Tombusvirus 5′ UTR

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
SymbolTombus_5
RfamRF00171
Other data
RNA typeCis-reg
Domain(s)Viruses
SOSO:0000204
PDB structuresPDBe

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.

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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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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