The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme

Nucleic Acids Research

Volumn 36, Issue 9, 2008, Pages 2990-3000

  Brown, Abigail L ^a   Perrotta, Anne T ^a   Wadkins, Timothy S ^a   Been, Michael D ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PLASMID DNA; POLYADENYLATED RNA; RIBOZYME; VIRUS RNA;

ARTICLE; DNA FLANKING REGION; DOWNSTREAM PROCESSING; GEL ELECTROPHORESIS; GENE MAPPING; HEPATITIS DELTA VIRUS; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; RNA CLEAVAGE; RNA REPLICATION; RNA SELF CLEAVAGE; RNA SEQUENCE; RNA STABILITY; RNA STRUCTURE; SEQUENCE ANALYSIS; VIRUS MUTATION;

5' UNTRANSLATED REGIONS; BASE PAIRING; BASE SEQUENCE; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HEPATITIS DELTA VIRUS; KINETICS; MAGNESIUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; POLY A; RNA PRECURSORS; RNA, CATALYTIC; RNA, VIRAL;

HEPATITIS DELTA VIRUS;

EID: 44349185564     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn156     Document Type: Article

References (40)

1. Branch,A.D. and Robertson,H.D. (1984) A replication cycle for viroids and other small infectious RNA's, Science, 223, 450-455.
2. Taylor,J.M. (1992) The structure and replication of hepatitis delta virus. Annu. Rev. Microbiol., 46, 253-276.
3. Lai,M.M. (1995) The molecular biology of hepatitis delta virus. Annu. Rev. Biochem., 64, 259-286.
4. Hsieh,S.Y., Chao,M., Coates,L. and Tayior,J. (1990) Hepatitis delta virus genome replication: A polyadenylated mRNA for delta antigen. J. Virol., 64, 3192-3198.
5. Hsieh,S.Y. and Taylor,J. (1991) Regulation of polyadenylation of hepatitis delta virus antigenomic RNA. J. Virol., 65, 6438-6446.
6. Bird,G., Fong,N., Gatlin,J.C., Farabaugh,S. and Bentley,D.L. (2005) Ribozyme cleavage reveals connections between mRNA release from the site of transcription and pre-mRNA processing. Mol. Cell, 20, 747-758.
7. Rigo,F., Kazerouninia,A., Naga,A. and Martinson,H.G. (2005) The RNA tether from poly(A) signal to the polymerase mediates coupling of transcription to cleavage and polyadenylation. Mol. Cell, 20 733-745.
8. Macnaughton,T.B., Shi,S.T., Modahl,L.E. and Lai,M.M. (2002) Rolling circle replication ot hepatitis delta virus RNA is carried out by two different cellular RNA polymerases. J. Virol., 76, 3920-3927.
9. Nie,X., Chang,J. and Taylor,J.M. (2004) Alternative processing of hepatitis delta virus antigenomic RNA tanscript. J. Virol., 78 4517-4524.
10. McCracken,S., Fong,N., Yankulov,K., Ballantyne,S., Pan,G., Greenblatt,J., Patterson,S.D., Wickens,M. and Bentley,D.L. (1997) The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature, 385, 357-361.
11. Calvo,O. and Manley,J.L. (2003) Strange bedfellows: Polyadenylation factors at the promoter. Genes Dev., 17, 1321-1327.
12. Modahl,L.E., Macnaughton,T.B., Zhu,N., Johnson,D.L. and Lai,M.M. (2000) RNA-Dependent replication and transcription of hepatitis delta virus RNA involve distinct cellular RNA polymerases. Mol. Cell Biol., 20 6030-6039.
13. Kuo,M.Y., Sharmeen,L., Dinter-Gottlieb,G. and Taylor,J. (1988) Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J. Virol., 62, 4439-4444.
14. Perrotta,A.T. and Been,M.D. (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.
15. Chadalavada,D.M., Knudsen,S.M., Nakano,S. and Bevilacqua,P.C. (2000) A role for utpstream RNA structure in facilitating the catalylic fold of the genomic hepatitis delta virus ribozyme. J. Mol. Biol., 301 349-367.
16. Chadalavada,D.M., Senchak,S.E. and Bevilacqua,P.C. (2002) The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. J. Mol. Biol., 317, 559-575.
17. Colgan,D.F. and Manley,J.L. (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev., 11, 2755-2766.
18. Wadkins,T.S. and Been,M.D. (2002) Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus. Cell. Mol. Life Sci., 59, 112-125.
19. Pan.J. and Woodson,S.A. (1998) Folding intermediates of a self-splicing RNA: Mispairing of the catalytic core. J. Mol. Biol., 280, 597-609.
20. Berkhout,B., Klaver,B. and Das,A.T. (1995) A conserved hairpain tructure predicted for the poly(A) signal of human and simian immunodeficiency viruses. Virology, 207, 276-281.
21. Das,A.T., Klaver,B. and Berkhout,B. (1999) A hairpin structure in the R region of the human immunodefiency virus type 1 RNA genome is instrumental in polyadenylation site selection. J. Virol., 73 81-91.
22. Klasens,B.L. Thiesen.M., Virtanen,A. and Berkhout,B. (1999) The ability of the HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structure. Nucleic Acids Res., 27, 446-454.
23. Davanloo,P., Rosenberg,A.H., Dunn,J.J. and Studier,F.W. (1984) Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc. Natl Acad. Sci. USA, 81, 2035-2039.
24. Perrotta,A.T., Nikiforova,O. and Been,M.D. (1999) A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduces kinetic trapping of inactive conformations. Nucleic Acids Res., 27, 795-802.
25. Perrotta,A.T. and Been,M.D. (1992) Cleavage of oligoribonucleiotides by a ribozyme derived from the hepatitis delta virus RNA sequence. Biochemistry, 31, 16-21.
26. Kunkel,T.A., Roberts,J.D. and Zakour,R.A. 1987) Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol., 154, 367-382.
27. Vieira,J. and Messing,J. (1987) Production of single-stranded plasmid DNA. Methods Enzymol., 153, 3-11.
28. Perrotta,A.T. and Been,M.D. (1991) A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature, 350, 434-436.
29. Bruce,A.G. and Uhlenbeck,O.C. (1978) Reactions at the termini of tRNA with T4 RNA ligase. Nucleic Acids Res., 5, 3665-3677.
30. Perrotta,A.T. and Been,M.D. (2007) A single nucleotide linked to a switch in metal ion reactivity preference in the HDV ribozymes. Biochemistry, 46, 5124-5130.
31. Shih,I.H. and Been,M.D. (1999) Ribozyme cleavage of a 2,5-phosphodiester linkage: Mechanism and a restricted divalent metal-ion requirement. RNA, 5, 1140-1148.
32. Brown,T.S., Chadalavada,D.M. and Bevilacqua,P.C. (2004) Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength. J. Mol. Biol., 341, 695-712.
33. Walter,F., Murchie,A.I. and Lilley,D.M. (1998) Folding of the four-way RNA junction of the hairpin ribozyme. Biochemistry, 37, 17629-17636.
34. 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, 708-712.
35. Winkler,W.C., Nahvi,A., Roth,A., Collins,J.A. and Breaker,R.R. (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature, 428, 281-286.
36. Wilkinson,S.R. and Been,M.D. (2005) A pseudoknot in the 3′ non-core region of the glmS ribozyme enhances self-cleavage activity. RNA, 11, 1788-1794.
37. Roth,A., Nahvi,A., Lee,M., Jona,I. and Breaker,R.R. (2006) Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA, 12, 607-619.
38. Lazinski,D.W. and Taylor,J.M. (1995) Intracellular cleavage and ligation of hepatitis delta virus genomic RNA: Regulation of ribozyme activity by cis-acting sequences and host factors. J. Virol., 69, 1190-1200.
39. Lazinski,D.W. and Taylor,J.M. (1995) Regulation of the hepatitis delta virus ribozymes: To cleave or not to cleave? RNA, 1, 225-233.
40. Salchi-Ashtiani,K., LuptaK,A., Litovchick,A. and Szostak,J.W. (2006) A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science, 313, 1788-1792.