Plant virus xrRNAs

xrRNAs in Plant Viruses (Tombusviridae and Solemoviridae)

Plant-infecting positive-strand RNA viruses from the Tombusviridae and Solemoviridae families contain Exoribonuclease-Resistant RNAs (xrRNAs), typically located at the beginning of the 3′ UTR or within the intergenic region (IGR) between open reading frames (ORF1 and ORF2)[1][2]. These plant-virus xrRNAs are distinct in sequence and secondary structure from flavivirus xrRNAs, representing a clear example of convergent evolution toward the same functional outcome of exoribonuclease resistance. They are classified as class 3 xrRNAs.

Plant-virus class 3 xrRNAs consist of a single stem-loop containing a pseudoknot between the apical stem and the 3′ end, reinforced by a conserved T-loop/D-loop interaction[3][4][5]. Some variants additionally include a short downstream SL that is dispensable for nuclease-resistance. Despite the differences in sequence and secondary structure, the resulting three-dimensional fold forms a similar protective ring around the 5′ end that blocks degradation[6].

xrRNAs have been identified in Red clover necrotic mosaic virus (RCNMV), as well as in major agricultural pathogens including Potato leafroll virus (PLRV), Maize chlorotic mottle virus (MCMV), and Maize yellow dwarf virus-RMV (MYDV-RMV, formerly BYDV-RMV)[1][6]. Loss of xrRNA function leads to severely impaired viral replication, emphasizing their essential role in viral fitness and translational regulation[6].

References

  1. ^ a b Steckelberg, Anna-Lena; Vicens, Quentin; Kieft, Jeffrey S. (18 December 2018). "Exoribonuclease-Resistant RNAs Exist within both Coding and Noncoding Subgenomic RNAs". mBio. 9 (6): e02461–18. doi:10.1128/mBio.02461-18. ISSN 2150-7511. PMC 6299227. PMID 30563900.
  2. ^ Iwakawa, Hiro-Oki; Mizumoto, Hiroyuki; Nagano, Hideaki; Imoto, Yuka; Takigawa, Kazuma; Sarawaneeyaruk, Siriruk; Kaido, Masanori; Mise, Kazuyuki; Okuno, Tetsuro (2008). "A viral noncoding RNA generated by cis-element-mediated protection against 5'->3' RNA decay represses both cap-independent and cap-dependent translation". Journal of Virology. 82 (20): 10162–10174. doi:10.1128/JVI.01027-08. ISSN 1098-5514. PMC 2566255. PMID 18701589.
  3. ^ Steckelberg, Anna-Lena; Akiyama, Benjamin M.; Costantino, David A.; Sit, Tim L.; Nix, Jay C.; Kieft, Jeffrey S. (19 June 2018). "A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure". Proceedings of the National Academy of Sciences of the United States of America. 115 (25): 6404–6409. doi:10.1073/pnas.1802429115. ISSN 1091-6490. PMC 6016793. PMID 29866852.
  4. ^ Steckelberg, Anna-Lena; Vicens, Quentin; Costantino, David A.; Nix, Jay C.; Kieft, Jeffrey S. (2020). "The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold". RNA (New York, N.Y.). 26 (12): 1767–1776. doi:10.1261/rna.076224.120. ISSN 1469-9001. PMC 7668246. PMID 32848042.
  5. ^ Gezelle, Jeanine G.; Korn, Sophie M.; McDonald, Jayden T.; Gong, Zhen; Erickson, Anna; Huang, Chih-Hung; Yang, Feiyue; Cronin, Matt; Kuo, Yen-Wen; Wimberly, Brian T.; Steckelberg, Anna-Lena (27 August 2025). "A conserved viral RNA fold enables nuclease resistance across kingdoms of life". Nucleic Acids Research. 53 (16): gkaf840. doi:10.1093/nar/gkaf840. ISSN 1362-4962. PMC 12397905. PMID 40884403.{{cite journal}}: CS1 maint: article number as page number (link)
  6. ^ a b c Gezelle, Jeanine G.; Korn, Sophie M.; McDonald, Jayden T.; Gong, Zhen; Erickson, Anna; Huang, Chih-Hung; Yang, Feiyue; Cronin, Matt; Kuo, Yen-Wen; Wimberly, Brian T.; Steckelberg, Anna-Lena (27 August 2025). "A conserved viral RNA fold enables nuclease resistance across kingdoms of life". Nucleic Acids Research. 53 (16): gkaf840. doi:10.1093/nar/gkaf840. ISSN 1362-4962. PMC 12397905. PMID 40884403.{{cite journal}}: CS1 maint: article number as page number (link)
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