Viroid
Encyclopedia
Viroids are plant
pathogens that consist of a short stretch (a few hundred nucleobase
s) of highly complementary, circular, single-stranded RNA
without the protein coat
that is typical for virus
es. The smallest discovered is a 220 nucleobase
scRNA (small cytoplasmic RNA) associated with the rice yellow mottle sobemovirus (RYMV). In comparison, the genome of the smallest known viruses capable of causing an infection by themselves are around 2 kilobases in size. The human pathogen hepatitis D
is similar to viroids.
Viroids were discovered and given this name by Theodor Otto Diener, a plant pathologist at the Agricultural Research Service in Maryland, in 1971.
Viroid RNA does not code for any protein
. The replication mechanism involves RNA polymerase II
, an 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 template. Some viroids are ribozymes, having catalytic properties which allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.
The first viroid to be identified was the potato spindle tuber viroid
(PSTVd). Some 33 species have been identified.
s in plants without encoding any protein
products within their sequences. Evidence now suggests that RNA silencing
is involved in the process. First, changes to the viroid genome
can dramatically alter its virulence
. This reflects the fact that any siRNA
s produced would have less complementary base pairing with target messenger RNA
. Secondly, siRNA
s 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.
This evidence 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 actually contain sequences capable of complementary base pairing with the plant's own messenger RNAs and induction of degradation or inhibition of translation is what causes the classic viroid symptoms.
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
pathogens that consist of a short stretch (a few hundred nucleobase
Nucleobase
Nucleobases are a group of nitrogen-based molecules that are required to form nucleotides, the basic building blocks of DNA and RNA. Nucleobases provide the molecular structure necessary for the hydrogen bonding of complementary DNA and RNA strands, and are key components in the formation of stable...
s) of highly complementary, circular, single-stranded RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
without the protein coat
Capsid
A capsid is the protein shell of a virus. It consists of several oligomeric structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The capsid encloses the genetic...
that is typical for virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
es. The smallest discovered is a 220 nucleobase
Nucleobase
Nucleobases are a group of nitrogen-based molecules that are required to form nucleotides, the basic building blocks of DNA and RNA. Nucleobases provide the molecular structure necessary for the hydrogen bonding of complementary DNA and RNA strands, and are key components in the formation of stable...
scRNA (small cytoplasmic RNA) associated with the rice yellow mottle sobemovirus (RYMV). In comparison, the genome of the smallest known viruses capable of causing an infection by themselves are around 2 kilobases in size. The human pathogen hepatitis D
Hepatitis D
Hepatitis D, also referred to as hepatitis D virus and classified as Hepatitis delta virus, is a disease caused by a small circular enveloped RNA virus. It is one of five known hepatitis viruses: A, B, C, D, and E. HDV is considered to be a subviral satellite because it can propagate only in the...
is similar to viroids.
Viroids were discovered and given this name by Theodor Otto Diener, a plant pathologist at the Agricultural Research Service in Maryland, in 1971.
Viroid RNA does not code for any protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
. The replication mechanism involves RNA polymerase II
RNA polymerase II
RNA polymerase II is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase...
, an enzyme normally associated with synthesis of messenger RNA
Messenger RNA
Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein...
from DNA, which instead catalyzes "rolling circle" synthesis of new RNA using the viroid's RNA as template. Some viroids are ribozymes, having catalytic properties which allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.
The first viroid to be identified was the potato spindle tuber viroid
Potato spindle tuber viroid
The Potato spindle tuber viroid was the first viroid to be identified. PSTVd is a small, circular RNA molecule closely related to the Chrysanthemum stunt viroid. Present within the viroidal RNA is the Pospiviroid RY motif stem loop. The natural hosts are potatoes and tomatoes...
(PSTVd). Some 33 species have been identified.
Taxonomy
- Family PospiviroidaePospiviroidaeThe Pospiviroidae are a family of viroids, including the first viroid to be discovered, PSTVd. Their secondary structure is key to their biological activity. The classification of this family is based on differences in the conserved central region sequence...
- Genus PospiviroidPospiviroidPospiviroid is a genus of viroid which most commonly infects tubers. It belongs to the family pospiviroidae.The first viroid discovered was a pospiviroid, the PSTVd species ....
; type species: Potato spindle tuber viroidPotato spindle tuber viroidThe Potato spindle tuber viroid was the first viroid to be identified. PSTVd is a small, circular RNA molecule closely related to the Chrysanthemum stunt viroid. Present within the viroidal RNA is the Pospiviroid RY motif stem loop. The natural hosts are potatoes and tomatoes... - Genus HostuviroidHostuviroidHostuviroid is a genus of viroids that includes the hop stunt viroids, a group of viroids that infects many different types of plants, including the common hop plant.Some hostuviroids:Citrus gummy bark viroidGrapevine viroid...
; type species: Hop stunt viroidHop stunt viroidThe hop stunt viroid is a viroid species that infects the common hop plant, citrus plants and grapevines, among others. It is a member of the Pospiviroidae family and the Hostuviroid genus.... - Genus Cocadviroid; type species: Coconut cadang-cadang viroid
- Genus Apscaviroid; type species: Apple scar skin viroid
- Genus Coleviroid; type species: Coleus blumei viroid 1
- Genus Pospiviroid
- Family AvsunviroidaeAvsunviroidaeThe Avsunviroidae are a family of viroids. At present three members are known of. They consist of RNA genomes between 246-375 nucleotides in length. They are single stranded covalent circles and have intramolecular base pairing. All members lack a central conserved region.-Replication:Replication...
- Genus Avsunviroid; type species: Avocado sunblotch viroidAvocado sunblotch viroidAvocado sunblotch viroid is an important disease affecting avocado trees.Infections result in lower yields and poorer quality fruit. ASBV is the smallest known viroid that infects plants and is transmitted by pollen and infected seeds or budwood....
- Genus Pelamoviroid; type species: Peach latent mosaic viroidPeach latent mosaic viroidPeach latent mosaic viroid is a type species from 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...
- Genus Elaviroid; type species: Eggplant latent viroid
- Genus Avsunviroid; type species: Avocado sunblotch viroid
Viroids and RNA silencing
There has long been confusion over how viroids are able to induce symptomSymptom
A symptom is a departure from normal function or feeling which is noticed by a patient, indicating the presence of disease or abnormality...
s in plants without encoding any protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
products within their sequences. Evidence now suggests that RNA silencing
RNA silencing
RNA silencing refers to a family of gene silencing effects by which the expression of one or more genes is downregulated or entirely suppressed by the introduction of an antisense RNA molecule...
is involved in the process. First, changes to the viroid genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
can dramatically alter its virulence
Virulence
Virulence is by MeSH definition the degree of pathogenicity within a group or species of parasites as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenicity of an organism - its ability to cause disease - is determined by its...
. This reflects the fact that any siRNA
Sírna
Sírna Sáeglach , son of Dian mac Demal, son of Demal mac Rothechtaid, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland...
s produced would have less complementary base pairing with target messenger RNA
Messenger RNA
Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein...
. Secondly, siRNA
Sírna
Sírna Sáeglach , son of Dian mac Demal, son of Demal mac Rothechtaid, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland...
s corresponding to sequences from viroid genomes have been isolated from infected plants. Finally, transgenic expression of the noninfectious hpRNA of potato spindle tuber viroid
Potato spindle tuber viroid
The Potato spindle tuber viroid was the first viroid to be identified. PSTVd is a small, circular RNA molecule closely related to the Chrysanthemum stunt viroid. Present within the viroidal RNA is the Pospiviroid RY motif stem loop. The natural hosts are potatoes and tomatoes...
develops all the corresponding viroid like symptoms.
This evidence indicates that when viroids replicate via a double stranded intermediate RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
, they are targeted by a dicer
Dicer
Dicer is an endoribonuclease in the RNase III family that cleaves double-stranded RNA and pre-microRNA into short double-stranded RNA fragments called small interfering RNA about 20-25 nucleotides long, usually with a two-base overhang on the 3' end...
enzyme and cleaved into siRNAs that are then loaded onto the RNA-induced silencing complex
RNA-induced silencing complex
RNA-Induced Silencing Complex, or RISC, is a multiprotein complex that incorporates one strand of a small interfering RNA or micro RNA . RISC uses the siRNA or miRNA as a template for recognizing complementary mRNA. When it finds a complementary strand, it activates RNase and cleaves the RNA...
. The viroid siRNAs actually contain sequences capable of complementary base pairing with the plant's own messenger RNAs and induction of degradation or inhibition of translation is what causes the classic viroid symptoms.
See also
- VirusVirusA virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
- VirusoidVirusoidVirusoids are circular single-stranded RNAs dependent on plant viruses for replication and encapsidation. The genome of virusoids consist of several hundred nucleotides and only encodes structural proteins....
- Virus classificationVirus classificationVirus classification is the process of naming viruses and placing them into a taxonomic system. Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate and proposals. This is mainly due to the pseudo-living nature of viruses, which...
- Satellite (biology)Satellite (biology)A satellite is a subviral agent composed of nucleic acid that depends on the co-infection of a host cell with a helper or master virus for its multiplication. When a satellite encodes the coat protein in which its nucleic acid is encapsidated it is referred to as a satellite virus...
- PrionPrionA prion is an infectious agent composed of protein in a misfolded form. This is in contrast to all other known infectious agents which must contain nucleic acids . The word prion, coined in 1982 by Stanley B. Prusiner, is a portmanteau derived from the words protein and infection...
- MicroparasiteMicroparasiteA microparasite is a parasite that complete a full life cycle within one host and can be transmitted directly to conspecific hosts. They often reproduce within a host's cells and are generally too small to be seen with the naked eye. Most are viruses, bacteria and fungi with a smaller number being...
- Plant pathology