Viroids

Introduction image

Viroids are the sub-viral agents, which are smaller and infectious particles. These are somewhat similar like viruses but possesses some unique properties in its evolutionary origin, morphology and function. In the year 1917, Diener was the first scientist who discovered and termed the non-bacterial infectious plant pathogen as “Viroids”.

Potato spindle tuber viroids (PSTV) was the first viroid discovered by T.O. Diener and W.B. Raymer in the year 1967. PSTV caused massive damage in potatoes. Its discovery led to the existence of some infectious entities smaller than the viruses.

Content: Viroids

  1. Meaning
  2. Properties
  3. Classification
  4. Genome
  5. Replication

Meaning of Viroids

Viroids can define as the small, non-cellular sub-viral agents that exist as obligate intracellular parasites like viruses, but differs in a property by lacking a protein coat. It is approximately 200-400 nucleotides long. These primarily infects, replicates and induces serious disease in the higher plants. The pathogenicity of viroids differs within the distinct host species. Viroids can cause latent or can induce chronic infections in their host plants.

Properties

  1. Viroids are the smallest infectious agents that only consist of tiny circular RNA.
  2. Its RNA is covalently closed and not coated by protein subunits.
  3. These are similar to small nuclear RNA, which only comprises a single stranded circular RNA molecule.
  4. A plant pathologist, Theodor Diener discovered viroids in the year 1971. Till date, it is not cleared of how these viroids induce disease in any species.
  5. Sometimes viroids show severe problems in one plant without showing any symptoms in other plants of the same species.
  6. It does not encode the protein.
  7. Some of Nucleotide sequencing of viroids are the same as those observed in transposons and retroviruses.
  8. Viroids are the acellular particles, which are smaller in comparison to the viruses.
  9. These are considered as the molecular fossils of the RNA dominated by DNA and protein.
  10. Like viruses, viroids also go through the cell to cell movement via plasmodesmata and systemic transport via the phloem.
  11. The replication process of viroids follows the same pathway as in viruses, as these also function as the obligate intracellular parasites.
  12. Its replication requires RNA polymerase II for the synthesis of messenger RNA from DNA, by using viroid RNA as a template.
  13. These can induce symptoms in higher plants via a mechanism known as “RNA silencing”.

Classification

Viroids classify into the two families depending upon the site of replication.

Classification of viroids

Popsiviroidae

The members belong to this family replicate inside the nucleus and refers as “Nuclear viroids” and formerly called as group-B viroids.

  • Pospiviroid: It a genus that includes a type species (Potato spindle tuber viroid) with a genome size of 356 to 375 nt.
  • Hostuviroid: It a genus that includes a type species (Hop stunt viroid) with a genome size of 295 to 303 nt.
  • Cocadviroid: It a genus that includes a type species (Coconut cadangcadang viroid) with a genome size of 246 to 301 nt.
  • Apscaviroid: It a genus that includes a type species (Apple scar skin viroid) with a genome size of 306 to 369 nt.
  • Coleviroid: It a genus that includes a type species (Co/ens blumei viroid) with a genome size of 248 to 361 nt.

Avsunviroidae

The members belong to this family replicate inside the chloroplast and refers as “Chloroplastic viroids” and formerly called as group-A viroids.

  • Avsunviroid: It a genus that includes a type species (Avocado sun-blotch viroid) with a genome size of 246 to 250 nt.
  • Pelamoviroid: It is a genus that includes a type species (Peach latent mosaic viroid) with a genome size of 337 to 399 nt.

Thus the site of replication differs within the type of plant species, but the replication mechanism follows the same strategy that involves three steps RNA-based replication. Its replication cycle is dependent upon the following three enzymatic activities:

  • Host DNA-dependent RNA polymerases
  • Processing enzymes
  • RNA ligase

Distinction Between Viruses and Viroids

  1. Viruses are nucleoprotein particle, while viroids are the infectious RNA particle.
  2. Unlike viruses, viroids are of small size and having low molecular weight.
  3. Viroid only contains an RNA genome, whereas viruses can contain DNA or RNA.
  4. The infectious RNA replicates autonomously (without no helper virus) in the susceptible host cells.

Viroid Genome

Its genome size is of low molecular weight (1.1-1.3X105 Da). It can be characterized by the absence of protein coating surrounding the viral genome, as its genome lacks AUG codon that mediates the protein synthesis.

Viroid comprises of a small fragment of RNA molecule that is generally present as naked and circularized RNA. The genomic RNA consists of 250-370 nucleotides. The nucleotides in the RNA genome is usually paired, forming a dsRNA via intramolecular complementary regions.

Therefore, the viroids resemble a rod-like structure, where the dsRNA appears as a closed, folded and 3D structure.

structural organization of viroid

Viroid genome generally comprises five domains, like:

  • Pathogenicity domain (P)
  • Left terminal domain (TL)
  • Central conserved domain (CCR)
  • Variable domain (V)
  • Rigid terminal domain (TR)

The folded regions of the viroid help in the protection of the RNA against the action of cellular enzymes.

Replication of Viroids

The replication of viroid in the higher plants occurs via three enzyme based-RNA rolling circle mechanism. Symmetric replication occurs in Avsunviroids, whereas asymmetric replication in Pospiviroids. RNA polymerase, an RNase and an RNA ligase are needed for the viroid replication. Symmetric and Asymmetric Replication are the two replicative mechanisms of Viroid.

Replication of viroid

Asymmetric Replication

Members of Popsiviroidae family undergo asymmetric replication, for which it first requires a host cell enzyme (RNA polymerase II). The RNA polymerase II will create a nick in the cellular DNA by forming both positive and negative strands. The positive circular strand will function as a template for the formation of new RNA via a rolling circle mechanism.

Then, it initiates the synthesis of mRNA from the cellular DNA by making the use of viroid circular (+) RNA strand to make a large linear multimeric (-) strand. After that, Pospiviroids form (+) sense RNA from this long linear molecule via asymmetric replication pathway.

The (+) RNA strand of viroid is sensitive to the RNase activity of the host cell. Thus, the RNase enzyme cleaves the (+) RNA strand of viroid into a unit viroid lengths. Then the unit fragments of the (+) RNA strand molecule undergoes ligation to form the (+) circular RNA.

Symmetric Replication

Avsunviroids lack a central conserved region and possess a ribozyme activity instead of RNA polymerase. Hence in this, the large multimeric (-) RNA strand is self-cleaved by the associated ribozyme activity. Thus, these possess the property of auto cleavage.

Then, the replication intermediates are ligated to form a (-) circularized RNA. After that, a second rolling circle event takes place that makes a long linear (+) RNA strand that is again cleaved by the ribozyme activity. Then the fragments of viroid RNA undergo ligation to form the (+) circular RNA.

Genome replication can occur in two possible ways:

RNA-directed replication: It is one of the mechanisms, where the RNA polymerase synthesizes the RNA molecules directed by the RNA itself.

Central dogma

DNA-directed replication: It is another mechanism, where the viroid RNA forms after the transcription of host cell DNA, complementary to the viroid RNA. The viroid RNA can produce new DNA in the infected cell via association of reverse transcriptase enzyme. The reverse transcriptase enzyme functions as an RNA directed DNA polymerase, which can produce viroid RNA by using the infected DNA as a template.

After the study of these two replication modes, two conclusions have been made that the viroids can replicate via direct RNA to RNA copying, and the host cell machinery possibly promotes the replication of viroid RNA.

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