Kinetics of hairpin ribozyme cleavage in yeast

RNA

Volumn 3, Issue 9, 1997, Pages 961-973

  Donahue, Christine P ^a   Fedor, Martha J ^a,b  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Antisense RNA; Hairpin rlbozyme; Kinetic analysis; mRNA degradation; Poly A removal; RNA stability

Indexed keywords

MESSENGER RNA; RIBOZYME;

ARTICLE; CATALYSIS; ENZYME SPECIFICITY; ENZYME SUBSTRATE COMPLEX; MOLECULAR STABILITY; NONHUMAN; PRIORITY JOURNAL; REACTION ANALYSIS; RNA DEGRADATION;

ANTISENSE ELEMENTS (GENETICS); BASE SEQUENCE; KINETICS; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PHOSPHOGLYCERATE KINASE; POLY A; RNA CAPS; RNA, CATALYTIC; RNA, MESSENGER; YEASTS;

EID: 0030865308     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (53)

1. Beelman CA, Parker R. 1995. Degradation of mRNA in eukaryotes. Cell 81:179-183.
2. Bertrand EL, Rossi JJ. 1994. Facilitation of hammerhead ribozyme catalysis by the nucleocapsid protein of HIV-1 and the heterogeneous nuclear ribonucleoprotein Al. EMBO J 13:2904-2912.
3. Brehm SL, Cech TR. 1983. Fate of an intervening sequence ribonucleic acid: Excision and cyclization of the Tetrahymena ribosomal ribonucleic acid intervening sequence in vivo. Biochemistry 22:2390-2397.
4. Burke JM, Butcher SE, Sargueil B. 1996. Structural analysis and modifications of the hairpin ribozyme. Nucleic Acids Mol Biol 10:129-143.
5. Buzayan JM, Gerlach WL, Bruening G. 1986. Nonenzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature 323:349-353.
6. Celander DW, Cech TR. 1991. Visualizing the higher order folding of a catalytic RNA molecule. Science 252:401-407.
7. Chen B, Przybyla AE. 1994. An efficient site-directed mutagenesis method based on PCR. Bio Techniques 17:657-659.
8. Chowrira BM, Berzal-Herranz A, Burke J. 1991. Novel guanosine requirement for catalysis by the hairpin ribozyme. Nature 354:320-322.
9. Chowrira BM, Berzal-Herranz A, Burke JM. 1993. Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme. Biochemistry 32:1088-1095.
10. Coetzee T, Herschlag D, Belfort M. 1994. E. coli proteins, including the ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. Genes & Dev 8:1575-1588.
11. Crisell P, Thompson S, James W. 1993. Inhibition of HIV-1 replication by ribozymes that show poor activity in vitro. Nucleic Acids Res 21:5251-5255.
12. Eick D, Piechaczyk M, Henglein B, Blanchard JM, Traub B, Kofler E, Wiest S, Lenoir GM, Bornkamm GW. 1985. Aberrant c-myc RNAs of Burkitt's lymphoma cells have longer half-lives. EMBO J 4:3717-3725.
13. Fedor MJ, Lue NF, Kornberg RD. 1988. Statistical positioning of nucleosomes by specific protein-binding to an upstream activat-ing sequence in yeast. J Mol Biol 204:109-127.
14. Fedor MJ, Uhlenbeck OC. 1990. Substrate sequence effects on "hammerhead" RNA catalytic efficiency. Proc Natl Acad Sci USA 87:1668-1672.
15. Feldstein PA, Bruening G. 1993. Catalytically active geometry in the reversible circularization of "mini-monomer" RNAs derived from the complementary strand of tobacco ringspot virus satellite RNA. Nucleic Acids Res 22:1991-1998.
16. Feldstein PA, Buzayan JM, Bruening G. 1989. Two sequences participating in the autocatalytic processing of satellite tobacco ringspot virus complementary RNA. Gene 82:53-61.
17. Grosshans CA, Cech TR. 1989. Metal ion requirements for sequencespecific endoribonuclease activity of the Tetrahymena ribozyme. Biochemistry 28:6888-6894.
18. Hampel A, Tritz R. 1989. RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry 28:4929-4933.
19. Hegg LA, Fedor MJ. 1995. Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes. Biochemistry 34:15813-15828.
20. Herrick D, Parker R, Jacobson A. 1990. Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae. Mol Cell Biol 10:2269-2284.
21. Homann M, Tabler M, Tzortzakaki S, Sczakiel G. 1994. Extension of helix II of an HIV-1-directed hammerhead ribozyme with long antisense flanks does not alter kinetic parameters in vitro but causes loss of the inhibitory potential in living cells. Nucleic Acids Res 22:351-357.
22. Jacobson A, Peltz SW. 1996. Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells. Annu Rev Biochem 65:693-739.
23. Kaiser C, Michaelis S, Mitchell A. 1994. Methods in yeast genetics. New York: Cold Spring Harbor Laboratory Press, pp 151-152.
24. Keese P, Symons RH. 1987. The structure of viroids and virusoids. In: Semancik JS, ed. Viroids and viroid-like pathogens. Boca Raton: CRC Press, pp 1-47.
25. Köhrer KB, Domdey H. 1991. Preparation of high molecular weight RNA. Methods Enzymol 394:398-405.
26. Long DM, Uhlenbeck OC. 1993. Self-cleaving RNA. FASEB J 7:25-30.
27. Lowell JE, Rudner DZ, Sachs A, 1992. 3′-UTR-dependent deadenylation by the yeast poly(A) nuclease. Genes & Dev 6:2088-2099.
28. Madhani HD, Guthrie C. 1992. A novel base-pairing interaction between U2 and U6 snRNA suggests a mechanism for the catalytic activation of the spliceosome. Cell 72:803-817.
29. Milligan JF, Uhlenbeck OC. 1989. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol 180:51-62.
30. Mohr G, Zhang A, Gianelos JA, Belfort M, Lambowitz AM. 1992. The Neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell 69:483-494.
31. Muhlrad D, Decker CJ, Parker R. 1995. Turnover mechanisms of the stable yeast PGK1 mRNA. Mol Cell Biol 15:2145-2156.
32. Muhlrad D, Parker R. 1994. Premature translational termination triggers mRNA decapping. Nature 370:578-581.
33. Noller HF, Hoffarth V, Zimniak L. 1992. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256:1416-1418.
34. Nonet M, Scafe S, Sexton J, Young R. 1987. Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol Cell Biol 7:1602-1611.
35. Pan T. 1995. Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 34:902-909.
36. Pan T, Long DM, Uhlenbeck OC. 1993. Divalent metal ions in RNA folding and catalysis. In: Gesteland RF, Atkins JF, eds. The RNA world. New York: Cold Spring Harbor Laboratory Press, pp 271-302.
37. Parker R, Herrick D, Peltz SW, Jacobson A. 1991. Measurement of mRNA decay rates in Saccharomyces cerevisiae. Methods Enzymol 194:415-423.
38. Peltz SW, Jacobson A. 1993. mRNA turnover in Saccharomyces cerevisiae. In: Brawerman G, Belasco J, eds. Control of mRNA stability. New York: Academic Press, pp 291-328.
39. Piccirilli JA, Vyle JS, Caruthers MH, Cech TR. 1993. Metal ion catalysis by the Tetrahymena ribozyme. Nature 361:85-88.
40. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual. New York: Cold Spring Harbor Laboratory Press.
41. Sikorski RS, Hieter P. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
42. Smith D, Burgin AB, Haas ES, Pace N. 1992. Influence of metal ions on the ribonuclease P reaction. Distinguishing substrate binding from catalysis. J Biol Chem 267:2429-2436.
43. Stevens A. 1980. Purification and characterization of a Saccharomyces cerevisiae exoribonuclease which yields 5′-mononucleotides by a 5′ to 3′ mode of hydrolysis. J Biol Chem 255:3080-3085.
44. Symons RH. 1992. Small catalytic RNAs. Annu Rev Biochem 62:641-671.
45. Tsuchihashi Z, Koshla M, Herschlag D. 1993. Protein enhancement of hammerhead ribozyme catalysis. Science 262:99-102.
46. Uhlenbeck OC. 1995. Keeping RNA happy. RNA 2:4-6.
47. Weeks KM, Cech TR. 1995. Protein facilitation of group I splicing by assembly of the catalytic core and the 5′ splice site domain. Cell 82:221-230.
48. Welch PJ, Hampel A, Barber J, Wong-Staal F, Yu M. 1996. Inhibition of HIV replication by the hairpin ribozyme. Nucleic Acids and Mol Biol 10:314-327.
49. Wisdom R, Lee W. 1991. The protein-coding region of c-myc mRNA contains a sequence that specifies rapid mRNA turnover and induction by protein synthesis inhibitors. Genes & Dev 5:232-243.
50. Yanisch-Perron C. 1985. Improved M13 phage cloning vectors and host strains: Nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119.
51. Zarrinkar PP, Williamson JR. 1994. Kinetic intermediates in RNA. Science 265:918-924.
52. Zhang F, Ramsay ES, Woodson SA. 1995. In vivo facilitation of Tetrahymena group I intron splicing in Escherichia coli pre-ribosomal RNA. RNA 3:284-292.
53. Zuker M. 1994. Prediction of RNA secondary structure by energy minimization. Methods Mol Biol 25:267-294.