Pairwise coupling analysis of helical junction hydrogen bonding interactions in luteoviral RNA pseudoknots

Biochemistry

Volumn 45, Issue 37, 2006, Pages 11162-11171

  Cornish, Peter V ^a,b   Giedroc, David P ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b United States of America   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; GENES; HYDROGEN BONDS; SUBSTITUTION REACTIONS;

COUPLING ANALYSIS; HELICAL JUNCTIONS; RIBOSOMAL FRAMESHIFTING; RNA PSEUDOKNOTS;

RNA;

ADENOSINE; CYTIDINE; GUANINE; HYDROXYL GROUP; MESSENGER RNA; VIRUS RNA;

ARTICLE; BASE PAIRING; BEET WESTERN YELLOW VIRUS; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; CONTROLLED STUDY; DOUBLE MUTANT CYCLE APPROACH; ENERGY; FRAMESHIFT MUTATION; HELICAL JUNCTION; HYDROGEN BOND; IN VITRO STUDY; LUTEOVIRUS; MUTATION RATE; NONHUMAN; P1 GENE; P2 GENE; PAIRWISE COUPLING ANALYSIS; PLANT VIRUS; PRIORITY JOURNAL; RIBOSOMAL FRAMESHIFTING; RNA ANALYSIS; RNA CONFORMATION; RNA PSEUDOKNOT; RNA SEQUENCE; RNA STRUCTURE; SUGARCANE YELLOW LEAF VIRUS; VIRUS GENE;

HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; LUTEOVIRUS; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID CONFORMATION; RNA, MESSENGER; RNA, VIRAL;

BEET WESTERN YELLOWS VIRUS; SUGARCANE YELLOW LEAF VIRUS;

EID: 33748774169     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi060430n     Document Type: Article

References (34)

1. Kervestin, S., and Amrani, N. (2004) Translational regulation of gene expression, Genome Biol. 5, 359.
2. Tucker, B. J., and Breaker, R. R. (2005) Riboswitches as versatile gene control elements, Curr. Opin. Struct. Biol. 15, 342-348.
3. Baranov, P. V., Gesteland, R. F., and Atkins, J. F. (2002) Receding: Translational bifurcations in gene expression, Gene 286, 187-201.
4. Stahl, G., McCarty, G. P., and Farabaugh, P. J. (2002) Ribosome structure: Revisiting the connection between translational accuracy and unconventional decoding, Trends Biochem. Sci. 27, 178-183.
5. Felsenstein, K. M., and Goff, S. P. (1988) Expression of the gag-pol fusion protein of Moloney murine leukemia virus without gag protein does not induce virion formation or proteolytic processing, J. Virol. 62, 2179-2182.
6. Dinman, J. D., and Wickner, R. B. (1992) Ribosomal frameshifting efficiency and gag/gag-pol ratio are critical for yeast M1 double-stranded RNA virus propagation, J. Virol. 66, 3669-3676.
7. Biswas, P., Jiang, X., Pacchia, A. L., Dougherty, J. P., and Peltz, S. W. (2004) The human immunodeficiency virus type 1 ribosomal frameshifting site is an invariant sequence determinant and an important target for antiviral therapy, J. Virol. 78, 2082-2087.
8. Hung, M., Patel, P., Davis, S., and Green, S. R. (1998) Importance of ribosomal frameshifting for human immunodeficiency virus type 1 particle assembly and replication, J. Virol. 72, 4819-4824.
9. Shehu-Xhilaga, M., Crowe, S. M., and Mak, J. (2001) Maintenance of the Gag/Gag-Pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity, J. Virol. 75, 1834-1841.
10. Giedroc, D. P., Theimer, C. A., and Nixon, P. L. (2000) Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting, J. Mol. Biol. 298, 167-185.
11. Brierley, I., Jenner, A. J., and Inglis, S. C. (1992) Mutational analysis of the "slippery-sequence" component of a coronavirus ribosomal frameshifting signal, J. Mol. Biol. 227, 463-479.
12. Yusupova, G. Z., Yusupov, M. M., Cate, J. H., and Noller, H. F. (2001) The path of messenger RNA through the ribosome, Cell 106, 233-241.
13. Takyar, S., Hickerson, R. P., and Noller, H. F. (2005) mRNA helicase activity of the ribosome, Cell 120, 49-58.
14. Plant, E. P., Jacobs, K. L., Harger, J. W., Meskauskas, A., Jacobs, J. L., Baxter, J. L., Petrov, A. N., and Dinman, J. D. (2003) The 9-Å solution: How mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting, RNA 9, 168-174.
15. Smith, H. G., and Barker, H. (1999) The Luteoviridae, 1st ed., CABI Publishing, New York.
16. Cornish, P. V., Hennig, M., and Giedroc, D. P. (2005) A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting, Proc. Natl. Acad. Sci. U.S.A. 102, 12694-12699.
17. Nixon, P., Rangan, A., Kim, Y., Rich, A., Hoffman, D., Hennig, M., and Giedroc, D. (2002) Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot, J. Mol. Biol. 322, 621-633.
18. Su, L., Chen, L., Egli, M., Berger, J. M., and Rich, A. (1999) Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot, Nat. Struct. Biol. 6, 285-292.
19. Pallan, P. S., Marshall, W. S., Harp, J., Jewett, F. C., III, Wawrzak, Z., Brown, B. A., II, Rich, A., and Egli, M. (2005) Crystal Structure of a Luteoviral RNA Pseudoknot and Model for a Minimal Ribosomal Frameshifting Motif, Biochemistry 44, 11315-11322.
20. Nixon, P. L., Cornish, P. V., Suram, S. V., and Giedroc, D. P. (2002) Thermodynamic analysis of conserved loop-stem interactions in P1-P2 frameshifting RNA pseudoknots from plant Luteoviridae, Biochemistry 41, 10665-10674.
21. Kim, Y. G., Maas, S., Wang, S. C., and Rich, A. (2000) Mutational study reveals that tertiary interactions are conserved in ribosomal frameshifting pseudoknots of two luteoviruses, RNA 6, 1157-1165.
22. Kim, Y. G., Su, L., Maas, S., O'Neill, A., and Rich, A. (1999) Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency, Proc. Natl. Acad. Sci. U.S.A. 96, 14234-14239.
23. Cornish, P. V., Stammler, S. N., and Giedroc, D. P. (2006) The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical, RNA, in press.
24. Chen, X., Chamorro, M., Lee, S. I., Shen, L. X., Hines, J. V., Tinoco, I., Jr., and Varmus, H. E. (1995) Structural and functional studies of retroviral RNA pseudoknots involved in ribosomal frameshifting: Nucleotides at the junction of the two stems are important for efficient ribosomal frameshifting, EMBO J. 14, 842-852.
25. Brierley, I., Rolley, N. J., Jenner, A. J., and Inglis, S. C. (1991) Mutational analysis of the RNA pseudoknot component of a coronavirus ribosomal frameshifting signal, J. Mol. Biol. 220, 889-902.
26. Nixon, P. L., and Giedroc, D. P. (2000) Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot, J. Mol. Biol. 296, 659-671.
27. Theimer, C. A., and Giedroc, D. P. (1999) Equilibrium unfolding pathway of an H-type RNA pseudoknot which promotes programmed -1 ribosomal frameshifting, J. Mol. Biol. 289, 1283-1299.
28. Theimer, C. A., and Giedroc, D. P. (2000) Contribution of the intercalated adenosine at the helical junction to the stability of the gag-pro frameshifting pseudoknot from mouse mammary tumor virus, RNA 6, 409-421.
29. Leontis, N. B., Stombaugh, J., and Westhof, E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices, Nucleic Acids Res. 30, 3497-3531.
30. a shifting, RNA 11, 157-172.
31. Moody, E. M., and Bevilacqua, P. C. (2003) Folding of a stable DNA motif involves a highly cooperative network of interactions, J. Am. Chem. Soc. 125, 16285-16293.
32. Lindqvist, M., Sarkar, M., Winqvist, A., Rozners, E., Stromberg, R., and Graslund, A. (2000) Optical spectroscopic study of the effects of a single deoxyribose substitution in a ribose backbone: Implications in RNA-RNA interaction, Biochemistry 39, 1693-1701.
33. Egli, M., Minasov, G., Su, L., and Rich, A. (2002) Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution, Proc. Natl. Acad. Sci. U.S.A. 99, 4302-4307.
34. Namy, O., Moran, S. I., Stuart, D. I., Gilbert, R. J. C., and Brierley, I. (2006) A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting. Nature 441, 244-247.