RNA structures required for production of subgenomic flavivirus RNA

Anneke Funk, Katherine Truong, Tomoko Nagasaki, Shessy Torres, Nadia Floden, Ezequiel Balmori Melian, Judy Edmonds, Hongping Dong, Pei-Yong Shi, Alexander A. Khromykh

Research output: Contribution to journalArticle

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Abstract

Flaviviruses are a group of single-stranded, positive-sense RNA viruses causing ∼100 million infections per year. We have recently shown that flaviviruses produce a unique, small, noncoding RNA (∼0.5 kb) derived from the 3′ untranslated region (UTR) of the genomic RNA (gRNA), which is required for flavivirus-induced cytopathicity and pathogenicity (G. P. Pijlman et al., Cell Host Microbe, 4: 579-591, 2008). This RNA (subgenomic flavivirus RNA [sfRNA]) is a product of incomplete degradation of gRNA presumably by the cellular 5′-3′ exoribonuclease XRN1, which stalls on the rigid secondary structure stem-loop II (SL-II) located at the beginning of the 3′ UTR. Mutations or deletions of various secondary structures in the 3′ UTR resulted in the loss of full-length sfRNA (sfRNA1) and production of smaller and less abundant sfRNAs (sfRNA2 and sfRNA3). Here, we investigated in detail the importance of West Nile virus Kunjin (WNVKUN) 3′ UTR secondary structures as well as tertiary interactions for sfRNA formation. We show that secondary structures SL-IV and dumbbell 1 (DB1) downstream of SL-II are able to prevent further degradation of gRNA when the SL-II structure is deleted, leading to production of sfRNA2 and sfRNA3, respectively. We also show that a number of pseudoknot (PK) interactions, in particular PK1 stabilizing SL-II and PK3 stabilizing DB1, are required for protection of gRNA from nuclease degradation and production of sfRNA. Our results show that PK interactions play a vital role in the production of nuclease-resistant sfRNA, which is essential for viral cytopathicity in cells and pathogenicity in mice.

Original languageEnglish (US)
Pages (from-to)11407-11417
Number of pages11
JournalJournal of Virology
Volume84
Issue number21
DOIs
StatePublished - 2010
Externally publishedYes

Fingerprint

Flavivirus
RNA
3' Untranslated Regions
3' untranslated regions
RNA Stability
Flaviviridae
genomics
stems
nucleases
Virulence
degradation
positive sense, single-stranded RNA viruses
exoribonucleases
Small Untranslated RNA
West Nile virus
pathogenicity
Sequence Deletion
RNA Viruses
Ribonucleases
cells

ASJC Scopus subject areas

  • Immunology
  • Virology
  • Medicine(all)

Cite this

Funk, A., Truong, K., Nagasaki, T., Torres, S., Floden, N., Melian, E. B., ... Khromykh, A. A. (2010). RNA structures required for production of subgenomic flavivirus RNA. Journal of Virology, 84(21), 11407-11417. https://doi.org/10.1128/JVI.01159-10

RNA structures required for production of subgenomic flavivirus RNA. / Funk, Anneke; Truong, Katherine; Nagasaki, Tomoko; Torres, Shessy; Floden, Nadia; Melian, Ezequiel Balmori; Edmonds, Judy; Dong, Hongping; Shi, Pei-Yong; Khromykh, Alexander A.

In: Journal of Virology, Vol. 84, No. 21, 2010, p. 11407-11417.

Research output: Contribution to journalArticle

Funk, A, Truong, K, Nagasaki, T, Torres, S, Floden, N, Melian, EB, Edmonds, J, Dong, H, Shi, P-Y & Khromykh, AA 2010, 'RNA structures required for production of subgenomic flavivirus RNA', Journal of Virology, vol. 84, no. 21, pp. 11407-11417. https://doi.org/10.1128/JVI.01159-10
Funk A, Truong K, Nagasaki T, Torres S, Floden N, Melian EB et al. RNA structures required for production of subgenomic flavivirus RNA. Journal of Virology. 2010;84(21):11407-11417. https://doi.org/10.1128/JVI.01159-10
Funk, Anneke ; Truong, Katherine ; Nagasaki, Tomoko ; Torres, Shessy ; Floden, Nadia ; Melian, Ezequiel Balmori ; Edmonds, Judy ; Dong, Hongping ; Shi, Pei-Yong ; Khromykh, Alexander A. / RNA structures required for production of subgenomic flavivirus RNA. In: Journal of Virology. 2010 ; Vol. 84, No. 21. pp. 11407-11417.
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