Ribozyme cleavage of a 2',5'-phosphodiester linkage: Mechanism and a restricted divalent metal-ion requirement

RNA

Volumn 5, Issue 9, 1999, Pages 1140-1148

  Shih, I Hung ^a   Been, Michael D ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Catalytic RNA; Divalent metal ions; HDV; Hepatitis delta virus; Self cleavage

Indexed keywords

CALCIUM ION; MAGNESIUM ION; MANGANESE; RIBOZYME; TRANS ACTING FACTOR;

ARTICLE; CHEMICAL BINDING; CHEMICAL REACTION KINETICS; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ASSAY; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME SPECIFICITY; HEPATITIS DELTA VIRUS; MOLECULAR DYNAMICS; NONHUMAN; PH; PRIORITY JOURNAL; REACTION ANALYSIS; RNA CLEAVAGE;

BASE SEQUENCE; BINDING SITES; CALCIUM; HEPATITIS DELTA VIRUS; HYDROGEN-ION CONCENTRATION; KINETICS; MAGNESIUM; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES; PHOSPHORIC ACID ESTERS; RNA, CATALYTIC; RNA, VIRAL; SEQUENCE ANALYSIS, RNA; TIME FACTORS; TRANS-ACTIVATORS;

DELTA VIRUS; HEPATITIS DELTA VIRUS;

EID: 0032832044     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299990763     Document Type: Article

References (32)

1. Chen P-J, Kalpana G, Goldberg J, Mason W, Werner B, Gerin J, Taylor J. 1986. Structure and replication of the genome of the hepatitis δ virus. Proc Natl Acad Sci USA 83:8774-8778.
2. Chowrira BM, Burke JM. 1991. Binding and cleavage of nucleic acids by the "Hairpin" ribozyme. Biochemistry 30:8518-8522.
3. Dahm SC, Derrick WB, Uhlenbeck OC. 1993. Evidence for the role of solvated metal hydroxide in the hammerhead cleavage. Biochemistry 32:13040-13045.
4. Dahm SC, Uhlenbeck OC. 1991. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30:9464-9469.
5. Davanloo P, Rosenberg AH, Dunn JJ, Studier FW. 1984. Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc Natl Acad Sci USA 81:2035-2039.
6. Ellis KJ, Morrison JF. 1982. Buffers of constant ionic strength for studying pH-dependent processes. Methods Enzymol 87:405-426.
7. Fauzi H, Kawakami J, Nishikawa F, Nishikawa S. 1997. Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme. Nucleic Acids Res 25:3124-3130.
8. Feldstein PA, Buzayan JM, van Tol H, DeBear J, Gough GR, Gilham PT, Bruening G. 1990. Specific association between an endoribonucleolytic sequence from a satellite RNA and a substrate analogue containing a 2′-5′ phosphodiester. Proc Natl Acad Sci USA 87:2623-2627.
9. Ferré-D'Amaré AR, Zhou K, Doudna JA. 1998. Crystal structure of a hepatitis delta virus ribozyme. Nature 395:567-574.
10. Herschlag D, Cech TR. 1990. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 2. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site. Biochemistry 29:10172-10180.
11. Hertel K, Herschlag D, Uhlenbeck OC. 1994. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry 33:3374-3385.
12. Kuo MY-P, Sharmeen L, Dinter-Gottlieb G, Taylor J. 1988. Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J Virol 62:4439-4444.
13. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15:8783-8798.
14. Moore MJ, Sharp PA. 1992. Site-specific modification of pre-mRNA: The 2′-hydroxyl groups at the splice sites. Science 256:992-997.
15. Neel OD, Robertson HD. 1997. Pathways of RNA ligation in the replication of the hepatitis delta agent. Nucleic Acids Symp Ser 36:154-155.
16. Nesbitt S, Hegg LA, Fedor MJ. 1997. An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem Biol 4:619-630.
17. Perrin DD, Dempsey B. 1974. Buffers for pH and metal ion control. London: Chapman and Hall Ltd.
18. Perrotta AT, Been MD. 1990. The self-cleaving domain from the genomic RNA of hepatitis delta virus: Sequence requirements and the effects of denaturant. Nucleic Acids Res 18:6821-6827.
19. Perrotta AT, Been MD. 1991. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature 350:434-436.
20. Perrotta AT, Been MD. 1992. Cleavage of oligoribonucleotides by a ribozyme derived from the hepatitis δ virus RNA sequence. Biochemistry 31:16-21.
21. Piccirilli JA, Vyle JS, Caruthers MH, Cech TR. 1993. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature 361:85-88.
22. Pyle AM. 1993. Ribozymes: A distinct class of metalloenzymes. Science 261:709-714.
23. Rizzetto M, Hoyer B, Canese MG, Shih JW-K, Purcell RH, Gerin JL. 1980. Delta agent: Association of delta antigen with hepatitis B surface antigen and RNA in serum of delta-infected chimpanzees. Proc Natl Acad Sci USA 77:6124-6128.
24. Rosenstein SR, Been MD. 1996. Hepatitis delta virus ribozymes fold to generate a solvent-inaccessible core with essential nucleotides near the cleavage-site phosphate. Biochemistry 35:11403-11413.
25. Scott EC, Uhlenbeck OC. 1999. A re-investigation of the thio effect at the hammerhead cleavage site. Nucleic Acids Res 27:479-484.
26. Sharmeen L, Kuo, MY-P, Dinter-Gottlieb G, Taylor J. 1988. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol 62:2674-2679.
27. Sharmeen L, Kuo MY-P, Taylor J. 1989. Self-ligating RNA sequences on the antigenome of human hepatitis delta virus. J Virol 63:1428-1430.
28. Suh Y-A, Kumar PKR, Taira K, Nishikawa S. 1993. Self-cleavage activity of the genomic HDV ribozyme in the presence of various divalent metal ions. Nucleic Acids Res 21:3277-3280.
29. Wadkins TS, Perrotta AT, Ferré-D'Amaré AR, Doudna JA, Been MD. 1999. A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. RNA 5:720-727.
30. Wang K-S, Choo Q-L, Weiner AJ, Ou J-H, Najarian RC, Thayer RM, Mullenbach GT, Denniston KJ, Gerin JL, Houghton M. 1986. Structure, sequence, and expression of the hepatitis delta (δ) viral genome. Nature 323:508-514.
31. Weinstein LB, Jones BCNM, Cosstick R, Cech TR. 1997. A second catalytic metal ion in a group I ribozyme. Nature 388:805-808.
32. Wu H-N, Lin Y-J, Lin F-P, Makino S, Chang M-F, Lai MMC. 1989. Human hepatitis δ virus RNA subfragments contain an autocleavage activity. Proc Natl Acad Sci USA 86:1831-1835.