Biology:Tombusvirus 5′ UTR
| Tombusvirus 5′ UTR | |
|---|---|
 Predicted secondary structure and sequence conservation of Tombus_5 | |
| Identifiers | |
| Symbol | Tombus_5 |
| Rfam | RF00171 |
| Other data | |
| RNA type | Cis-reg |
| Domain(s) | Viruses |
| SO | 0000204 |
| PDB structures | PDBe |
Tombusvirus 5′ UTR is an important cis-regulatory region of the Tombus virus genome.
Tomato bushy stunt virus is the prototype member of the Tombusviridae family. The genome of this virus is positive sense single stranded RNA. Replication occurs via a negative strand RNA intermediate. In addition to viral proteins p33 and the RNA-dependent RNA polymerase p92, and unknown host factors, conserved and structural regions within the 5′ untranslated region (5′ UTR) are important for regulating genome replication.[citation needed]
2 RNA domains in the 5′ UTR have been reported, a 5′ T-shaped domain (TSD) followed by a stem-loop (SL5)[1][2] and a downstream domain (DSD).[3] TSD-DSD interactions are proposed to be involved in the mediation of viral RNA replication.[3]
An interesting feature of Tombusvirus is its ability to support the replication of defective interfering (DI) RNAs. These sub-viral replicons are small, non-coding, deletion mutants of the viral genome that maintain cis-acting RNA elements necessary for replication [1]
Other non-coding RNA structures in Tombusvirus include the 3′ UTR region IV[4] and an internal replication element.[5]
References
- ↑ 1.0 1.1 "An RNA domain within the 5′ untranslated region of the tomato bushy stunt virus genome modulates viral RNA replication". J. Mol. Biol. 305 (4): 741–756. 2001. doi:10.1006/jmbi.2000.4298. PMID 11162089.
- ↑ "Structural properties of a multifunctional T-shaped RNA domain that mediate efficient tomato bushy stunt virus RNA replication". J. Virol. 78 (19): 10490–10500. 2004. doi:10.1128/JVI.78.19.10490-10500.2004. PMID 15367615.
- ↑ 3.0 3.1 "A second functional RNA domain in the 5′ UTR of the Tomato bushy stunt virus genome: intra- and interdomain interactions mediate viral RNA replication". RNA 9 (10): 1232–1245. 2003. doi:10.1261/rna.5630203. PMID 13130137.
- ↑ "3′-Terminal RNA secondary structures are important for accumulation of tomato bushy stunt virus DI RNAs". Virology 313 (2): 567–580. 2003. doi:10.1016/S0042-6822(03)00349-0. PMID 12954222.
- ↑ Monkewich, S; Lin HX; Fabian MR; Xu W; Na H; Ray D; Chernysheva OA; Nagy PD et al. (2005). "The p92 Polymerase Coding Region Contains an Internal RNA Element Required at an Early Step in Tombusvirus Genome Replication". J Virol 79 (8): 4848–4858. doi:10.1128/JVI.79.8.4848-4858.2005. PMID 15795270.
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