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Volumn 8, Issue 5, 2011, Pages

HDV-like self-cleaving ribozymes

Author keywords

Catalytic RNA; Motif search; R2 retrotransposon

Indexed keywords

CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN; CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 3; RIBOZYME; UNCLASSIFIED DRUG; VIRUS PROTEIN; VIRUS RNA;

EID: 80052822183     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.8.5.16226     Document Type: Review
Times cited : (71)

References (48)
  • 1
    • 0017565349 scopus 로고
    • Immunofluorescence detection of new antigen-antibody system (delta/anti-delta) associated to hepatitis B virus in liver and in serum of HBsAg carriers
    • Rizzetto M, Canese MG, Arico S, Crivelli O, Trepo C, Bonino F, et al. Immunofluorescence detection of new antigen-antibody system (delta/anti-delta) associated to hepatitis B virus in liver and in serum of HBsAg carriers. Gut 1977; 18:997-1003. (Pubitemid 8263407)
    • (1977) Gut , vol.18 , Issue.12 , pp. 997-1003
    • Rizzetto, M.1    Canese, M.G.2    Arico, S.3
  • 3
    • 0023747377 scopus 로고
    • Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage
    • Sharmeen L, Kuo MY, Dinter-Gottlieb G, Taylor J. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol 1988; 62:2674-9.
    • (1988) J Virol , vol.62 , pp. 2674-2679
    • Sharmeen, L.1    Kuo, M.Y.2    Dinter-Gottlieb, G.3    Taylor, J.4
  • 4
    • 0024209351 scopus 로고
    • Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus
    • Kuo MY, Sharmeen L, Dinter-Gottlieb G, Taylor J. Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J Virol 1988; 62:4439-44. (Pubitemid 19006103)
    • (1988) Journal of Virology , vol.62 , Issue.12 , pp. 4439-4444
    • Kuo, M.Y.-P.1    Sharmeen, L.2    Dinter-Gottlieb, G.3    Taylor, J.4
  • 5
    • 0025882069 scopus 로고
    • A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA
    • Perrotta AT, Been MD. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature 1991; 350:434-6. (Pubitemid 21912248)
    • (1991) Nature , vol.350 , Issue.6317 , pp. 434-436
    • Perrotta, A.T.1    Been, M.D.2
  • 6
    • 0033053643 scopus 로고    scopus 로고
    • A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes
    • DOI 10.1017/S1355838299990209
    • Wadkins TS, Perrotta AT, Ferre-D'Amare AR, Doudna JA, Been MD. A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. RNA 1999; 5:720-7. (Pubitemid 29283775)
    • (1999) RNA , vol.5 , Issue.6 , pp. 720-727
    • Wadkins, T.S.1    Perrotta, A.T.2    Ferre-D'Amare, A.R.3    Doudna, J.A.4    Been, M.D.5
  • 7
    • 0027535112 scopus 로고
    • Replication of hepatitis delta virus RNA: Effect of mutations of the autocatalytic cleavage sites
    • Macnaughton TB, Wang YJ, Lai MM. Replication of hepatitis delta virus RNA: effect of mutations of the autocatalytic cleavage sites. J Virol 1993; 67:2228-34. (Pubitemid 23088399)
    • (1993) Journal of Virology , vol.67 , Issue.4 , pp. 2228-2234
    • MacNaughton, T.B.1    Wang, Y.-J.2    Lai, M.M.C.3
  • 8
    • 0028332817 scopus 로고
    • Cis- and trans-acting ribozymes from a human pathogen, hepatitis delta virus
    • Been MD. Cis- and trans-acting ribozymes from a human pathogen, hepatitis delta virus. Trends Biochem Sci 1994; 19:251-6.
    • (1994) Trends Biochem Sci , vol.19 , pp. 251-256
    • Been, M.D.1
  • 9
    • 0036200431 scopus 로고    scopus 로고
    • Rolling circle replication of hepatitis delta virus RNA is carried out by two different cellular RNA polymerases
    • DOI 10.1128/JVI.76.8.3920-3927.2002
    • Macnaughton TB, Shi ST, Modahl LE, Lai MM. Rolling circle replication of hepatitis delta virus RNA is carried out by two different cellular RNA polymerases. J Virol 2002; 76:3920-7. (Pubitemid 34250556)
    • (2002) Journal of Virology , vol.76 , Issue.8 , pp. 3920-3927
    • Macnaughton, T.B.1    Shi, S.T.2    Modahl, L.E.3    Lai, M.M.C.4
  • 11
    • 0025082875 scopus 로고
    • Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions
    • DOI 10.1021/bi00487a002
    • Rosenstein SP, Been MD. Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions. Biochemistry 1990; 29:8011-6. (Pubitemid 20283281)
    • (1990) Biochemistry , vol.29 , Issue.35 , pp. 8011-8016
    • Rosenstein, S.P.1    Been, M.D.2
  • 12
    • 44349185564 scopus 로고    scopus 로고
    • The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme
    • DOI 10.1093/nar/gkn156
    • Brown AL, Perrotta AT, Wadkins TS, Been MD. The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme. Nucleic Acids Res 2008; 36:2990-3000. (Pubitemid 351737191)
    • (2008) Nucleic Acids Research , vol.36 , Issue.9 , pp. 2990-3000
    • Brown, A.L.1    Perrotta, A.T.2    Wadkins, T.S.3    Been, M.D.4
  • 13
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • DOI 10.1038/26912
    • Ferre-D'Amare AR, Zhou K, Doudna JA. Crystal structure of a hepatitis delta virus ribozyme. Nature 1998; 395:567-74. (Pubitemid 28475703)
    • (1998) Nature , vol.395 , Issue.6702 , pp. 567-574
    • Ferre-D'Amare, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 14
    • 2442641641 scopus 로고    scopus 로고
    • A conformational switch controls hepatitis delta virus ribozyme catalysis
    • DOI 10.1038/nature02522
    • Ke A, Zhou K, Ding F, Cate JH, Doudna JA. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 2004; 429:201-5. (Pubitemid 38656198)
    • (2004) Nature , vol.429 , Issue.6988 , pp. 201-205
    • Ke, A.1    Zhou, K.2    Ding, F.3    Cate, J.H.D.4    Doudna, J.A.5
  • 15
    • 77955258795 scopus 로고    scopus 로고
    • A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
    • Chen JH, Yajima R, Chadalavada DM, Chase E, Bevilacqua PC, Golden BL. A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage. Biochemistry 2010; 49:6508-18.
    • (2010) Biochemistry , vol.49 , pp. 6508-6518
    • Chen, J.H.1    Yajima, R.2    Chadalavada, D.M.3    Chase, E.4    Bevilacqua, P.C.5    Golden, B.L.6
  • 16
    • 0025597973 scopus 로고
    • The self-cleaving domain from the genomic RNA of hepatitis delta virus: Sequence requirements and the effects of denaturant
    • Perrotta AT, Been MD. The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant. Nucleic Acids Res 1990; 18:6821-7. (Pubitemid 120006063)
    • (1990) Nucleic Acids Research , vol.18 , Issue.23 , pp. 6821-6827
    • Perrotta, A.T.1    Been, M.D.2
  • 17
    • 0026495873 scopus 로고
    • Secondary structure of the self-cleaving RNA of hepatitis delta virus: Applications to catalytic RNA design
    • Been MD, Perrotta AT, Rosenstein SP. Secondary structure of the self-cleaving RNA of hepatitis delta virus: applications to catalytic RNA design. Biochemistry 1992; 31:11843-52.
    • (1992) Biochemistry , vol.31 , pp. 11843-11852
    • Been, M.D.1    Perrotta, A.T.2    Rosenstein, S.P.3
  • 18
    • 0027222970 scopus 로고
    • Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme
    • Thill G, Vasseur M, Tanner NK. Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme. Biochemistry 1993; 32:4254-62. (Pubitemid 23137731)
    • (1993) Biochemistry , vol.32 , Issue.16 , pp. 4254-4262
    • Thill, G.1    Vasseur, M.2    Tanner, N.K.3
  • 19
    • 0034636981 scopus 로고    scopus 로고
    • A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme
    • Chadalavada DM, Knudsen SM, Nakano S, Bevilacqua PC. A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme. J Mol Biol 2000; 301:349-67.
    • (2000) J Mol Biol , vol.301 , pp. 349-367
    • Chadalavada, D.M.1    Knudsen, S.M.2    Nakano, S.3    Bevilacqua, P.C.4
  • 20
    • 0036289258 scopus 로고    scopus 로고
    • The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots
    • DOI 10.1006/jmbi.2002.5434
    • Chadalavada DM, Senchak SE, Bevilacqua PC. The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. J Mol Biol 2002; 317:559-75. (Pubitemid 34722169)
    • (2002) Journal of Molecular Biology , vol.317 , Issue.4 , pp. 559-575
    • Chadalavada, D.M.1    Senchak, S.E.2    Bevilacqua, P.C.3
  • 21
    • 4344584210 scopus 로고    scopus 로고
    • Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength
    • DOI 10.1016/j.jmb.2004.05.071, PII S0022283604006527
    • Brown TS, Chadalavada DM, Bevilacqua PC. Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength. J Mol Biol 2004; 341:695-712. (Pubitemid 39118405)
    • (2004) Journal of Molecular Biology , vol.341 , Issue.3 , pp. 695-712
    • Brown, T.S.1    Chadalavada, D.M.2    Bevilacqua, P.C.3
  • 22
    • 0033081861 scopus 로고    scopus 로고
    • A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduces kinetic trapping of inactive conformations
    • DOI 10.1093/nar/27.3.795
    • Perrotta AT, Nikiforova O, Been MD. A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduceskinetic trapping of inactive conformations. Nucleic Acids Res 1999; 27:795-802. (Pubitemid 29209367)
    • (1999) Nucleic Acids Research , vol.27 , Issue.3 , pp. 795-802
    • Perrotta, A.T.1    Nikiforova, O.2    Been, M.D.3
  • 23
    • 0033555361 scopus 로고    scopus 로고
    • Detailed analysis of stem I and its 5' and 3' neighbor regions in the trans-acting HDV ribozyme
    • DOI 10.1093/nar/27.2.403
    • Nishikawa F, Roy M, Fauzi H, Nishikawa S. Detailed analysis of stem I and its 5′ and 3′ neighbor regions in the trans-acting HDV ribozyme. Nucleic Acids Res 1999; 27:403-10. (Pubitemid 29210001)
    • (1999) Nucleic Acids Research , vol.27 , Issue.2 , pp. 403-410
    • Nishikawa, F.1    Roy, M.2    Fauzi, H.3    Nishikawa, S.4
  • 27
    • 0030798881 scopus 로고    scopus 로고
    • Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme
    • DOI 10.1093/nar/25.15.3124
    • Fauzi H, Kawakami J, Nishikawa F, Nishikawa S. Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme. Nucleic Acids Res 1997; 25:3124-30. (Pubitemid 27331408)
    • (1997) Nucleic Acids Research , vol.25 , Issue.15 , pp. 3124-3130
    • Fauzi, H.1    Kawakami, J.2    Nishikawa, F.3    Nishikawa, S.4
  • 29
    • 33747612153 scopus 로고    scopus 로고
    • Addition of an extra substrate binding site and partial destabilization of stem structures in HDV ribozyme give rise to high sequence-specificity for its target RNA
    • DOI 10.1080/15257770600684183, PII R1420144154H9K17
    • Hori T, Guo F, Uesugi S. Addition of an extra substrate binding site and partial destabilization of stem structures in HDV ribozyme give rise to high sequence-specificity for its target RNA. Nucleosides Nucleotides Nucleic Acids 2006; 25:489-501. (Pubitemid 44264717)
    • (2006) Nucleosides, Nucleotides and Nucleic Acids , vol.25 , Issue.4-6 , pp. 489-501
    • Hori, T.1    Guo, F.2    Uesugi, S.3
  • 30
    • 33749034196 scopus 로고    scopus 로고
    • A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene
    • DOI 10.1126/science.1129308
    • Salehi-Ashtiani K, Luptak A, Litovchick A, Szostak JW. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science 2006; 313:1788-92. (Pubitemid 44454155)
    • (2006) Science , vol.313 , Issue.5794 , pp. 1788-1792
    • Salehi-Ashtiani, K.1    Luptak, A.2    Litovchick, A.3    Szostak, J.W.4
  • 32
    • 0042423675 scopus 로고    scopus 로고
    • Two previously undescribed members of the mouse CPEB family of genes and their inducible expression in the principal cell layers of the hippocampus
    • DOI 10.1073/pnas.1133424100
    • Theis M, Si K, Kandel ER. Two previously undescribed members of the mouse CPEB family of genes and their inducible expression in the principal cell layers of the hippocampus. Proc Natl Acad Sci USA 2003; 100:9602-7. (Pubitemid 37033974)
    • (2003) Proceedings of the National Academy of Sciences of the United States of America , vol.100 , Issue.16 , pp. 9602-9607
    • Theis, M.1    Si, K.2    Kandel, E.R.3
  • 33
    • 80052820608 scopus 로고    scopus 로고
    • Mammalian self-cleaving ribozymes
    • Lilley DMJ, Eckstein F, Eds. Cambridge, UK: Royal Society of Chemistry
    • Luptak A, Szostak JW. Mammalian self-cleaving ribozymes. In: Lilley DMJ, Eckstein F, Eds. Ribozymes and RNA catalysis. Cambridge, UK: Royal Society of Chemistry 2007.
    • (2007) Ribozymes and RNA Catalysis
    • Luptak, A.1    Szostak, J.W.2
  • 34
    • 77953894191 scopus 로고    scopus 로고
    • The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting
    • Chadalavada DM, Gratton EA, Bevilacqua PC. The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting. Biochemistry 2010; 49:5321-30.
    • (2010) Biochemistry , vol.49 , pp. 5321-5330
    • Chadalavada, D.M.1    Gratton, E.A.2    Bevilacqua, P.C.3
  • 36
    • 33644879170 scopus 로고    scopus 로고
    • Antigenomic delta ribozyme variants with mutations in the catalytic core obtained by the in vitro selection method
    • Legiewicz M, Wichlacz A, Brzezicha B, Ciesiolka J. Antigenomic delta ribozyme variants with mutations in the catalytic core obtained by the in vitro selection method. Nucleic Acids Res 2006; 34:1270-80.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1270-1280
    • Legiewicz, M.1    Wichlacz, A.2    Brzezicha, B.3    Ciesiolka, J.4
  • 37
    • 32644448356 scopus 로고    scopus 로고
    • Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence
    • DOI 10.1093/nar/gkj463
    • Nehdi A, Perreault JP. Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence. Nucleic Acids Res 2006; 34:584-92. (Pubitemid 43240246)
    • (2006) Nucleic Acids Research , vol.34 , Issue.2 , pp. 584-592
    • Nehdi, A.1    Perreault, J.-P.2
  • 39
    • 0025095711 scopus 로고
    • Pattern searching/alignment with RNA primary and secondary structures: An effective descriptor for tRNA
    • Gautheret D, Major F, Cedergren R. Pattern searching/ alignment with RNA primary and secondary structures: an effective descriptor for tRNA. Comput Appl Biosci 1990; 6:325-31. (Pubitemid 20370013)
    • (1990) Computer Applications in the Biosciences , vol.6 , Issue.4 , pp. 325-331
    • Gautheret, D.1    Major, F.2    Cedergren, R.3
  • 40
    • 77957168895 scopus 로고    scopus 로고
    • Computational discovery of folded RNA domains in genomes and in vitro selected libraries
    • Riccitelli NJ, Lupták A. Computational discovery of folded RNA domains in genomes and in vitro selected libraries. Methods 2010.
    • (2010) Methods
    • Riccitelli, N.J.1    Lupták, A.2
  • 41
    • 77953379568 scopus 로고    scopus 로고
    • R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript
    • Eickbush DG, Eickbush TH. R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript. Mol Cell Biol 2010; 30:3142-50.
    • (2010) Mol Cell Biol , vol.30 , pp. 3142-3150
    • Eickbush, D.G.1    Eickbush, T.H.2
  • 42
    • 0021459207 scopus 로고
    • The rare transcripts of interrupted rRNA genes in drosophila melanogaster are processed or degraded during synthesis
    • Jamrich M, Miller OL Jr. The rare transcripts of interrupted rRNA genes in Drosophila melanogaster are processed or degraded during synthesis. EMBO J 1984; 3:1541-5.
    • (1984) EMBO J , vol.3 , pp. 1541-1545
    • Jamrich, M.1    Miller Jr., O.L.2
  • 43
    • 0033081843 scopus 로고    scopus 로고
    • Conserved features at the 5' end of Drosophila R2 retrotransposable elements: Implications for transcription and translation
    • George JA, Eickbush TH. Conserved features at the 5 end of Drosophila R2 retrotransposable elements: implications for transcription and translation. Insect Mol Biol 1999; 8:3-10. (Pubitemid 29032130)
    • (1999) Insect Molecular Biology , vol.8 , Issue.1 , pp. 3-10
    • George, J.A.1    Eickbush, T.H.2
  • 44
    • 0032853242 scopus 로고    scopus 로고
    • In vitro selection of functional nucleic acids
    • DOI 10.1146/annurev.biochem.68.1.611
    • Wilson DS, Szostak JW. In vitro selection of functional nucleic acids. Annu Rev Biochem 1999; 68:611-47. (Pubitemid 29449205)
    • (1999) Annual Review of Biochemistry , vol.68 , pp. 611-647
    • Wilson, D.S.1    Szostak, J.W.2
  • 45
    • 0035498871 scopus 로고    scopus 로고
    • In vitro evolution suggests multiple origins for the hammerhead ribozyme
    • DOI 10.1038/35102081
    • Salehi-Ashtiani K, Szostak JW. In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature 2001; 414:82-4. (Pubitemid 33041627)
    • (2001) Nature , vol.414 , Issue.6859 , pp. 82-84
    • Salehi-Ashtiani, K.1    Szostak, J.W.2
  • 46
    • 77956229148 scopus 로고    scopus 로고
    • Ubiquitous presence of the hammerhead ribozyme motif along the tree of life
    • de la Pena M, Garcia-Robles I. Ubiquitous presence of the hammerhead ribozyme motif along the tree of life. Rna-a Publication of the Rna Society 2010; 16:1943-50.
    • (2010) Rna-a Publication of the Rna Society , vol.16 , pp. 1943-1950
    • De La Pena, M.1    Garcia-Robles, I.2
  • 47
    • 78650501783 scopus 로고    scopus 로고
    • From alpaca to zebrafish: Hammerhead ribozymes wherever you look
    • Seehafer C, Kalweit A, Steger G, Graf S, Hammann C. From alpaca to zebrafish: hammerhead ribozymes wherever you look. RNA 2011; 17:21-6.
    • (2011) RNA , vol.17 , pp. 21-26
    • Seehafer, C.1    Kalweit, A.2    Steger, G.3    Graf, S.4    Hammann, C.5
  • 48
    • 79953141245 scopus 로고    scopus 로고
    • Structure-based Search Reveals Hammerhead Ribozymes in the Human Microbiome
    • Jimenez RM, Delwart E, Luptak A. Structure-based Search Reveals Hammerhead Ribozymes in the Human Microbiome. J Biol Chem 2011; 286:7737-43.
    • (2011) J Biol Chem , vol.286 , pp. 7737-7743
    • Jimenez, R.M.1    Delwart, E.2    Luptak, A.3


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