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 × 10⁵ 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.