Virusoids are circular single-stranded RNA(s) dependent on viruses for replication and encapsidation. The genome of virusoids consist of several hundred (200–400) nucleotides and does not code for any proteins.
Picornaviruses are a group of related nonenveloped RNA viruses which infect vertebrates including fish, mammals, and birds. They are viruses that represent a large family of small, positive-sense, single-stranded RNA viruses with a 30 nm icosahedral capsid. The viruses in this family can cause a range of diseases including the common cold, poliomyelitis, meningitis, hepatitis, and paralysis.
Cauliflower mosaic virus (CaMV) is a member of the genus Caulimovirus, one of the six genera in the family Caulimoviridae, which are pararetroviruses that infect plants. Pararetroviruses replicate through reverse transcription just like retroviruses, but the viral particles contain DNA instead of RNA.
A satellite is a subviral agent that depends on the coinfection of a host cell with a helper virus for its replication. Satellites can be divided into two major classes: satellite viruses and satellite nucleic acids. Satellite viruses, which are most commonly associated with plants, are also found in mammals, arthropods, and bacteria. They encode structural proteins to enclose their genetic material, which are therefore distinct from the structural proteins of their helper viruses. Satellite nucleic acids, in contrast, do not encode their own structural proteins, but instead are encapsulated by proteins encoded by their helper viruses. The genomes of satellites range upward from 359 nucleotides in length for satellite tobacco ringspot virus RNA (STobRV).
VPg is a protein that is covalently attached to the 5′ end of positive strand viral RNA and acts as a primer during RNA synthesis in a variety of virus families including Picornaviridae, Potyviridae and Caliciviridae. There are some studies showing that a possible VPg protein is also present in astroviridae, however, experimental evidence for this has not yet been provided and requires further study. The primer activity of VPg occurs when the protein becomes uridylated, providing a free hydroxyl that can be extended by the virally encoded RNA-dependent RNA polymerase. For some virus families, VPg also has a role in translation initiation by acting like a 5' mRNA cap.
Ribosome shunting is a mechanism of translation initiation in which ribosomes bypass, or "shunt over", parts of the 5' untranslated region to reach the start codon. However, a benefit of ribosomal shunting is that it can translate backwards allowing more information to be stored than usual in an mRNA molecule. Some viral RNAs have been shown to use ribosome shunting as a more efficient form of translation during certain stages of viral life cycle or when translation initiation factors are scarce. Some viruses known to use this mechanism include adenovirus, Sendai virus, human papillomavirus, duck hepatitis B pararetrovirus, rice tungro bacilliform viruses, and cauliflower mosaic virus. In these viruses the ribosome is directly translocated from the upstream initiation complex to the start codon (AUG) without the need to unwind RNA secondary structures.
Potyvirus is a genus of positive-strand RNA viruses in the family Potyviridae. Plants serve as natural hosts. Like begomoviruses, members of this genus may cause significant losses in agricultural, pastoral, horticultural, and ornamental crops. More than 200 species of aphids spread potyviruses, and most are from the subfamily Aphidinae. The genus contains 190 species and potyviruses account for about thirty percent of all currently known plant viruses.
Tombusvirus is a genus of viruses, in the family Tombusviridae. Plants serve as natural hosts. There are 17 species in this genus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt virus.
The bamboo mosaic virus satellite RNA cis-regulatory element is an RNA element found in the 5' UTR of the genome of the bamboo mosaic virus. This element is thought to be essential for efficient RNA replication.
The Citrus tristeza virus replication signal is a regulatory element involved in a viral replication signal which is highly conserved in citrus tristeza viruses. Replication signals are required for viral replication and are usually found near the 5' and 3' termini of protein coding genes. This element is predicted to form ten stem loop structures some of which are essential for functions that provide for efficient viral replication.
The Potato virus X cis-acting regulatory element is a cis-acting regulatory element found in the 3' UTR of the Potato virus X genome. This element has been found to be required for minus strand RNA accumulation and is essential for efficient viral replication.
The Rubella virus 3′ cis-acting element RNA family represents a cis-acting element found at the 3′ UTR in the rubella virus. This family contains three conserved step loop structures. Calreticulin (CAL), which is known to bind calcium in most eukaryotic cells, is able to specifically bind to the first stem loop of this RNA. CAL binding is thought to be related to viral pathogenesis and in particular arthritis which occurs frequently in rubella infections in adults and is independent of viral viability. All stem loop structures are thought to be important for efficient viral replication and deletion of stem loop three is known to be lethal.
Tombusvirus 5′ UTR is an important cis-regulatory region of the Tombus virus genome.
Tombus virus defective interfering (DI) RNA region 3 is an important cis-regulatory region identified in the 3' UTR of Tombusvirus defective interfering particles (DI).
The Upstream pseudoknot (UPSK) domain is an RNA element found in the turnip yellow mosaic virus, beet virus Q, barley stripe mosaic virus and tobacco mosaic virus, which is thought to be needed for efficient transcription. Disruption of the pseudoknot structure gives rise to a 50% drop in transcription efficiency. This element acts in conjunction with the Tymovirus/Pomovirus tRNA-like 3' UTR element to enhance translation.
Potexvirus is a genus of pathogenic viruses in the order Tymovirales, in the family Alphaflexiviridae. Plants serve as natural hosts. There are 48 species in this genus, three of which are assigned to a subgenus. Diseases associated with this genus include: mosaic and ringspot symptoms. The genus name comes from POTato virus X).
Bamboo mosaic virus (BaMV) is a plant pathogenic virus in the genus Potexvirus and the family Alphaflexiviridae. BaMV is a filamentous, flexuous rod, 490 nm in length and 15 nm in width. The virus has been fully sequenced and it is 6366 nucleotides long.
Alphaflexiviridae is a family of viruses in the order Tymovirales. Plants and fungi serve as natural hosts. There are 65 species in this family, assigned to six genera. Diseases associated with this family include: mosaic and ringspot symptoms.
Cis-acting replication elements bring together the 5′ and 3′ ends during replication of positive-sense single-stranded RNA viruses and double-stranded RNA viruses.
