UPSK RNA

UPSK RNA
	Predicted secondary structure and sequence conservation of UPSK
Identifiers
Symbol	UPSK
Rfam	RF00390
Other data
RNA type	Cis-reg
Domain(s)	Viruses
SO	SO:0000233
PDB structures	PDBe

The Upstream pseudoknot (UPSK) domain is an RNA element found in the turnip yellow mosaic virus, beet virus Q,[1] barley stripe mosaic virus[2] and tobacco mosaic virus,[3] which is thought to be needed for efficient transcription. Disruption of the pseudoknot structure gives rise to a 50% drop in transcription efficiency.[4] This element acts in conjunction with the Tymovirus/Pomovirus tRNA-like 3' UTR element to enhance translation.[5]

References

Koenig R, Pleij CW, Beier C, Commandeur U (August 1998). "Genome properties of beet virus Q, a new furo-like virus from sugarbeet, determined from unpurified virus". J. Gen. Virol. 79 (8): 2027–2036. doi:10.1099/0022-1317-79-8-2027. PMID 9714254.
Solovyev AG, Savenkov EI, Agranovsky AA, Morozov SY (May 1996). "Comparisons of the genomic cis-elements and coding regions in RNA beta components of the hordeiviruses barley stripe mosaic virus, lychnis ringspot virus, and poa semilatent virus". Virology. 219 (1): 9–18. doi:10.1006/viro.1996.0217. PMID 8623558.
Felden B, Florentz C, Giegé R, Westhof E (March 1996). "A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5' upstream pseudoknots in the 3' terminus of tobacco mosaic virus RNA". RNA. 2 (3): 201–212. PMC 1369363. PMID 8608444.
Deiman, BA; Kortlever RM; Pleij CW (1997). "The role of the pseudoknot at the 3' end of turnip yellow mosaic virus RNA in minus-strand synthesis by the viral RNA-dependent RNA polymerase". J Virol. 71 (8): 5990–5996. doi:10.1128/JVI.71.8.5990-5996.1997. PMC 191855. PMID 9223489.
Matsuda, D; Dreher TW (2004). "The tRNA-like structure of Turnip yellow mosaic virus RNA is a 3'-translational enhancer". Virology. 321 (1): 36–46. doi:10.1016/j.virol.2003.10.023. PMID 15033563.

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