A secondary structure model for the 3'-untranslated region of ilarvirus RNAs

Viral Genomes: Diversity, Properties and Parameters

Volumn , Issue , 2009, Pages 65-83

  Chen, Shih Cheng ^a   Gultyaev, Alexander P ^a   Pleij, Cornelis W A ^a   Olsthoorn, René C L ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

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[No Author keywords available]

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EID: 84892909854     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (45)

1. Aparicio F, Sánchez-Navarro JA, Olsthoorn RCL, Pallás V, Bol JF. 2001. Recognition of cisacting sequences in RNA 3 of Prunus necrotic ringspot virus by the replicase of Alfalfa mosaic virus. J Gen Virol. 82: 947-951.
2. Aparicio F, Vilar M, Perez-Payá E, Pallás V. 2003. The coat protein of prunus necrotic ringspot virus specifically binds to and regulates the conformation of its genomic RNA. Virology. 313: 213-223.
3. Bink HHJ, Hellendoorn K, van der Meulen J, Pleij CWA. 2002. Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA. Proc. Natl. Acad. Sci. USA. 99: 13465-13470.
4. Bol JF. 2005. Replication of alfamo-and ilarviruses: role of the coat protein. Annu Rev Phytopathol. 43: 39-62.
5. Chen SC, van den Born E, van den Worm SHE, Pleij CWA, Snijder EJ, Olsthoorn RCL. 2007. New structure model for the packaging signal in the genome of group IIa coronaviruses. J Virol. 81: 6771-6774.
6. Chen S-J. 2008. RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu. Rev. Biophys. 37: 197-214.
7. Codoñer FM, Elena SF. 2008. The promiscuous evolutionary history of the family Bromoviridae. J Gen Virol. 89: 1739-1747.
8. Dreher TW. 2008. Role of tRNA-like structures in controlling plant virus replication. Virus Res. doi: 10.1016/j.virusres.2008.06.010
9. Fabian MR, White KA. 2004. 5'-3' RNA-RNA interaction facilitates cap-and poly(A) tailindependent translation of tomato bushy stunt virus mRNA: a potential common mechanism for tombusviridae. J. Biol. Chem. 279: 28862-28872.
10. Gultyaev AP, van Batenburg FH, Pleij CWA. 1995. The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol. 250: 37-51.
11. Gultyaev AP, van Batenburg FH, Pleij CWA. 1999 An approximation of loop free energy values of RNA H-pseudoknots. RNA. 5: 609-617.
12. Guo L, Allen EM, Miller WA. 2001. Base-pairing between untranslated regions facilitates translation of uncapped, nonpolyadenylated viral RNA. Mol. Cell. 7: 1103-1109.
13. Haasnoot PC, Bol JF, Olsthoorn RC. 2003. A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA-protein interactions. Proc Natl Acad Sci U S A 100: 12596-600.
14. Jaspars EMJ. 1999. Genome activation in alfamo-and ilarviruses. Arch Virol. 144: 843-863.
15. Joshi RL, Joshi S, Chapeville F, Haenni AL. 1983. tRNA-like structures of plant viral RNAs: conformational requirements for adenylation and aminoacylation. EMBO J. 2: 1123-1127.
16. Kieft JS. 2008. Viral IRES RNA structures and ribosome interactions. Trends Biochem Sci. 33: 274-283.
17. Kim CH, Kao CC, Tinoco I Jr. 2000. RNA motifs that determine specificity between a viral replicase and its promoter. Nat Struct Biol. 7: 415-423.
18. Klovins J, van Duin J. 1999. A long-range pseudoknot in Qbeta RNA is essential for replication. J Mol Biol. 294: 875-884.
19. Koper-Zwarthoff EC, Bol JF. 1980. Nucleotide sequence of the putative recognition site for coat protein in the RNAs of alfalfa mosaic virus and tobacco streak virus. Nucleic Acids Res. 8: 3307-3318.
20. Krab IM, Caldwell C, Gallie DR, Bol JF. 2005. Coat protein enhances translational efficiency of Alfalfa mosaic virus RNAs and interacts with the eIF4G component of initiation factor eIF4F. J Gen Virol. 86: 1841-1849.
21. Kramvis A, Kew MC. 1998. Structure and function of the encapsidation signal of hepadnaviridae. J Viral Hepat. 5: 357-367.
22. Meulewaeter F, van Lipzig R, Gultyaev AP, Pleij CWA, Van Damme D, Cornelissen M, van Eldik G. 2004. Conservation of RNA structures enables TNV and BYDV 5' and 3' elements to cooperate synergistically in cap-independent translation. Nucleic Acids Res. 32: 1721-1730.
23. Miller WA, White KA. 2006. Long-distance RNA-RNA interactions in plant virus gene expression and replication. Annu Rev Phytopathol. 44: 447-467.
24. Neeleman L, Olsthoorn RCL, Linthorst HJM, Bol JF. 2001. Translation of a nonpolyadenylated viral RNA is enhanced by binding of viral coat protein or polyadenylation of the RNA. Proc Natl Acad Sci U S A. 98: 14286-14291.
25. Olsthoorn RCL, Bol JF. 2002. Role of an essential triloop hairpin and flanking structures in the 3' untranslated region of Alfalfa mosaic virus RNA in in vitro transcription. J Virol. 76: 8747-8756.
26. Olsthoorn RCL, Haasnoot PCJ, Bol JF. 2004. Similarities and differences between the subgenomic and minus-strand promoters of an RNA plant virus. J Virol. 78: 4048-4053.
27. Olsthoorn RCL, Mertens S, Brederode FT, Bol JF. 1999. A conformational switch at the 3' end of a plant virus RNA regulates viral replication. EMBO J. 18: 4856-4864.
28. Petrillo JE, Rocheleau G, Kelley-Clarke B, Gehrke L. 2005. Evaluation of the conformational switch model for alfalfa mosaic virus RNA replication. J Virol. 79: 5743-5751.
29. Pickett GG, Peabody DS. 1993. Encapsidation of heterologous RNAs by bacteriophage MS2 coat protein. Nucleic Acids Res. 21: 4621-4626.
30. Pleij CWA, Rietveld K, Bosch L. 1985. A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res. 13: 1717-1731.
31. Quigley GJ, Gehrke L, Roth DA, Auron PE. 1984. Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data. Nucleic Acids Res. 12: 347-366.
32. Rampitsch C, Eastwell KC. 1997. The complete nucleotide sequence of prune dwarf ilarvirus RNA-1. Arch Virol. 142: 1911-8.
33. Reusken CBEM, Bol JF. 1996. Structural elements of the 3'-terminal coat protein binding site in alfalfa mosaic virus RNAs. Nucleic Acids Res. 24: 2660-2665.
34. Sanchez-Navarro JA, Pallas V. 1997. Evolutionary relationships in the ilarviruses: nucleotide sequence of Prunus necrotic ringspot virus RNA 3. Arch Virol. 142: 749-763.
35. Scott SW, Zimmerman MT, Ge X. 1998. The sequence of RNA 1 and RNA 2 of tobacco streak virus: additional evidence for the inclusion of alfalfa mosaic virus in the genus Ilarvirus. Arch Virol. 143: 1187-1198.
36. Scott SW, Zimmerman MT. 2001. American plum line pattern is a distinct ilarvirus. Acta Hortic. 550: 221-228.
37. Shiel PJ, Berger PH. 2000. The complete nucleotide sequence of apple mosaic virus (ApMV) RNA 1 and RNA 2: ApMV is more closely related to alfalfa mosaic virus than to other ilarviruses. J Gen Virol. 81: 273-8.
38. Shu Z, Bevilacqua PC. 1999. Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library. Biochemistry. 38: 15369-15379.
39. Simmonds P, Tuplin A, Evans DJ. 2004. Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence. RNA. 10: 1337-1351.
40. Sivakumaran K, Bao Y, Roossinck MJ, Kao CC. 2000. Recognition of the core RNA promoter for minus-strand RNA synthesis by the replicases of Brome mosaic virus and Cucumber mosaic virus. J Virol. 74: 10323-10331.
41. Turner DR, Joyce LE, Butler PJG. 1988. The Tobacco Mosaic Virus Assembly Origin RNA Functional Characteristics Defined by Directed Mutagenesis. J Mol Biol. 203: 531-547.
42. van Rossum CMA, Reusken CBEM, Brederode FT, Bol JF. 1997. The 3' untranslated region of alfalfa mosaic virus RNA3 contains a core promoter for minus-strand RNA synthesis and an enhancer element. J Gen Virol. 78: 3045-3049.
43. van Vloten-Doting L. 1975. Coat protein is required for infectivity of tobacco streak virus: biological equivalence of the coat proteins of tobacco streak and alfalfa mosaic viruses. Virology. 65: 215-25.
44. Zoll J, Heus HA, van Kuppeveld FJM, Melchers WJG. 2008. The structure-function relationship of the enterovirus 3'-UTR. Virus Res. Available online 30 August 2008.
45. Zuidema D, Jaspars EMJ. 1984. Comparative investigations on the coat protein binding sites of the genomic RNAs of alfalfa mosaic and tobacco streak viruses. Virology 135: 43-52.