메뉴 건너뛰기




Volumn 13, Issue 12, 2007, Pages 2189-2201

Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions

Author keywords

Catalysis; Cotranscriptional; Evolution; HDV; Ribozyme

Indexed keywords

HEPATITIS DELTA ANTIGEN; RIBOZYME;

EID: 36248964100     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.778107     Document Type: Article
Times cited : (43)

References (48)
  • 2
    • 0026495873 scopus 로고
    • Secondary structure of the self-cleaving RNA of hepatitis delta virus: Applications to catalytic RNA design
    • Been, M.D., Perrotta, A.T., and Rosenstein, S.P. 1992. Secondary structure of the self-cleaving RNA of hepatitis delta virus: Applications to catalytic RNA design. Biochemistry 31: 11843-11852.
    • (1992) Biochemistry , vol.31 , pp. 11843-11852
    • Been, M.D.1    Perrotta, A.T.2    Rosenstein, S.P.3
  • 3
    • 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
    • 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.
    • (2004) J. Mol. Biol , vol.341 , pp. 695-712
    • Brown, T.S.1    Chadalavada, D.M.2    Bevilacqua, P.C.3
  • 4
    • 18344411608 scopus 로고
    • Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing
    • Buzayan, J.M., Gerlach, W.L., and Bruening, G. 1986. Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing. Proc. Natl. Acad. Sci. 83: 8859-8862.
    • (1986) Proc. Natl. Acad. Sci , vol.83 , pp. 8859-8862
    • Buzayan, J.M.1    Gerlach, W.L.2    Bruening, G.3
  • 5
    • 1942489258 scopus 로고    scopus 로고
    • Informational complexity and functional activity of RNA structures
    • Carothers, J.M., Oestreich, S.C., Davis, J.H., and Szostak, J.W. 2004. Informational complexity and functional activity of RNA structures. J. Am. Chem. Soc. 126: 5130-5137.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 5130-5137
    • Carothers, J.M.1    Oestreich, S.C.2    Davis, J.H.3    Szostak, J.W.4
  • 6
    • 0034636981 scopus 로고    scopus 로고
    • A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme
    • Chadalavada, D.M., Knudsen, S.M., Nakano, S., and Bevilacqua, P.C. 2000. A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme. J. Mol. Biol. 301: 349-367.
    • (2000) J. Mol. Biol , vol.301 , pp. 349-367
    • Chadalavada, D.M.1    Knudsen, S.M.2    Nakano, S.3    Bevilacqua, P.C.4
  • 7
    • 0036289258 scopus 로고    scopus 로고
    • The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots
    • 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.
    • (2002) J. Mol. Biol , vol.317 , pp. 559-575
    • Chadalavada, D.M.1    Senchak, S.E.2    Bevilacqua, P.C.3
  • 8
    • 0036434479 scopus 로고    scopus 로고
    • A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence
    • Diegelman-Parente, A. and Bevilacqua, P.C. 2002. A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence. J. Mol. Biol. 324: 1-16.
    • (2002) J. Mol. Biol , vol.324 , pp. 1-16
    • Diegelman-Parente, A.1    Bevilacqua, P.C.2
  • 9
    • 0030747157 scopus 로고    scopus 로고
    • RNA virus mutations and fitness for survival
    • Domingo, E. and Holland, J.J. 1997. RNA virus mutations and fitness for survival. Annu. Rev. Microbiol. 51: 151-178.
    • (1997) Annu. Rev. Microbiol , vol.51 , pp. 151-178
    • Domingo, E.1    Holland, J.J.2
  • 10
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferre-D'Amare, A.R., Zhou, K., and Doudna, J.A. 1998. Crystal structure of a hepatitis delta virus ribozyme. Nature 395: 567-574.
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferre-D'Amare, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 11
    • 0023663396 scopus 로고
    • Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites
    • 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.
    • (1987) Cell , vol.49 , pp. 211-220
    • Forster, A.C.1    Symons, R.H.2
  • 12
    • 33751430926 scopus 로고    scopus 로고
    • The human RNA polymerase II interacts with the terminal stem-loop regions of the hepatitis delta virus RNA genome
    • Greco-Stewart, V.S., Miron, P., Abrahem, A., and Pelchat, M. 2007. The human RNA polymerase II interacts with the terminal stem-loop regions of the hepatitis delta virus RNA genome. Virology 357: 68-78.
    • (2007) Virology , vol.357 , pp. 68-78
    • Greco-Stewart, V.S.1    Miron, P.2    Abrahem, A.3    Pelchat, M.4
  • 13
    • 0032500589 scopus 로고    scopus 로고
    • Identification and characterization of the RNA chaperone activity of hepatitis delta antigen peptides
    • Huang, Z.S. and Wu, H.N. 1998. Identification and characterization of the RNA chaperone activity of hepatitis delta antigen peptides. J. Biol. Chem. 273: 26455-26461.
    • (1998) J. Biol. Chem , vol.273 , pp. 26455-26461
    • Huang, Z.S.1    Wu, H.N.2
  • 14
    • 0037458726 scopus 로고    scopus 로고
    • Selective strand annealing and selective strand exchange promoted by the N-terminal domain of hepatitis delta antigen
    • Huang, Z.S., Su, W.H., Wang, J.L., and Wu, H.N. 2003. Selective strand annealing and selective strand exchange promoted by the N-terminal domain of hepatitis delta antigen. J. Biol. Chem. 278: 5685-5693.
    • (2003) J. Biol. Chem , vol.278 , pp. 5685-5693
    • Huang, Z.S.1    Su, W.H.2    Wang, J.L.3    Wu, H.N.4
  • 15
    • 10044240495 scopus 로고    scopus 로고
    • Characterization and application of the selective strand annealing activity of the N-terminal domain of hepatitis delta antigen
    • Huang, Z.S., Chen, A.Y., and Wu, H.N. 2004. Characterization and application of the selective strand annealing activity of the N-terminal domain of hepatitis delta antigen. FEBS Lett. 578: 345-350.
    • (2004) FEBS Lett , vol.578 , pp. 345-350
    • Huang, Z.S.1    Chen, A.Y.2    Wu, H.N.3
  • 16
    • 0034612331 scopus 로고    scopus 로고
    • Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme
    • Isambert, H. and Siggia, E.D. 2000. Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme. Proc. Natl. Acad. Sci. 97: 6515-6520.
    • (2000) Proc. Natl. Acad. Sci , vol.97 , pp. 6515-6520
    • Isambert, H.1    Siggia, E.D.2
  • 17
    • 2442641641 scopus 로고    scopus 로고
    • A conformational switch controls hepatitis delta virus ribozyme catalysis
    • Ke, A., Zhou, K., Ding, F., Cate, J.H., and Doudna, J.A. 2004. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 429: 201-205.
    • (2004) Nature , vol.429 , pp. 201-205
    • Ke, A.1    Zhou, K.2    Ding, F.3    Cate, J.H.4    Doudna, J.A.5
  • 18
    • 0033607261 scopus 로고    scopus 로고
    • Thermodynamics of single mismatches in RNA duplexes
    • Kierzek, R., Burkard, M.E., and Turner, D.H. 1999. Thermodynamics of single mismatches in RNA duplexes. Biochemistry 38: 14214-14223.
    • (1999) Biochemistry , vol.38 , pp. 14214-14223
    • Kierzek, R.1    Burkard, M.E.2    Turner, D.H.3
  • 19
    • 0032482923 scopus 로고    scopus 로고
    • Promoter escape limits the rate of RNA polymerase II transcription and is enhanced by TFIIE, TFIIH, and ATP on negatively supercoiled DNA
    • Kugel, J.F. and Goodrich, J.A. 1998. Promoter escape limits the rate of RNA polymerase II transcription and is enhanced by TFIIE, TFIIH, and ATP on negatively supercoiled DNA. Proc. Natl. Acad. Sci. 95: 9232-9237.
    • (1998) Proc. Natl. Acad. Sci , vol.95 , pp. 9232-9237
    • Kugel, J.F.1    Goodrich, J.A.2
  • 20
    • 0029071510 scopus 로고
    • The molecular biology of hepatitis delta virus
    • Lai, M.M. 1995. The molecular biology of hepatitis delta virus. Annu. Rev. Biochem. 64: 259-286.
    • (1995) Annu. Rev. Biochem , vol.64 , pp. 259-286
    • Lai, M.M.1
  • 21
    • 36248976299 scopus 로고    scopus 로고
    • Hepatitis delta antigen: Biochemical properties and functional roles in HDV replication
    • eds. H. Handa and Y. Yamaguchi, pp, Landes Bioscience, Georgetown, TX
    • Lai, M.M. 2006. Hepatitis delta antigen: Biochemical properties and functional roles in HDV replication. In Hepatitis delta virus (eds. H. Handa and Y. Yamaguchi), pp. 38-51. Landes Bioscience, Georgetown, TX.
    • (2006) Hepatitis delta virus , pp. 38-51
    • Lai, M.M.1
  • 22
    • 0028339955 scopus 로고
    • Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem II deletions
    • Long, D.M. and Uhlenbeck, O.C. 1994. Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem II deletions. Proc. Natl. Acad. Sci. 91: 6977-6981.
    • (1994) Proc. Natl. Acad. Sci , vol.91 , pp. 6977-6981
    • Long, D.M.1    Uhlenbeck, O.C.2
  • 24
    • 0019331859 scopus 로고
    • DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription
    • Martin, F.H. and Tinoco Jr., I. 1980. DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res. 8: 2295-2299.
    • (1980) Nucleic Acids Res , vol.8 , pp. 2295-2299
    • Martin, F.H.1    Tinoco Jr., I.2
  • 25
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
    • (1999) J. Mol. Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 26
    • 0034712097 scopus 로고    scopus 로고
    • General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
    • Nakano, S., Chadalavada, D.M., and Bevilacqua, P.C. 2000. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science 287: 1493-1497.
    • (2000) Science , vol.287 , pp. 1493-1497
    • Nakano, S.1    Chadalavada, D.M.2    Bevilacqua, P.C.3
  • 29
    • 0033578330 scopus 로고    scopus 로고
    • Folding of a large ribozyme during transcription and the effect of the elongation factor NusA
    • Pan, T., Artsimovitch, I., Fang, X.W., Landick, R., and Sosnick, T.R. 1999. Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc. Natl. Acad. Sci. 96: 9545-9550.
    • (1999) Proc. Natl. Acad. Sci , vol.96 , pp. 9545-9550
    • Pan, T.1    Artsimovitch, I.2    Fang, X.W.3    Landick, R.4    Sosnick, T.R.5
  • 30
    • 0025597973 scopus 로고
    • The self-cleaving domain from the genomic RNA of hepatitis delta virus: Sequence requirements and the effects of denaturant
    • doi: 10.1093/nar/8.10.2295
    • 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. doi: 10.1093/nar/8.10.2295.
    • (1990) Nucleic Acids Res , vol.18 , pp. 6821-6827
    • Perrotta, A.T.1    Been, M.D.2
  • 31
    • 0025882069 scopus 로고
    • A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA
    • 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.
    • (1991) Nature , vol.350 , pp. 434-436
    • Perrotta, A.T.1    Been, M.D.2
  • 32
    • 34247560640 scopus 로고    scopus 로고
    • A single nucleotide linked to a switch in metal ion reactivity preference in the HDV ribozymes
    • 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.
    • (2007) Biochemistry , vol.46 , pp. 5124-5130
    • Perrotta, A.T.1    Been, M.D.2
  • 33
    • 0025082875 scopus 로고
    • Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions
    • Rosenstein, S.P. and Been, M.D. 1990. Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions. Biochemistry 29: 8011-8016.
    • (1990) Biochemistry , vol.29 , pp. 8011-8016
    • Rosenstein, S.P.1    Been, M.D.2
  • 34
    • 0023042012 scopus 로고
    • Information content of binding sites on nucleotide sequences
    • Schneider, T.D., Stormo, G.D., Gold, L., and Ehrenfeucht, A. 1986. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188: 415-431.
    • (1986) J. Mol. Biol , vol.188 , pp. 415-431
    • Schneider, T.D.1    Stormo, G.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 36
    • 36248936329 scopus 로고    scopus 로고
    • Structure and replication of hepatitis delta virus RNA
    • eds. H. Handa and Y. Yamaguchi, pp, Landes Bioscience, Georgetown, TX
    • Taylor, J.M. 2006. Structure and replication of hepatitis delta virus RNA. In Hepatitis delta virus (eds. H. Handa and Y. Yamaguchi), pp. 20-37. Landes Bioscience, Georgetown, TX.
    • (2006) Hepatitis delta virus , pp. 20-37
    • Taylor, J.M.1
  • 37
    • 10244257563 scopus 로고    scopus 로고
    • Autophosphorylation sites participate in the activation of the double-stranded-RNA-activated protein kinase PKR
    • Taylor, D.R., Lee, S.B., Romano, P.R., Marshak, D.R., Hinnebusch, A.G., Esteban, M., and Mathews, M.B. 1996. Autophosphorylation sites participate in the activation of the double-stranded-RNA-activated protein kinase PKR. Mol. Cell. Biol. 16: 6295-6302.
    • (1996) Mol. Cell. Biol , vol.16 , pp. 6295-6302
    • Taylor, D.R.1    Lee, S.B.2    Romano, P.R.3    Marshak, D.R.4    Hinnebusch, A.G.5    Esteban, M.6    Mathews, M.B.7
  • 38
    • 0027222970 scopus 로고
    • Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme
    • Thill, G., Vasseur, M., and Tanner, N.K. 1993. Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme. Biochemistry 32: 4254-4262.
    • (1993) Biochemistry , vol.32 , pp. 4254-4262
    • Thill, G.1    Vasseur, M.2    Tanner, N.K.3
  • 39
    • 36248933916 scopus 로고    scopus 로고
    • Turner, D.H., Sugimoto, N., and Freier, S.M. 1990. Thermodynamics and kinetics of base-pairing and of DNA and RNA self-assembly and helix coil transition. In Nucleic acids (ed. W. Saenger), 1C of Landolt-Bornstein Series, pp. 201-227. Springer-Verlag, Berlin.
    • Turner, D.H., Sugimoto, N., and Freier, S.M. 1990. Thermodynamics and kinetics of base-pairing and of DNA and RNA self-assembly and helix coil transition. In Nucleic acids (ed. W. Saenger), vol. 1C of Landolt-Bornstein Series, pp. 201-227. Springer-Verlag, Berlin.
  • 40
    • 0031008221 scopus 로고    scopus 로고
    • Basic mechanisms of transcript elongation and its regulation
    • Uptain, S.M., Kane, C.M., and Chamberlin, M.J. 1997. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66: 117-172.
    • (1997) Annu. Rev. Biochem , vol.66 , pp. 117-172
    • Uptain, S.M.1    Kane, C.M.2    Chamberlin, M.J.3
  • 41
    • 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
    • Wadkins, T.S., Perrotta, A.T., Ferre-D'Amare, A.R., Doudna, J.A., and Been, M.D. 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.
    • (1999) RNA , vol.5 , 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
  • 42
    • 0344237409 scopus 로고    scopus 로고
    • Nucleic acid binding properties of the nucleic acid chaperone domain of hepatitis delta antigen
    • doi: 10.1093/nar/gkg857
    • Wang, C.C., Chang, T.C., Lin, C.W., Tsui, H.L., Chu, P.B., Chen, B.S., Huang, Z.S., and Wu, H.N. 2003. Nucleic acid binding properties of the nucleic acid chaperone domain of hepatitis delta antigen. Nucleic Acids Res. 31: 6481-6492. doi: 10.1093/nar/gkg857.
    • (2003) Nucleic Acids Res , vol.31 , pp. 6481-6492
    • Wang, C.C.1    Chang, T.C.2    Lin, C.W.3    Tsui, H.L.4    Chu, P.B.5    Chen, B.S.6    Huang, Z.S.7    Wu, H.N.8
  • 43
    • 84974692676 scopus 로고    scopus 로고
    • Hepatitis delta antigen and RNA polymerase II
    • eds. H. Handa and Y. Yamaguchi, pp, Landes Bioscience, Georgetown, TX
    • Yamaguchi, Y. and Handa, H. 2006. Hepatitis delta antigen and RNA polymerase II. In Hepatitis delta virus (eds. H. Handa and Y. Yamaguchi), pp. 66-75. Landes Bioscience, Georgetown, TX.
    • (2006) Hepatitis delta virus , pp. 66-75
    • Yamaguchi, Y.1    Handa, H.2
  • 45
    • 34250698885 scopus 로고    scopus 로고
    • Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity
    • Yamaguchi, Y., Mura, T., Chanarat, S., Okamoto, S., and Handa, H. 2007. Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity. Genes Cells 12: 863-875.
    • (2007) Genes Cells , vol.12 , pp. 863-875
    • Yamaguchi, Y.1    Mura, T.2    Chanarat, S.3    Okamoto, S.4    Handa, H.5
  • 46
    • 0022649937 scopus 로고
    • The intervening sequence RNA of Tetrahymena is an enzyme
    • Zaug, A.J. and Cech, T.R. 1986. The intervening sequence RNA of Tetrahymena is an enzyme. Science 231: 470-475.
    • (1986) Science , vol.231 , pp. 470-475
    • Zaug, A.J.1    Cech, T.R.2
  • 47
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • doi: 10.1093/nar/gkg595
    • Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415. doi: 10.1093/nar/gkg595.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 48
    • 0002287019 scopus 로고    scopus 로고
    • Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
    • RNA biochemistry and biotechnology eds. J. Barciszewski and Brian F.C. Clark, pp, Kluwer Academic Publishers, Dordrecht, The Netherlands
    • Zuker, M., Mathews, D.H., and Turner, D.H. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In RNA biochemistry and biotechnology (eds. J. Barciszewski and Brian F.C. Clark), pp. 11-43. NATO ASI Series, Kluwer Academic Publishers, Dordrecht, The Netherlands.
    • (1999) NATO ASI Series , pp. 11-43
    • Zuker, M.1    Mathews, D.H.2    Turner, D.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.