Diverse roles and interactions of RNA structures during the replication of positive-stranded RNA viruses of humans and animals

Journal of General Virology

Volumn 96, Issue 7, 2015, Pages 1497-1503

  Tuplin, Andrew ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; VIRUS RNA;

ARTICLE; BASE PAIRING; FLAVIVIRUS; GENE FUNCTION; GENETIC VARIABILITY; HUMAN; IMMUNE EVASION; INNATE IMMUNITY; INTERACTIONS WITH RNA; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; NUCLEAR REPROGRAMMING; NUCLEOTIDE SEQUENCE; PICORNAVIRIDAE; POSITIVE-STRAND RNA VIRUS; PRIORITY JOURNAL; RNA RNA INTERACTION; RNA STRUCTURE; RNA TRANSLATION; TRANSLATION INITIATION; VIRAL GENETICS; VIRUS GENOME; VIRUS IMMUNITY; VIRUS REPLICATION; ANIMAL; CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; PLANT; RNA VIRUS;

ANIMALIA; RNA VIRUSES;

ANIMALS; BASE PAIRING; GENE EXPRESSION REGULATION, VIRAL; HUMANS; NUCLEIC ACID CONFORMATION; PLANTS; RNA VIRUSES; RNA, VIRAL; VIRUS REPLICATION;

EID: 84938390516     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.000066     Document Type: Article

References (46)

1. Alvarez, D. E., De Lella Ezcurra, A. L., Fucito, S. & Gamarnik, A. V. (2005a). Role of RNA structures present at the 3’UTR of dengue virus on translation, RNA synthesis, and viral replication. Virology 339, 200-212
2. Alvarez, D. E., Lodeiro, M. F., Ludueña, S. J., Pietrasanta, L. I. & Gamarnik, A. V. (2005b). Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol 79, 6631-6643
3. Atkinson, N. J., Witteveldt, J., Evans, D. J. & Simmonds, P. (2014). The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication. Nucleic Acids Res 42, 4527-4545.
4. Burrill, C. P., Westesson, O., Schulte, M. B., Strings, V. R., Segal, M. & Andino, R. (2013). Global RNA structure analysis of poliovirus identifies a conserved RNA structure involved in viral replication and infectivity. J Virol 87, 11670-11683
5. Chapman, E. G., Costantino, D. A., Rabe, J. L., Moon, S. L., Wilusz, J., Nix, J. C. & Kieft, J. S. (2014). The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production. Science 344, 307-310
6. Chase, A. J., Daijogo, S. & Semler, B. L. (2014). Inhibition of poliovirus-induced cleavage of cellular protein PCBP2 reduces the levels of viral RNA replication. J Virol 88, 3192-3201
7. Diviney, S., Tuplin, A., Struthers, M., Armstrong, V., Elliott, R. M., Simmonds, P. & Evans, D. J. (2008). A hepatitis C virus cis-acting replication element forms a long-range RNA-RNA interaction with upstream RNA sequences in NS5B. J Virol 82, 9008-9022
8. Fayzulin, R. & Frolov, I. (2004). Changes of the secondary structure of the 59 end of the Sindbis virus genome inhibit virus growth in mosquito cells and lead to accumulation of adaptive mutations. J Virol 78, 4953-4964
9. Filomatori, C. V., Lodeiro, M. F., Alvarez, D. E., Samsa, M. M., Pietrasanta, L. & Gamarnik, A. V. (2006). A 59 RNA element promotes dengue virus RNA synthesis on a circular genome. Genes Dev 20, 2238-2249
10. Filomatori, C. V., Iglesias, N. G., Villordo, S. M., Alvarez, D. E. & Gamarnik, A. V. (2011). RNA sequences and structures required for the recruitment and activity of the dengue virus polymerase. J Biol Chem 286, 6929-6939
11. Firth, A. E., Wills, N. M., Gesteland, R. F. & Atkins, J. F. (2011). Stimulation of stop codon readthrough: frequent presence of an extended 39 RNA structural element. Nucleic Acids Res 39, 6679-6691
12. Friebe, P., Boudet, J., Simorre, J. P. & Bartenschlager, R. (2005). Kissing-loop interaction in the 39 end of the hepatitis C virus genome essential for RNA replication. J Virol 79, 380-392
13. Gebhard, L. G., Filomatori, C. V. & Gamarnik, A. V. (2011). Functional RNA elements in the dengue virus genome. Viruses 3, 1739-1756
14. Giedroc, D. P. & Cornish, P. V. (2009). Frameshifting RNA pseudoknots: structure and mechanism. Virus Res 139, 193-208
15. Gorchakov, R., Hardy, R., Rice, C. M. & Frolov, I. (2004). Selection of functional 59 cis-acting elements promoting efficient sindbis virus genome replication. J Virol 78, 61-75
16. Groat-Carmona, A. M., Orozco, S., Friebe, P., Payne, A., Kramer, L. & Harris, E. (2012). A novel coding-region RNA element modulates infectious dengue virus particle production in both mammalian and mosquito cells and regulates viral replication in Aedes aegypti mosquitoes. Virology 432, 511-526
17. Han, J. Q., Townsend, H. L., Jha, B. K., Paranjape, J. M., Silverman, R. H. & Barton, D. J. (2007). A phylogenetically conserved RNA structure in the poliovirus open reading frame inhibits the antiviral endoribonuclease RNase L. J Virol 81, 5561-5572
18. Harvey, S. C., Zeng, Y. & Heitsch, C. E. (2013). The icosahedral RNA virus as a grotto: organizing the genome into stalagmites and stalactites. J Biol Phys 39, 163-172
19. Hyde, J. L., Gardner, C. L., Kimura, T., White, J. P., Liu, G., Trobaugh, D. W., Huang, C., Tonelli, M., Paessler, S. & other authors (2014). A viral RNA structural element alters host recognition of nonself RNA. Science 343, 783-787
20. Jan, E. & Sarnow, P. (2002). Factorless ribosome assembly on the internal ribosome entry site of cricket paralysis virus. J Mol Biol 324, 889-902
21. Keel, A. Y., Jha, B. K. & Kieft, J. S. (2012). Structural architecture of an RNA that competitively inhibits RNase L. RNA 18, 88-99
22. Khromykh, A. A., Meka, H., Guyatt, K. J. & Westaway, E. G. (2001). Essential role of cyclization sequences in flavivirus RNA replication. J Virol 75, 6719-6728
23. Lee, H., Shin, H., Wimmer, E. & Paul, A. V. (2004). cis-acting RNA signals in the NS5B C-terminal coding sequence of the hepatitis C virus genome. J Virol 78, 10865-10877.
24. Lo, M. K., Tilgner, M., Bernard, K. A. & Shi, P. Y. (2003). Functional analysis of mosquito-borne flavivirus conserved sequence elements within 39 untranslated region of West Nile virus by use of a reporting replicon that differentiates between viral translation and RNA replication. J Virol 77, 10004-10014
25. López de Quinto, S., Sáiz, M., de la Morena, D., Sobrino, F. & Martínez-Salas, E. (2002). IRES-driven translation is stimulated separately by the FMDV 39-NCR and poly(A) sequences. Nucleic Acids Res 30, 4398-4405
26. Manzano, M., Reichert, E. D., Polo, S., Falgout, B., Kasprzak, W., Shapiro, B. A. & Padmanabhan, R. (2011). Identification of cisacting elements in the 39-untranslated region of the dengue virus type 2 RNA that modulate translation and replication. J Biol Chem 286, 22521-22534.
27. Merino, E. J., Wilkinson, K. A., Coughlan, J. L. & Weeks, K. M. (2005). RNA structure analysis at single nucleotide resolution by selective 29-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc 127, 4223-4231
28. Oakland, T. E., Haselton, K. J. & Randall, G. (2013). EWSR1 binds the hepatitis C virus cis-acting replication element and is required for efficient viral replication. J Virol 87, 6625-6634
29. Ogram, S. A. & Flanegan, J. B. (2011). Non-template functions of viral RNA in picornavirus replication. Curr Opin Virol 1, 339-346
30. Olsthoorn, R. & van Duin, J. (2011). Bacteriophages with ssRNA: eLS
31. Pathak, K. B., Pogany, J. & Nagy, P. D. (2011). Non-template functions of the viral RNA in plant RNA virus replication. Curr Opin Virol 1, 332-338
32. Plant, E. P. & Dinman, J. D. (2008). The role of programmed-1 ribosomal frameshifting in coronavirus propagation. Front Biosci 13, 4873-4881
33. Polacek, C., Friebe, P. & Harris, E. (2009). Poly(A)-binding protein binds to the non-polyadenylated 39 untranslated region of dengue virus and modulates translation efficiency. J Gen Virol 90, 687-692
34. Romero-López, C. & Berzal-Herranz, A. (2012). The functional RNA domain 5BSL3.2 within the NS5B coding sequence influences hepatitis C virus IRES-mediated translation. Cell Mol Life Sci 69, 103-113
35. Schnettler, E., Sterken, M. G., Leung, J. Y., Metz, S. W., Geertsema, C., Goldbach, R. W., Vlak, J. M., Kohl, A., Khromykh, A. A. & Pijlman, G. P. (2012). Noncoding flavivirus RNA displays RNA interference suppressor activity in insect and Mammalian cells. J Virol 86, 13486-13500
36. Serrano, P., Pulido, M. R., Sáiz, M. & Martínez-Salas, E. (2006). The 39 end of the foot-and-mouth disease virus genome establishes two distinct long-range RNA-RNA interactions with the 59 end region. J Gen Virol 87, 3013-3022
37. Simmonds, P., Tuplin, A. & Evans, D. J. (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
38. Song, Y., Liu, Y., Ward, C. B., Mueller, S., Futcher, B., Skiena, S., Paul, A. V. & Wimmer, E. (2012). Identification of two functionally redundant RNA elements in the coding sequence of poliovirus using computer-generated design. Proc Natl Acad Sci U S A 109, 14301-14307
39. Strauss, E. G., Rice, C. M. & Strauss, J. H. (1983). Sequence coding for the alphavirus nonstructural proteins is interrupted by an opal termination codon. Proc Natl Acad Sci U S A 80, 5271-5275
40. Tuplin, A., Struthers, M., Simmonds, P. & Evans, D. J. (2012). A twist in the tail: SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication. Nucleic Acids Res 40, 6908-6921
41. Villordo, S. M. & Gamarnik, A. V. (2009). Genome cyclization as strategy for flavivirus RNA replication. Virus Res 139, 230-239
42. Villordo, S. M. & Gamarnik, A. V. (2013). Differential RNA sequence requirement for dengue virus replication in mosquito and mammalian cells. J Virol 87, 9365-9372
43. Villordo, S. M., Alvarez, D. E. & Gamarnik, A. V. (2010). A balance between circular and linear forms of the dengue virus genome is crucial for viral replication. RNA 16, 2325-2335
44. Wilkinson, K. A., Merino, E. J. & Weeks, K. M. (2006). Selective 29-hydroxyl acylation analyzed by primer extension (SHAPE): quant-itative RNA structure analysis at single nucleotide resolution. Nat Protoc 1, 1610-1616
45. Witteveldt, J., Blundell, R., Maarleveld, J. J., McFadden, N., Evans, D. J. & Simmonds, P. (2014). The influence of viral RNA secondary structure on interactions with innate host cell defences. Nucleic Acids Res 42, 3314-3329
46. You, S., Stump, D. D., Branch, A. D. & Rice, C. M. (2004). A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. J Virol 78, 1352-1366