Tombusvirus 5′ UTR

{{Infobox rfam

| Name = Tombusvirus 5′ UTR

| image = RF00171.jpg

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| caption = Predicted secondary structure and sequence conservation of Tombus_5

| Symbol = Tombus_5

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| Rfam = RF00171

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| RNA_type = Cis-reg

| Tax_domain = Viruses

| GO =

| SO = {{SO|0000204}}

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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.{{cn|date=November 2022}}

2 RNA domains in the 5′ UTR have been reported, a 5′ T-shaped domain (TSD) followed by a stem-loop (SL5){{cite journal |vauthors=Wu B, Vanti WB, White KA | title = An RNA domain within the 5′ untranslated region of the tomato bushy stunt virus genome modulates viral RNA replication | journal = J. Mol. Biol. | volume = 305 | issue = 4 | pages = 741–756 | year = 2001 | pmid = 11162089 | doi = 10.1006/jmbi.2000.4298 }}{{cite journal |vauthors=Ray D, Na H, White KA | title = Structural properties of a multifunctional T-shaped RNA domain that mediate efficient tomato bushy stunt virus RNA replication | journal = J. Virol. | volume = 78 | issue = 19 | pages = 10490–10500 | year = 2004 | pmid = 15367615 | doi = 10.1128/JVI.78.19.10490-10500.2004 | pmc = 516415}} and a downstream domain (DSD).{{cite journal |vauthors=Ray D, Wu B, White KA | title = A second functional RNA domain in the 5′ UTR of the Tomato bushy stunt virus genome: intra- and interdomain interactions mediate viral RNA replication | journal = RNA | volume = 9 | issue = 10 | pages = 1232–1245 | year = 2003 | pmid = 13130137 | doi = 10.1261/rna.5630203 | pmc = 1370487 }} TSD-DSD interactions are proposed to be involved in the mediation of viral RNA replication.

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

Other non-coding RNA structures in Tombusvirus include the 3′ UTR region IV{{cite journal |vauthors=Fabian MR, Na H, Ray D, White KA | title = 3′-Terminal RNA secondary structures are important for accumulation of tomato bushy stunt virus DI RNAs | journal = Virology | volume = 313 | issue = 2 | pages = 567–580 | year = 2003 | pmid = 12954222 | doi =10.1016/S0042-6822(03)00349-0 | doi-access = free }} and an internal replication element.{{cite journal | last = Monkewich | first = S |author2=Lin HX |author3=Fabian MR |author4=Xu W |author5=Na H |author6=Ray D |author7=Chernysheva OA |author8=Nagy PD |author9=White KA | year = 2005 | title = The p92 Polymerase Coding Region Contains an Internal RNA Element Required at an Early Step in Tombusvirus Genome Replication | journal = J Virol | volume = 79 | pages = 4848–4858 | pmid = 15795270 | doi = 10.1128/JVI.79.8.4848-4858.2005 | issue = 8 | pmc = 1069561}}