Viroids and virusoids

SIGNIFICANCE: Viroids are naked strands of RNA, 270 to 380 nucleotides long, that are circular and do not code for any proteins. However, some viroids are catalytic RNAs (ribozymes), able to cleave and ligate themselves. In spite of their simplicity, they are able to cause disease in susceptible plants, many of them economically important. Virusoids are similar to viroids, except that they require a helper virus to infect a plant and reproduce.

General Characteristics of Viroids and Virusoids

Viroids, and some virusoids, are circular, single-stranded RNA molecules, which normally appear as rods but when denatured by heating appear as closed circles. The rod-shaped structure is formed by extensive within the RNA molecule, and the secondary structure is divided into five structural domains. One domain is called the pathogenicity (P) domain, because differences among variant strains of the same species of viroid seem to correlate with differences in pathogenicity. Virusoids may also comprise linear RNA or, rarely, double-stranded circular RNA.

The difference between and is in their mode of transmission. Viroids have no protective covering of any kind and are no more than the RNA that makes up their genetic material. They depend on breaks in a plant’s epidermis or can travel with pollen or ovules to gain entry. Virusoids, also known as satellite RNAs, are packaged in the protein coat of other plant viruses, referred to as helpers, and are therefore dependent on the other virus.

Viroids are typically divided into two groups based on the nature of their RNA molecule. Group A is the smallest group, and their RNA has the ability to self-cleave. These include the avocado sunblotch and peach latent mosaic viroids. Group B contains all the other viroids, and their RNA is not capable of self-cleavage. Species in group B include the potato spindle tuber, coconut cadang, tomato plant macho, and citrus bent leaf viroids.

Virusoids are less well studied than viroids and, although more diverse, are most similar to group B viroids in that they cannot self-cleave. Examples include the tomato black ring virus viroid, the peanut stunt virus viroid, and the tobacco ringspot virus viroid. Because so little is known about virusoids, the remainder of this article will focus on viroids.

Viroid Pathogenesis

If infected leaves are homogenized in a blender and passed through an “ultrafilter” fine enough to exclude bacteria, the infection is easily transmitted to another plant by painting some of the filtrate on a leaf. Even billionfold dilutions of the filtrate retain the ability to cause infection, suggesting that it is being replicated. destroys infectivity, suggesting that the genetic material (RNA) is exposed to the medium, unlike viruses, which have a protective protein coat. When isolated from other cell components, an absorbance spectrum shows that viroids are pure nucleic acid, lacking a protein coat.

Although viroids are structurally simple and do not code for any proteins, they still cause disease. Although the molecular mechanisms of viroid pathogenesis are unknown, it is clear that the pathogenesis domain (P domain) is primarily responsible.

Changes in the sequence of nucleotides in the P domain have been correlated with pathogenicity. Some research suggests that the pathogenicity of a viroid strain is related to the resistance of the P domain to heat denaturation, with stability of this region being inversely related to severity. However, some evidence suggests that this may not be entirely true. In a series of substitutions introduced by researchers into the P region of an intermediate strain (that is, intermediate in pathogenicity) of potato spindle tuber viroid (PSTVd), four showed viroid infectivity and pathogenicity that were the same as those of a previously reported severe strain of PSTVd. Altogether, eight different mutant strains were analyzed, and resistance to and PSTVd pathogenicity were not correlated in all cases.

Research is under way to understand how viroids move from cell to cell and traverse the cytoplasm to the nucleus, where many viroids replicate. There is evidence that a possible interaction might involve viroid RNA activating an RNA-activated protein kinase in response to a nucleotide sequence similar to that of the normal RNA activator. Protein kinases are integral to intracellular signaling pathways that control many aspects of cell metabolism. Once researchers understand the signals that viroids use to get around, it may be possible to devise treatments against them. A better understanding of the process may also shed light on normal biochemical communication pathways in plant cells.

Viroid Replication

Viroids replicate by a rolling circle mechanism, a method also used by some viruses. The original strand is referred to as the “(+) strand,” and complementary copies of it are called “(−) strands.” Type A and B viroids replicate slightly differently. In type A viroids, the circular (+) strand is replicated by RNA-dependent to form several linear copies of the RNA (−) strand connected end to end. Site-specific self-cleavage produces individual (−) strands later circularized by a host RNA ligase. Each (−) strand is finally copied by the RNA polymerase to make several linear copies of (+) strand RNA. Cleavage of this last strand makes individual RNA (+) strands, which are then circularized. Self-cleavage in viroids represents one of the cases in which RNA acts as an enzyme. The RNA forms a “hammerhead” structure that enzymatically cleaves the longer RNAs at just the right sites.

Replication of type B viroids is apparently mediated by normal host DNA-dependent RNA polymerase, which mistakes the viroid RNA for DNA. The overall process is similar to what happens with type A viroids, except that the (−) strand is not cleaved but instead is copied directly, yielding a (+) strand that is cleaved by host RNase to form individual copies that are ligated to become circular.

Economic Impact of Viroids

Genetically engineered plants in the future might make proteins that would essentially confer immunity by preventing viroids from entering the nucleus. With no access to the nucleus, a viroid would be incapable of replicating, effectively preventing the damage normally associated with viroid infection. Currently, no such transgenic plants exist, and viroids can reduce agricultural productivity if outbreaks are not checked quickly. The typical treatment is simply to destroy the affected plants, as there is no cure.

Although predominantly negative, viroids may have some potentially positive benefits. They have already been used in unique ways to study plant genetics, and they may provide insights into how plant proteins and nucleic acids move in and out of cell nuclei. It may also be possible to harness the benefits of viroid infection for certain agricultural applications, such as dwarfing citrus trees. Considerably more will need to be learned about viroids before they can be adequately controlled or used for human benefit.

Key Terms

• RNA polymerasean enzyme that catalyzes the joining of ribonucleotides to make RNA using DNA or another RNA strand as a template
• RNasean enzyme that catalyzes the cutting of an RNA molecule

Bibliography

Dalakouras, Athanasios, Elena Dadami, and Michael Wassenegger. "Viroid-Induced DNA Methylation in Plants." Biomolecular Concepts 4.6 (2013): 557–65. Print.

Diener, T. O., R. A. Owens, and R. W. Hammond. “Viroids, the Smallest and Simplest Agents of Infectious Disease: How Do They Make Plants Sick?” Intervirology 35.1–4 (1993): 186–95. Print.

Duran-Vila, Núria, et al. “Structure and Evolution of Viroids.” Origin and Evolution of Viruses. Ed. Esteban Domingo, Colin R. Parrish, and John J. Holland. 2nd ed. Boston: Elsevier/Academic, 2008. Print.

Gómez, Gustavo, and Vicente Pallás. "Viroids: A Light in the Darkness of the lnc RNA-Directed Regulatory Networks in Plants." New Phytologist 198.1 (2013): 10–15. Print.

Hadidi, Ahmed, et al., eds. Viroids. Enfield: Science, 2003. Print.

Hammond, R. W. “Analysis of the Virulence Modulating Region of Potato Spindle Tuber Viroid (PSTVd) by Site-Directed Mutagenesis.” Virology 187.2 (1992): 654–62. Print.

Haseltine, William A. "Virusoids: Viruses' Very Own Parasites." Forbes, 3 Apr. 2023, www.forbes.com/sites/williamhaseltine/2023/04/03/virusoids-viruses-very-own-parasites/. Accessed 9 Sept. 2024.

Ma, Junfei, and Ying Wang. "Studies on Viroid Shed Light on the Role of RNA Three-Dimensional Structural Motifs in RNA Trafficking in Plants." Frontiers in Plant Science, 23 Mar. 2022, doi.org/10.3389/fpls.2022.836267. Accessed 9 Sept. 2024.

Owens, R. A., W. Chen, Y. Hu, and Y-H. Hsu. “Suppression of Potato Spindle Tuber Viroid Replication and Symptom Expression by Mutations, Which Stabilize the Pathogenicity Domain.” Virology 208.2 (1995): 554–64. Print.

Shors, Teri. “What About Prions and Viroids?” and “Plant Viruses.” Understanding Viruses. 2nd ed. Sudbury: Jones, 2013. Print.

Wassenegger, M., et al. “RNA-Directed De Novo Methylation of Genomic Sequences in Plants.” Cell 76.3 (1994): 567–76. Print.