of the viroid, expression is abnormal and disease results.

Viroids cause plant disease by triggering RNA interference.


Viroids: Origin, Meaning and Replication | Microbiology

In this article we will discuss about:- 1. Origin of Viroid 2. Meaning of Viroids 3. Viroid Genome 4. Replication.

Origin of Viroid:

So far no sufficient information is available that can lend support for the origin of viroids.

Following are some of the speculations regarding the origin of viroids:

(a) Viroids are supposed to be the primitive viruses and must have originated from cellular RNAs. This view has been emphasized by Watson (1987). In most of the healthy plants, RNA synthesis on RNA template must occur. Viroids would have originated from this RNA as they did not induce the biosynthetic machinery of their host from their own replication.

(b) Except tRNA and 5S RNA, several low molecular weight RNAs have been found to be associated with several virus infections such as, tobacco leaves infected by TMV, in E. coli infected by QB phage, in oncogenic RNA viruses, etc.

It is supposed that viroids would have been originated from virus induced low molecular weight RNAs which later on adapted as autonomously replicating infectious entities. Therefore viroids provide the evidence that they are the degenerated virus entities.

(c) With the discovery of spilt genes and RNA splicing in eukaryotes it has been suggested that viroids might have originated through circularization of spliced out introns. If such excised sequences would pursuit the extensive intra-molecular base-pairing (as viroids do) and if they are circularized they might become established and escape degradation. If such introns would compromise the appropriate recognition sequence they might be transcribed by host enzymes capable of functioning as an RNA polymerase and thus escape from the control mechanism of host cell.

Meaning of Viroids:

Diener (1971), a plant pathologist at the Agricultural Research Service in Maryland, for the first time discovered and named this diseases causing agent as ‘viroids’.

Viroids are small (200- 400 nucleotide long), circular RNA molecules with a rod-like secondary structure which possess no capsid or envelope arid are associated with certain plant diseases. Their replication strategy is similar to that of viruses as they are also obligate intracellular parasites.

Viroids are classified into two families as given below:

a. Family Pospiviroidae:

i. Genus Pospiviroid: type species: Potato spindle tuber viroid

ii. Genus Hostuviroid type species: Hop stunt viroid

iii. Genus Cocadviroid: type species: Coconut cadangcadang viroid

iv. Genus Apscaviroid type species: Apple scar skin viroid

v. Genus Coleviroid: type species: Co/ens blumei viroid

b. Family Avsunviroidae:

i. Genus Avsunviroid type species: Avocado sun-blotch viroid

ii. Genus Pelamoviroid: type species: Peach latent mosaic viroid

Fig. 16.22 Shows phylogenetic relationships between viroids, virusoids and satellites.

The classification described above is used on analysis of the central conserved region (CCR). Members of the Avsunviroidae lack a CCR region, whereas that of Pospiviroidae posses the CCR region. Until 1970s, viruses were considered as the smallest infectious agent.

The discovery of viroids has proved that the infectious entities smaller than virus exist in nature. For the first time T.O. Diener and W.B. Raymer (1967) discovered potato spindle tuber viroids (PSTV) which caused a disease in potatoes.

This disease resulted in loss of millions of dollars. Moreover, Diener (1971) advanced the concept of viroids on the basis of newly established properties of the infectious agent responsible for potato spindle tuber disease (Fig. 16.23.).

Their properties differ basically from those of conventional viruses in at least following five important features:

(i) The pathogen exists in vivo as an encapsulated in the RNA,

(ii) Virion like particles are not detected in the infected tissues,

(iii) The infectious RNA is of low molecular weight,

(iv) Despite its small size, the infectious RNA replicates autonomously in susceptible cells i.e. no helper virus is required, and

(v) The infectious RNA consists of one molecular species only.

(vi) Host Range: The other plants susceptible to viroids are potato, citrus, cucumber and chrysanthemum, hops, stunt, tomato banchy top, etc.

The host range of PSTV is the members of Solanaceae and Compositae. Recently, mild strains of PSTV were observed in cultivars Kufri, Chandramukhi, Kufri Jyoti of potato and wild solanums in Himachal Pradesh in India but these are not economically important in India as compared to the countries like USA, Canada, USSR and China. Symptoms vary according to the cultivars, strain and age of infection.

Stem and petiole are more acute than the other parts. Diseased tubers get elongated i.e. with pointed ends having numerous eyes and heavy brows. The viroids are contagious and spread mainly through mechanical injury/contact but also through pollen and true seeds from the infected plants. The control measures are the use of diseased free seeds, early roguing and avoiding cutting of potato tubers.

Viroid Genome:

Viroids are low molecular weight nucleic acid (1.1-1.3 × 10 5 Da). They are the only known pathogens that do not code for any protein. They differ from viruses in lacking protein coat The PSTV has been found to be present in nucleus of the infected cells but not the other subcellular organelles of potato. About 200 to 10,000 copies of PSTV are found in each cell.

These are just a small fragment of RNA molecule which are commonly circularized, and remain as naked RNA strand consisting of about 250-370 nucleotides. The genes lack the initiation codon (AUG) for protein synthesis.

Mostly the nucleotides are paired resulting in dsRNA molecule due to the presence of intra molecular complementary regions. Hence it appears as rods. The dsRNA has closed folded, three dimensional structure (Fig.16.24).

The closed single stranded circle has extensive intrastrand base pairing and interspersed unpaired loops. Viroids have five domains. Most changes in pathogenicity of viroids seem to arise from variation in the pathogenicity domain (P) and left terminal domain (TL).

The other domains are the central conserved region (CCR), variable domains (V), and rigid terminal domain (TR). The folded structure probably protects it from the attack by cellular enzymes. RNA does not code for any protein just like introns.

PSTV is restricted only to plants. However, no conclusive evidence is available for their presence in the animals. Moreover, a few animal diseases were suspected to be caused by viroids but no specific immunity occurred.

Replication of Viroids:

There is no convincing evidence for the replication of viroid genome. It is likely that nucleic acid codes for an enzyme replicase which is essential for its replications. Possibly, the members of Avsunviroids replicate in chloroplasts, whereas that of Pospiviroids replicate inside the nucleus and nucleolus.

Three enzymes are required for replication of viroids e.g. RNA polymerase, RNase and RNA ligase. RNA polymerase 11 is involved in synthesis of mRNA from DNA. Using viroid’s RNA as template, this enzyme catalyzes the synthesis of new RNA by rolling circle mechanism.

Members of the Avsunviroid lack a CCR and possess a ribozyme activity. Hence, they possess catalytic properties to carryout self-cleavage and ligation of genomes from larger replication intermediates. Probably Avsunviroids replicate via a symmetric rolling circle mechanism, whereas Pospiviroids use an asymmetric mechanism (Fig. 16.25).

Therefore, the infectious circular (+) RNA strand of a viroid serves as a template to make a large linear multimeric negative strand by using RNA polymerase II. Thereafter, Pospiviroids synthesize (+) sense RNA from this long linear molecule via asymmetric replication pathway. The (+) RNA strand is cleaved into a unit viroid lengths by RNase activity of the host. Then this molecule is ligated to form a circular viroid.

In Avsunviroid replication the long sense RNA is self cleaved by ribozyme activity. A negative circle is formed upon circularization of RNA. A second rolling circle event makes a long linear positive strand, which is again cleaved by the activity of ribozyme. Then the short viroid RNA is ligated to form the circular structure.

There are two possibilities for genome replications, RNA dependent replication and DNA dependent replication:

(a) RNA directed replication:

According to this scheme, it appears that RNA directed RNA polymerase are present to a limited extent in the normal cell of plant which may synthesize the RNA molecules directed by the RNA.

(b) DNA directed replication:

The viroids are transcribed from a cellular DNA of the host cell complementary to viroid RNA. In the infected cell new DNA may be produced with the infecting viroid RNA which serves as template. This makes the assumption for the presence of reverse transcriptase i.e. RNA directed DNA polymerase. From this the viroid RNAs are synthesized.

Branch and Robertson (1984) have analysed the viroid specific nucleic acids on tomato plants infected by PSTV. They conclude that (i) viroids replicate by direct RNA to RNA copying, (ii) the host cells possibly contain the machinery needed for replication of viroid RNA.


Biology 171

By the end of this section, you will be able to do the following:

  • Describe prions and their basic properties
  • Define viroids and their targets of infection

Prions and viroids are pathogens (agents with the ability to cause disease) that have simpler structures than viruses but, in the case of prions, still can produce deadly diseases.

Prions

Prions , so-called because they are proteinaceous, are infectious particles—smaller than viruses—that contain no nucleic acids (neither DNA nor RNA). Historically, the idea of an infectious agent that did not use nucleic acids was considered impossible, but pioneering work by Nobel Prize-winning biologist Stanley Prusiner has convinced the majority of biologists that such agents do indeed exist.

Fatal neurodegenerative diseases, such as kuru in humans and bovine spongiform encephalopathy (BSE) in cattle (commonly known as “mad cow disease”) were shown to be transmitted by prions. The disease was spread by the consumption of meat, nervous tissue, or internal organs between members of the same species. Kuru, native to humans in Papua New Guinea, was spread from human to human via ritualistic cannibalism. BSE, originally detected in the United Kingdom, was spread between cattle by the practice of including cattle nervous tissue in feed for other cattle. Individuals with kuru and BSE show symptoms of loss of motor control and unusual behaviors, such as uncontrolled bursts of laughter with kuru, followed by death. Kuru was controlled by inducing the population to abandon its ritualistic cannibalism.

On the other hand, BSE was initially thought to only affect cattle. Cattle dying of the disease were shown to have developed lesions or “holes” in the brain, causing the brain tissue to resemble a sponge. Later on in the outbreak, however, it was shown that a similar encephalopathy in humans, known as variant Creutzfeldt-Jakob disease (CJD), could be acquired from eating beef from animals infected with BSE, sparking bans by various countries on the importation of British beef and causing considerable economic damage to the British beef industry ((Figure)). BSE still exists in various areas, and although a rare disease, individuals that acquire CJD are difficult to treat. The disease can be spread from human to human by blood, so many countries have banned blood donation from regions associated with BSE.

The cause of spongiform encephalopathies, such as kuru and BSE, is an infectious structural variant of a normal cellular protein called PrP (prion protein). It is this variant that constitutes the prion particle. PrP exists in two forms, PrP c , the normal form of the protein, and PrP sc , the infectious form. Once introduced into the body, the PrP sc contained within the prion binds to PrP c and converts it to PrP sc . This leads to an exponential increase of the PrP sc protein, which aggregates. PrP sc is folded abnormally, and the resulting conformation (shape) is directly responsible for the lesions seen in the brains of infected cattle. Thus, although not without some detractors among scientists, the prion seems likely to be an entirely new form of infectious agent, the first one found whose transmission is not reliant upon genes made of DNA or RNA.


Viroids

Viroids are plant pathogens: small, single-stranded, circular RNA particles that are much simpler than a virus. They do not have a capsid or outer envelope, but like viruses can reproduce only within a host cell. Viroids do not, however, manufacture any proteins, and they only produce a single, specific RNA molecule. Human diseases caused by viroids have yet to be identified.

Viroids are known to infect plants ((Figure)) and are responsible for crop failures and the loss of millions of dollars in agricultural revenue each year. Some of the plants they infect include potatoes, cucumbers, tomatoes, chrysanthemums, avocados, and coconut palms.


Virologist
Virology is the study of viruses, and a virologist is an individual trained in this discipline. Training in virology can lead to many different career paths. Virologists are actively involved in academic research and teaching in colleges and medical schools. Some virologists treat patients or are involved in the generation and production of vaccines. They might participate in epidemiologic studies ((Figure)) or become science writers, to name just a few possible careers.


If you think you may be interested in a career in virology, find a mentor in the field. Many large medical centers have departments of virology, and smaller hospitals usually have virology labs within their microbiology departments. Volunteer in a virology lab for a semester or work in one over the summer. Discussing the profession and getting a first-hand look at the work will help you decide whether a career in virology is right for you. The American Society of Virology’s website is a good resource for information regarding training and careers in virology.

Section Summary

Prions are infectious agents that consist of protein, but no DNA or RNA, and seem to produce their deadly effects by duplicating their shapes and accumulating in tissues. They are thought to contribute to several progressive brain disorders, including mad cow disease and Creutzfeldt-Jakob disease. Viroids are single-stranded RNA pathogens that infect plants. Their presence can have a severe impact on the agriculture industry.

Free Response

Prions are responsible for variant Creutzfeldt-Jakob Disease, which has resulted in over 100 human deaths in Great Britain during the last 10 years. How do humans contract this disease?

This prion-based disease is transmitted through human consumption of infected meat.

How are viroids like viruses?

They both replicate in a cell, and they both contain nucleic acid.

A botanist notices that a tomato plant looks diseased. How could the botanist confirm that the agent causing disease is a viroid, and not a virus?

The botanist would need to isolate any foreign nucleic acids from infected plant cells, and confirm that an RNA molecule is the etiological agent of disease. The botanist would then need to demonstrate that the RNA can infect plant cells without a capsid, and that the RNA replicates, but is not translated to produce proteins.

Glossary


What are Viroids?

Viroid is an infectious single-stranded circular RNA particle. The first viroid identified was Potato Spindle Tuber Viroid (PsTVd). Up to now, thirty-three species of viroids have been identified. Viroids do not contain a protein capsid or envelope. They only contain RNA molecules. Since viroids are RNA particles, the ribonucleases can digest the viroids. The size of the viroid is smaller than a typical virus particle. Moreover, viroids need a host cell for reproduction. During reproduction, they produce only single-stranded RNA molecules.

Figure 02: Viroid Infection

Viroids do not cause human or animal diseases. They infect higher plants, causing diseases such as potato spindle tuber disease, chrysanthemum stunt disease, etc. These infectious RNA particles are responsible for crop failures and the loss of millions of money in agriculture annually. Potato, cucumber, tomato, chrysanthemums, avocado and coconut palms fall victim to viroid infections frequently. Viroid infections transmit by cross-contamination followed by mechanical damage of the plant. Some viroid infections are transmitted by aphids and leaf to leaf contact.


What are Viroids?

A viroid is an infectious RNA particle formed from a single-stranded circular RNA. Viroids were first discovered and named by the plant pathologist Theodor O. Diener in 1971. The first viroid identified was Potato Spindle Tuber Viroid (PsTVd) and thirty-three species of viroids have been identified up to now. Viroids do not contain a protein capsid or an envelope. They are made up of only RNA molecules. Since viroids are RNA particles, they can be digested by ribonucleases. But unlike prions, viroids cannot be destroyed by proteinase K and trypsin. The size of the viroid is smaller than a typical virus particle. Viorids need a host cell for reproduction. Other than a single stranded RNA molecule, they do not synthesize proteins.

Figure 02: Structure of Pospiviroid

Viroids do not cause human diseases. They infect higher plants and cause diseases like potato spindle tuber disease, and chrysanthemum stunt disease. These infectious RNA particles are responsible for crop failures and subsequently, the loss of millions of money in agriculture annually. Potato, cucumber, tomato, chrysanthemums, avocado and coconut palms are plants which are commonly subjected to viroid infections. Viroid infections are transmitted by cross contamination followed by mechanical damage to the plant. Some viroid infections are transmitted by aphids and leaf to leaf contact.


Viroids : Characteristics, Structure, Types and Replication

Viroids are the smallest known infectious agents consisting of a small, circular, RNA molecules.
A VIROIDs are a Virus(VIR) like(OID) particles.
Until 1970, viruses were considered as the smallest infectious agents. However, the discovery of viroids has proved that the infectious entities smaller than virus exist in nature.

Diener & Raymer first time discovered the Potato Spindle Tuber Viroid (PSTV). It was responsible for potato spindle tuber disease.

Most viroid cause plant discases & most common example is potato spindle tuber viroid. Today, 33 viroids are known.

The human disease known to be caused by viroid is hepatitis D. This viroid is enclosed in a hepatitis B virus capsid. For hepatitis D to occur, there must be simultaneous infection of cell with both the hepatitis B virus & the hepatitis D viroid.

Characteristics of Viroids :

1) Viroids are obligate intracellular parasite.
2) They are smaller than viruses. 3) Viroids are single stranded covalently closed circular RNA molecules.
4) They are only 246-400 nucleotides long.
5) Viroid RNA does not code for any protein.
6) They use host polymerase for replication.
6) They do not have capsid (protein coat).

Examples of Viroids

Structure of Viroid

• The viroids are single stranded circular RNA molecules.

• Most of the nucleotides in the RNA are base paired, producing a double stranded RNA molecules.

• The single stranded RNA circle has extensive intra-strand base pairing & unpaired loops at intervals.

• This structure protects the viroid from the action of ribonuclease.

• Structure of a viroid-circular single-stranded RNA with some pairing between complementary bases and loops where no such pairing occurs.

• There are two main groups of viroids on the basis of structure, these are self cleaving and non- self cleaving.

• Non-self cleaving viroids replicate in nucleus and fold into "dog bone" or rod-like structure.

Structure of Viroid

• Five domains identifiable in Non-self cleaving viroids
- Terminal left (TL)
- Terminal right (TR)
- Pathogenicity (P)
- Central (C)
- Variable (V)

Replication of Viroids

The replication of the viroid takes place in the nucleus of the host cell.

• Viroid RNA is a positive strand RNA and it replicates by the rolling circle mechanism in vivo.

• All components required for the replication are provided by the host.

• The rolling circle replication occurs by two mechanisms which are symmetric mode of replication and asymmetric mode of replication.

Symmetric mode of replication

Symmetric mode of replication is the most common mode of replication in viroids.

• According to Symmetric mode of replication, RNA directed RNA polymerase catalyses synthesis of new concatemeric negative(—) strand using the viroid position (+) RNA as a template.

• Viroids are ribozymes and therefore they catalyze their self cleavage.

• Self cleavage of concatemeric negative strand produce a monomeric subunits

• This is followed by the Ligation by host RNA ligase enzyme produce circular molecule.

• This circular negative strand is copied by the RNA polymerase to produce a concatemeric positive strand.

• Cleavage of concatemeric positive strand produces monomers.

• These monomers again circularize and produce positive RNA i.e. viroids.

Replication of Viroids

Asymmetric mode of replication

In the Symmetric mode of replication, the concatemeric negative strand is copied directly to a concatemeric positive strand.

• That means, Here self cleavage of monomers of negative strand is not carried out. Instead of that the intake of negative strand is used to synthesise the complementary concatemeric positive strand.


Do DNA viroids exist? - Biology

Viruses are not plants, animals, or bacteria, but they are the quintessential parasites of the living kingdoms. Although they may seem like living organisms because of their prodigious reproductive abilities, viruses are not living organisms in the strict sense of the word.

Without a host cell, viruses cannot carry out their life-sustaining functions or reproduce. They cannot synthesize proteins, because they lack ribosomes and must use the ribosomes of their host cells to translate viral messenger RNA into viral proteins. Viruses cannot generate or store energy in the form of adenosine triphosphate (ATP), but have to derive their energy, and all other metabolic functions, from the host cell. They also parasitize the cell for basic building materials, such as amino acids, nucleotides, and lipids (fats). Although viruses have been speculated as being a form of protolife, their inability to survive without living organisms makes it highly unlikely that they preceded cellular life during the Earth's early evolution. Some scientists speculate that viruses started as rogue segments of genetic code that adapted to a parasitic existence.

All viruses contain nucleic acid, either DNA or RNA (but not both), and a protein coat, which encases the nucleic acid. Some viruses are also enclosed by an envelope of fat and protein molecules. In its infective form, outside the cell, a virus particle is called a virion. Each virion contains at least one unique protein synthesized by specific genes in its nucleic acid. Viroids (meaning "viruslike") are disease-causing organisms that contain only nucleic acid and have no structural proteins. Other viruslike particles called prions are composed primarily of a protein tightly integrated with a small nucleic acid molecule.

Viruses are generally classified by the organisms they infect, animals, plants, or bacteria. Since viruses cannot penetrate plant cell walls, virtually all plant viruses are transmitted by insects or other organisms that feed on plants. Certain bacterial viruses, such as the T4 bacteriophage, have evolved an elaborate process of infection. The virus has a "tail" which it attaches to the bacterium surface by means of proteinaceous "pins." The tail contracts and the tail plug penetrates the cell wall and underlying membrane, injecting the viral nucleic acids into the cell. Viruses are further classified into families and genera based on three structural considerations: 1) the type and size of their nucleic acid, 2) the size and shape of the capsid, and 3) whether they have a lipid envelope surrounding the nucleocapsid (the capsid enclosed nucleic acid).

There are predominantly two kinds of shapes found amongst viruses: rods, or filaments, and spheres. The rod shape is due to the linear array of the nucleic acid and the protein subunits making up the capsid. The sphere shape is actually a 20-sided polygon (icosahedron).

The nature of viruses wasn't understood until the twentieth century, but their effects had been observed for centuries. British physician Edward Jenner even discovered the principle of inoculation in the late eighteenth century, after he observed that people who contracted the mild cowpox disease were generally immune to the deadlier smallpox disease. By the late nineteenth century, scientists knew that some agent was causing a disease of tobacco plants, but would not grow on an artificial medium (like bacteria) and was too small to be seen through a light microscope. Advances in live cell culture and microscopy in the twentieth century eventually allowed scientists to identify viruses. Advances in genetics dramatically improved the identification process.

Capsid - The capsid is the protein shell that encloses the nucleic acid with its enclosed nucleic acid, it is called the nucleocapsid. This shell is composed of protein organized in subunits known as capsomers. They are closely associated with the nucleic acid and reflect its configuration, either a rod-shaped helix or a polygon-shaped sphere. The capsid has three functions: 1) it protects the nucleic acid from digestion by enzymes, 2) contains special sites on its surface that allow the virion to attach to a host cell, and 3) provides proteins that enable the virion to penetrate the host cell membrane and, in some cases, to inject the infectious nucleic acid into the cell's cytoplasm. Under the right conditions, viral RNA in a liquid suspension of protein molecules will self-assemble a capsid to become a functional and infectious virus.

Envelope - Many types of virus have a glycoprotein envelope surrounding the nucleocapsid. The envelope is composed of two lipid layers interspersed with protein molecules (lipoprotein bilayer) and may contain material from the membrane of a host cell as well as that of viral origin. The virus obtains the lipid molecules from the cell membrane during the viral budding process. However, the virus replaces the proteins in the cell membrane with its own proteins, creating a hybrid structure of cell-derived lipids and virus-derived proteins. Many viruses also develop spikes made of glycoprotein on their envelopes that help them to attach to specific cell surfaces.

Nucleic Acid - Just as in cells, the nucleic acid of each virus encodes the genetic information for the synthesis of all proteins. While the double-stranded DNA is responsible for this in prokaryotic and eukaryotic cells, only a few groups of viruses use DNA. Most viruses maintain all their genetic information with the single-stranded RNA. There are two types of RNA-based viruses. In most, the genomic RNA is termed a plus strand because it acts as messenger RNA for direct synthesis (translation) of viral protein. A few, however, have negative strands of RNA. In these cases, the virion has an enzyme, called RNA-dependent RNA polymerase (transcriptase), which must first catalyze the production of complementary messenger RNA from the virion genomic RNA before viral protein synthesis can occur.

The Influenza (Flu) Virus - Next to the common cold, influenza or "the flu" is perhaps the most familiar respiratory infection in the world. In the United States alone, approximately 25 to 50 million people contract influenza each year. The symptoms of the flu are similar to those of the common cold, but tend to be more severe. Fever, headache, fatigue, muscle weakness and pain, sore throat, dry cough, and a runny or stuffy nose are common and may develop rapidly. Gastrointestinal symptoms associated with influenza are sometimes experienced by children, but for most adults, illnesses that manifest in diarrhea, nausea, and vomiting are not caused by the influenza virus though they are often inaccurately referred to as the "stomach flu." A number of complications, such as the onset of bronchitis and pneumonia, can also occur in association with influenza and are especially common among the elderly, young children, and anyone with a suppressed immune system.

The Human Immunodeficiency Virus (HIV) - The virus responsible for HIV was first isolated in 1983 by Robert Gallo of the United States and French scientist Luc Montagnier. Since that time, a tremendous amount of research focusing upon the causative agent of AIDS has been carried out and much has been learned about the structure of the virus and its typical course of action. HIV is one of a group of atypical viruses called retroviruses that maintain their genetic information in the form of ribonucleic acid ( RNA ). Through the use of an enzyme known as reverse transcriptase, HIV and other retroviruses are capable of producing deoxyribonucleic acid (DNA) from RNA, whereas most cells carry out the opposite process, transcribing the genetic material of DNA into RNA. The activity of the enzyme enables the genetic information of HIV to become integrated permanently into the genome (chromosomes) of a host cell.