Efficient, pH-Dependent RNA Ligation by the VS Ribozyme in Trans

Biochemistry

Volumn 43, Issue 4, 2004, Pages 1118-1125

  McLeod, Aileen C ^a   Lilley, David M J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DISSOCIATION; ENZYMES; PH EFFECTS; RNA;

CLEAVAGE ACTIVITY; DEPROTONATION;

BIOCHEMISTRY;

LIGASE; NUCLEIC ACID BASE; NUCLEOTIDE; RIBOZYME; RNA; UNCLASSIFIED DRUG; VARKUD SATELLITE RIBOZYME;

ARTICLE; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; PH; PKA; PRIORITY JOURNAL; PROTON TRANSPORT; RNA CLEAVAGE; RNA LIGATION; TRANS ISOMER;

EID: 0942279692     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi035790e     Document Type: Article

References (29)

1. Forster, A. C., and Symons, R. H. (1987) Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites, Cell 49, 211-220.
2. Hazeloff, J. P., and Gerlach, W. L. (1988) Simple RNA enzymes with new and highly specific endoribonuclease activities, Nature 334, 585-591.
3. Buzayan, J. M., Gerlach, W. L., and Bruening, G. (1986) Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA, Nature 323, 349-353.
4. Sharmeen, L., Kuo, M. Y., Dinter-Gottlieb, G., and Taylor, J. (1988) Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage, J. Virol. 62, 2674-2679.
5. Saville, B. J., and Collins, R. A. (1990) A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria, Cell 61, 685-696.
6. Li, Y., and Breaker, R. R. (1999) Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group, J. Am. Chem. Soc. 121, 5364-5372.
7. Murchie, A. I. H., Thomson, J. B., Walter, F., and Lilley, D. M. J. (1998) Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops, Mol. Cell 1, 873-881.
8. Fedor, M. J. (1999) Tertiary structure stabilization promotes hairpin ribozyme ligation, Biochemistry 38, 11040-11050.
9. Stage-Zimmermann, T. K., and Uhlenbeck, O. C. (2001) A covalent crosslink converts the hammerhead ribozyme from a ribonuclease to an RNA ligase, Nat. Struct. Biol. 8, 863-867.
10. Kennell, J. C., Saville, B. J., Mohr, S., Kuiper, M. T., Sabourin, J. R., Collins, R. A., and Lambowitz, A. M. (1995) The VS catalytic RNA replicates by reverse transcription as a satellite of a retroplasmid, Genes Dev. 9, 294-303.
11. Beattie, T. L., Olive, J. E., and Collins, R. A. (1995) A secondary-structure model for the self-cleaving region of Neurospora VS RNA, Proc. Natl. Acad. Sci. U.S.A. 92, 4686-4690.
12. Lafontaine, D. A., Norman, D. G., and Lilley, D. M. J. (2001) Structure, folding and activity of the VS ribozyme: Importance of the 2-3-6 helical junction, EMBO J. 20, 1415-1424.
13. Lafontaine, D. A., Norman, D. G., and Lilley, D. M. J. (2002) The global structure of the VS ribozyme, EMBO J. 21, 2461-2471.
14. Rastogi, T., Beattie, T. L., Olive, J. E., and Collins, R. A. (1996) A long-range pseudoknot is required for activity of the Neurospora VS ribozyme, EMBO J. 15, 2820-2825.
15. Lafontaine, D. A., Wilson, T. J., Norman, D. G., and Lilley, D. M. J. (2001) The A730 loop is an important component of the active site of the VS ribozyme, J. Mol. Biol. 312, 663-674.
16. Sood, V. D., and Collins, R. A. (2002) Identification of the catalytic subdomain of the VS ribozyme and evidence for remarkable sequence tolerance in the active site loop, J. Mol. Biol. 320, 443-454.
17. Jones, F. D., and Strobel, S. A. (2003) Ionization of a critical adenosine residue in the Neurospora Varkud Satellite ribozyme active site, Biochemistry 42, 4265-4276.
18. Saville, B. J., and Collins, R. A. (1991) RNA-mediated ligation of self-cleavage products of a Neurospora mitochondrial plasmid transcript, Proc. Natl. Acad. Sci. U.S.A. 88, 8826-8830.
19. Jones, F. D., Ryder, S. P., and Strobel, S. A. (2001) An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5′- and 3′-termini, Nucleic Acids Res. 29, 5115-5120.
20. Sood, V. D., and Collins, R. A. (2001) Functional equivalence of the uridine turn and the hairpin as building blocks of tertiary structure in the Neurospora VS ribozyme, J. Mol. Biol. 313, 1013-1019.
21. Rastogi, T., and Collins, R. A. (1998) Smaller, faster ribozymes reveal the catalytic core of Neurospora VS RNA, J. Mol. Biol. 277, 215-224.
22. Tan, E., Wilson, T. J., Nahas, M. K., Clegg, R. M., Lilley, D. M. J., and Ha, T. (2003) A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate, Proc. Natl. Acad. Sci. U.S.A. 100, 9308-9313.
23. Khvorova, A., Lescoute, A., Westhof, E., and Jayasena, S. D. (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity, Nat. Struct. Biol. 10, 1-5.
24. Lilley, D. M. J. (2003) Ribozymes-a snip too far?, Nat. Struct. Biol. 10, 672-673.
25. Dahm, S. C., Derrick, W. B., and Uhlenbeck, O. C. (1993) Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism, Biochemistry 32, 13040-13045.
26. Flinders, J., and Dieckmann, T. (2001) A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA, J. Mol. Biol. 308, 665-679.
27. Lafontaine, D. A., Wilson, T. J., Zhao, Z.-Y., and Lilley, D. M. J. (2002) Functional group requirements in the probable active site of the VS ribozyme, J. Mol. Biol. 323, 23-34.
28. Hiley, S. L., Sood, V. D., Fan, J., and Collins, R. A. (2002) 4-thio-U cross-linking identifies the active site of the VS ribozyme, EMBO J. 21, 4691-4698.
29. Milligan, J. F., Groebe, D. R., Witherall, G. W., and Uhlenbeck, O. C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates, Nucleic Acids Res. 15, 8783-8798.