Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3′ UTR of turnip crinkle virus

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 4, 2010, Pages 1385-1390

  Zuo, Xiaobing ^a   Wang, Jinbu ^a   Yu, Ping ^b   Eyler, Dan ^c   Xu, Huan ^a,g   Starich, Mary R ^a   Tiede, David M ^d   Simon, Anne E ^e   Kasprzak, Wojciech ^b   Schwieters, Charles D ^f   Shapiro, Bruce A ^a   Wang, Yun Xing ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

^e Bldg 142   (United States)

^f NATIONAL INSTITUTES OF HEALTH   (United States)

^g FUDAN UNIVERSITY   (China)

Author keywords

3 UTR RNA; New method; NMR; RNA structure; SAXS

Indexed keywords

VIRUS RNA;

ARTICLE; ENHANCER REGION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PLANT VIRUS; PRIORITY JOURNAL; RIBOSOME; RNA ANALYSIS; RNA STRUCTURE; SMALL ANGLE SCATTERING; TURNIP CRINKLE VIRUS; UNTRANSLATED REGION; VIRUS REPLICATION; VIRUS TRANSCRIPTION; X RAY CRYSTALLOGRAPHY;

3' UNTRANSLATED REGIONS; BASE SEQUENCE; CARMOVIRUS; ENHANCER ELEMENTS, GENETIC; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, VIRAL; VIRAL PROTEINS;

TURNIP CRINKLE VIRUS;

EID: 76549124254     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0908140107     Document Type: Article

References (35)

1. Kozak M Initiation of translation in prokaryotes and eukaryotes. Gene, 234:187-208.
2. Gallie DR (1991) The cap and poly(A) tail function synergistically to regulate mRNA translational efficiency. Genes Dev, 5:2108-2116.
3. Tarun SZ, Jr, Sachs AB (1995) A common function for mRNA 5′ and 3′ ends in translation initiation in yeast. Genes Dev, 9:2997-3007.
4. Tarun SZ, Jr, Sachs AB (1997) Binding of eukaryotic translation initiation factor 4E (eIF4E) to eIF4G represses translation of uncapped mRNA. Mol Cell Biol, 17:6876-6886.
5. Wells SE, Hillner PE, Vale RD, Sachs AB (1998) Circularization of mRNA by eukaryotic translation initiation factors. Mol Cell, 2:135-140.
6. Miller WA, Wang Z, Treder K (2007) The amazing diversity of capindependent translation elements in the 3′-untranslated regions of plant viral RNAs. Biochem Soc Trans, 35:1629-1633.
7. Stupina VA, et al. (2008) The 3′ proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits. RNA, 14:2379-2393.
8. Zhang G, Zhang J, Simon AE (2004) Repression and derepression of minus-strand synthesis in a plus-strand RNA virus replicon. J Virol, 78:7619-7633.
9. Zhang J, Zhang G, Guo R, Shapiro BA, Simon AE (2006) A pseudoknot in a preactive form of a viral RNA is part of a structural switch activating minus-strand synthesis. J Virol, 80:9181-9191.
10. McCormack JC, et al. (2008) Structural domains within the 3′ untranslated region of turnip crinkle virus. J Virol, 82:8706-8720.
11. Yuan X, Kerong Shi K, Meskauskas A, Simon AE The 3′ end of Turnip crinkle virus contains a highly interactive structure including a translational enhancer that is disrupted by binding to the RNA-dependent RNA polymerase. RNA, in press.
12. Montange RK, Batey RT (2008) Riboswitches: Emerging themes in RNA structure and function. Annu Rev Biophys, 37:117-133.
13. Wang J, et al. (2009) A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements. J Mol Biol, 393:717-734.
14. Puglisi JD, Wyatt JR, Tinoco I Jr. (1990) Conformation of an RNA pseudoknot. J Mol Biol, 214:437-453.
15. Cochrane JC, Lipchock SV, Strobel SA (2007) Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem Biol, 14:97-105.
16. Kazantsev AV, et al. (2005) Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci USA, 102:13392-13397.
17. Martick M, Scott WG (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell, 126:309-320.
18. Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR (2002) Transition state stabilization by a catalytic RNA. Science, 298:1421-1424.
19. Stahley MR, Strobel SA (2005) Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science, 309:1587-1590.
20. Schafer MA, et al. (2002) Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit. J Biol Chem, 277:19095-19105.
21. Yuan X, Shi K, Meskauskas A, Simon AE (2009) The 3′ end of Turnip crinkle virus contains a highly interactive structure including a translational enhancer that is disrupted by binding to the RNA-dependent RNA polymerase. RNA, 15:1849-1864.
22. Gebauer F, Hentze MW (2004) Molecular mechanisms of translational control. Nat Rev Mol Cell Biol, 5:827-835.
23. Na H, White KA (2006) Structure and prevalence of replication silencer-3′ terminus RNA interactions in Tombusviridae. Virology, 345:305-316.
24. Zhang J, Zhang G, McCormack JC, Simon AE (2006) Evolution of virus-derived sequences for high-level replication of a subviral RNA. Virology, 351:476-488.
25. Wu H, Feigon J (2007) H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification. Proc Natl Acad Sci USA, 104:6655-6660.
26. Butcher SE, Dieckmann T, Feigon J (1997) Solution structure of a GAAA tetraloop receptor RNA. EMBO J, 16:7490-7499.
27. Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA (2001) RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc Natl Acad Sci USA, 98:4899-4903.
28. Murray JB, Seyhan AA, Walter NG, Burke JM, Scott WG (1998) The hammerhead, hairpin, and VS ribozymes are catalytically proficient in monovalent cations alone. Chem Biol, 5:587-595.
29. Tanner MA, Cech TR (1995) An important RNA tertiary interaction of group I and group II introns is implicated in gram-positive RNase P RNAs. RNA, 1:349-350.
30. Costa M, Michel F (1995) Frequent use of the same tertiary motif by selffolding RNAs. EMBO J, 14:1276-1285.
31. Hammond JA, Rambo RP, Filbin ME, Kieft JS (2009) Comparison and functional implications of the 3D architectures of viral tRNA-like structures. RNA, 15: 294-307.
32. Fechter P, Rudinger-Thirion J, Florentz C, Giege R (2001) Novel features in the tRNA-like world of plant viral RNAs. Cell Mol Life Sci, 58:1547-1561.
33. Walsh JD, Cabello-Villegas J, Wang YX (2004) Periodicity in residual dipolar couplings and nucleic acid structures. J Am Chem Soc, 126:1938-1939.
34. Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J, 76:2879-2886.
35. Schwieters CD, Kuszewski JJ, Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Prog Nucl Magn Reson Spectrosc, 48:47-62.