Tombusvirus 5′ UTR is an important cis-regulatory region of the Tombus virus genome.
| 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 | SO:0000204 |
| PDB structures | PDBe |
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 edit
- ^ a b Wu B, Vanti WB, White KA (2001). "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. doi:10.1006/jmbi.2000.4298. PMID 11162089.
- ^ Ray D, Na H, White KA (2004). "Structural properties of a multifunctional T-shaped RNA domain that mediate efficient tomato bushy stunt virus RNA replication". J. Virol. 78 (19): 10490–10500. doi:10.1128/JVI.78.19.10490-10500.2004. PMC 516415. PMID 15367615.
- ^ a b Ray D, Wu B, White KA (2003). "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. doi:10.1261/rna.5630203. PMC 1370487. PMID 13130137.
- ^ Fabian MR, Na H, Ray D, White KA (2003). "3′-Terminal RNA secondary structures are important for accumulation of tomato bushy stunt virus DI RNAs". Virology. 313 (2): 567–580. 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; White KA (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. PMC 1069561. PMID 15795270.
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