In Vitro Secondary Structure of the Genomic RNA of Satellite Tobacco Mosaic Virus

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Athavale, Shreyas S ^a   Gossett, J Jared ^a,b   Bowman, Jessica C ^a   Hud, Nicholas V ^a   de Williams, Lorenan ^a   Harvey, Stephen C ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b Georgia Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC RNA; TRANSFER RNA; VIRUS RNA;

ANALYTIC METHOD; ARTICLE; ATOMIC FORCE MICROSCOPY; ELECTROPHILICITY; ENCAPSULATION; IN VITRO STUDY; NONHUMAN; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; RNA DEGRADATION; SELECTIVE 2' HYDROXYL ACYLATION ANALYZED BY PRIMER EXTENSION; TOBACCO MOSAIC VIRUS; VIRION; VIRUS CAPSID;

BASE PAIRING; GENOME; NUCLEIC ACID CONFORMATION; RNA, TRANSFER; RNA, VIRAL; TOBACCO; TOBACCO MOSAIC SATELLITE VIRUS; VIRION;

SATELLITE TOBACCO MOSAIC VIRUS;

EID: 84872803421     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054384     Document Type: Article

References (40)

1. Dodds JA, (1998) Satellite tobacco mosaic virus. Annual Review of Phytopathology 36: 295-310.
2. Schneemann A, (2006) The structural and functional role of RNA in icosahedral virus assembly. Annu Rev Microbiol 60: 51-67.
3. Gossele V, Fache I, Meulewaeter F, Cornelissen M, Metzlaff M, (2002) SVISS- a novel transient gene silencing system for gene function discovery and validation in tobacco plants. Plant Journal 32: 859-866.
4. Larson SB, Day J, Greenwood A, McPherson A, (1998) Refined structure of satellite tobacco mosaic virus at 1.8 Å resolution. J Mol Biol 277: 37-59.
5. Larson SB, McPherson A, (2001) Satellite tobacco mosaic virus RNA: Structure and implications for assembly. Curr Opinion Struct Biol 11: 59-65.
6. Kuznetsov YG, Dowell JJ, Gavira JA, Ng JD, McPherson A, (2010) Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus. Nucleic Acids Res 38: 8284-8294.
7. Schroeder SJ, Stone JW, Bleckley S, Gibbons T, Mathews DM, (2011) Ensemble of secondary structures for encapsidated satellite tobacco mosaic virus RNA consistent with chemical probing and crystallography constraints. Biophys J 101: 167-175.
8. Zeng Y, Larson SB, Heitsch CE, McPherson A, Harvey SC, (2012) A model for the structure of satellite tobacco mosaic virus. J Struct Biol 180: 110-116.
9. Felden B, Florentz C, McPherson A, Giege R, (1994) A histidine accepting tRNA-like fold at the 3′-end of satellite tobacco mosaic virus RNA. Nucleic Acids Res 22: 2882-2886.
10. Gultyaev AP, van Batenburg E, Pleij CW, (1994) Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs. J Gen Virol 75: 2851-2856.
11. Merino EJ, Wilkinson KA, Coughlan JL, Weeks KM, (2005) RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc 127: 4223-4231.
12. McGinnis JL, Dunkle JA, Cate JH, Weeks KM, (2012) The Mechanisms of RNA SHAPE Chemistry. J Am Chem Soc 134: 6617-6624.
13. Deigan KE, Li TW, Mathews DH, Weeks KM, (2009) Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A 106: 97-102.
14. Bindewald E, Wendeler M, Legiewicz M, Bona MK, Wang Y, et al. (2011) Correlating SHAPE signatures with three-dimensional RNA structures. RNA 17: 1688-1696.
15. Brion P, Westhof E, (1997) Hierarchy and dynamics of RNA folding. Annu Rev Biophys Biomol Struct 26: 113-137.
16. Draper DE, (2008) RNA folding: thermodynamic and molecular descriptions of the roles of ions. Biophys J 95: 5489-5495.
17. Bowman JC, Lenz TK, Hud NV, Williams LD, (2012) Cations in charge: magnesium ions in RNA folding and catalysis. Curr Opin Struct Biol 22: 262-272.
18. Reuter JS, Mathews DH, (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11: 129.
19. Kladwang W, VanLang CC, Cordero P, Das R, (2011) Understanding the errors of SHAPE-directed RNA structure modeling. Biochemistry 50: 8049-8056.
20. Cordero P, Kladwang W, Vanlang CC, Das R, (2012) Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry 51: 7037-7039.
21. Wilkinson KA, Vasa SM, Deigan KE, Mortimer SA, Giddings MC, et al. (2009) Influence of nucleotide identity on ribose 2′-hydroxyl reactivity in RNA. Rna-a Publication of the Rna Society 15: 1314-1321.
22. Xu W, Bolduc F, Hong N, Perreault J, (2012) The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids. Molecular Plant Pathology 10 (1111/J.1364-3703.2011.00776):: X.
23. Yoffe AM, Prinsen P, Gopal A, Knobler CM, Gelbart WM, et al. (2008) Predicting the sizes of large RNA molecules. Proc Natl Acad Sci U S A 105: 16153-16158.
24. Mirkov TE, Mathews DM, Du Plessis DH, Dodds JA, (1989) Nucleotide sequence and translation of satellite tobacco mosaic virus RNA. Virology 170: 139-146.
25. Vicens Q, Gooding AR, Laederach A, Cech TR, (2007) Local RNA structural changes induced by crystallization are revealed by SHAPE. RNA 13: 536-548.
26. Athavale SS, Petrov AS, Hsiao C, Watkins D, Prickett CD, et al. (2012) RNA Folding and Catalysis Mediated by Iron (II). PLoS ONE 7(5): e38024 doi:38010.31371/journal.pone.0038024.
27. Wilkinson KA, Merino EJ, Weeks KM, (2005) RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. J Am Chem Soc 127: 4659-4667.
28. Mortimer SA, Weeks KM, (2008) Time-resolved RNA SHAPE chemistry. J Am Chem Soc 130: 16178-16180.
29. Athavale SS, Gossett JJ, Hsiao C, Bowman JC, O'Neill E, et al. (2012) Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state. RNA 18: 752-758.
30. Mirkov TE, Kurath G, Mathews DM, Elliott K, Dodds JA, et al. (1990) Factors Affecting Efficient Infection of Tobacco with Invitro Rna Transcripts from Cloned Cdnas of Satellite Tobacco Mosaic-Virus. Virology 179: 395-402.
31. Routh G, Dodds JA, Fitzmaurice L, Mirkov TE, (1995) Characterization of Deletion and Frameshift Mutants of Satellite Tobacco Mosaic-Virus. Virology 212: 121-127.
32. Choi YG, Dreher TW, Rao ALN, (2002) tRNA elements mediate the assembly of an icosahedral RNA virus. Proceedings of the National Academy of Sciences of the United States of America 99: 655-660.
33. Dreher TW, (1999) Functions of the 3′-untranslated regions of positive strand RNA viral genomes. Annual Review of Phytopathology 37: 151-174.
34. Rao ALN, Dreher TW, Marsh LE, Hall TC, (1989) Telomeric Function of the Transfer Rna-Like Structure of Brome Mosaic-Virus Rna. Proceedings of the National Academy of Sciences of the United States of America 86: 5335-5339.
35. Söll D, RajBhandary U (1995) tRNA: structure, biosynthesis, and function. Washington, D.C.: ASM Press. xiii, 572 p.
36. Gallie DR, Feder JN, Schimke RT, Walbot V, (1991) Functional-Analysis of the Tobacco Mosaic-Virus Transfer Rna-Like Structure in Cytoplasmic Gene-Regulation. Nucleic Acids Res 19: 5031-5036.
37. Wang MB, Bian XY, Wu LM, Liu LX, Smith NA, et al. (2004) On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proceedings of the National Academy of Sciences of the United States of America 101: 3275-3280.
38. Sampson JR, (1988) Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci 85: 1033-1037.
39. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, et al. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America 101: 7287-7292.
40. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, et al. (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte Fur Chemie 125: 167-188.