메뉴 건너뛰기




Volumn 278, Issue 19, 2011, Pages 3739-3747

High-pressure analysis of a hammerhead ribozyme from Chrysanthemum chlorotic mottle viroid reveals two different populations of self-cleaving molecule

Author keywords

activation volume; hammerhead ribozyme; high pressure; kinetics; RNA

Indexed keywords

CIS ACTING ELEMENT; HAMMERHEAD RIBOZYME;

EID: 80052965567     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2011.08291.x     Document Type: Article
Times cited : (20)

References (46)
  • 1
    • 0023047510 scopus 로고
    • Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid
    • Hutchins C, Rathjen P, Forster A, &, Symons R, (1986) Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucleic Acids Res 14, 3627-3640.
    • (1986) Nucleic Acids Res , vol.14 , pp. 3627-3640
    • Hutchins, C.1    Rathjen, P.2    Forster, A.3    Symons, R.4
  • 4
    • 0029941783 scopus 로고    scopus 로고
    • Cloning and characterization of extended hammerheads from a diverse set of caudate amphibians
    • DOI 10.1016/0378-1119(96)00126-6
    • Zhang Y, &, Epstein LM, (1996) Cloning and characterization of extended hammerheads from a diverse set of caudate amphibians. Gene 172, 183-190. (Pubitemid 26190051)
    • (1996) Gene , vol.172 , Issue.2 , pp. 183-190
    • Zhang, Y.1    Epstein, L.M.2
  • 5
    • 0031806709 scopus 로고    scopus 로고
    • Schistosome satellite DNA encodes active hammerhead ribozymes
    • Ferbeyre G, Smith JM, &, Cedergren R, (1998) Schistosome satellite DNA encodes active hammerhead ribozymes. Mol Cell Biol 18, 3880-3888. (Pubitemid 28287911)
    • (1998) Molecular and Cellular Biology , vol.18 , Issue.7 , pp. 3880-3888
    • Ferbeyre, G.1    Smith, J.M.2    Cedergren, R.3
  • 7
    • 77949371176 scopus 로고    scopus 로고
    • Phylogenetic footprinting of non-coding RNA: Hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae)
    • Martinsen L, Johnsen A, Venanzetti F, &, Bachmann L, (2010) Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae). BMC Evol Biol 10, 3-11.
    • (2010) BMC Evol Biol , vol.10 , pp. 3-11
    • Martinsen, L.1    Johnsen, A.2    Venanzetti, F.3    Bachmann, L.4
  • 9
    • 49649109010 scopus 로고    scopus 로고
    • A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA
    • Martick M, Horan LH, Noller HF, &, Scott WG, (2008) A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA. Nature 454, 899-902.
    • (2008) Nature , vol.454 , pp. 899-902
    • Martick, M.1    Horan, L.H.2    Noller, H.F.3    Scott, W.G.4
  • 10
    • 77956226227 scopus 로고    scopus 로고
    • Intronic hammerhead ribozymes are ultraconserved in the human genome
    • de la Peña M, &, García-Robles I, (2010) Intronic hammerhead ribozymes are ultraconserved in the human genome. EMBO Rep 11, 711-716.
    • (2010) EMBO Rep , vol.11 , pp. 711-716
    • De La Peña, M.1    García-Robles, I.2
  • 11
    • 77956229148 scopus 로고    scopus 로고
    • Ubiquitous presence of the hammerhead ribozyme motif along the tree of life
    • de la Peña M, &, García-Robles I, (2010) Ubiquitous presence of the hammerhead ribozyme motif along the tree of life. RNA 16, 1943-1950.
    • (2010) RNA , vol.16 , pp. 1943-1950
    • De La Peña, M.1    García-Robles, I.2
  • 12
    • 79953141245 scopus 로고    scopus 로고
    • Structure-based search reveals hammerhead ribozymes in the human microbiome
    • Jimenez RM, Delwart E, &, Lupták A, (2011) Structure-based search reveals hammerhead ribozymes in the human microbiome. J Biol Chem 286, 7737-7743.
    • (2011) J Biol Chem , vol.286 , pp. 7737-7743
    • Jimenez, R.M.1    Delwart, E.2    Lupták, A.3
  • 13
    • 5644303570 scopus 로고    scopus 로고
    • Ribozyme mechanisms
    • (Majoral J-P, Ed.), Springer-Verlag, Berlin Heidelberg
    • Takagi Y, Ikeda Y, &, Taira K, (2004) Ribozyme mechanisms. In New Aspects in Phosphorus Chemistry IV (, Majoral J-P, Ed.), pp. 49-55. Springer-Verlag, Berlin Heidelberg.
    • (2004) New Aspects in Phosphorus Chemistry IV , pp. 49-55
    • Takagi, Y.1    Ikeda, Y.2    Taira, K.3
  • 15
    • 77956126717 scopus 로고    scopus 로고
    • Hammerhead ribozymes: True metal or nucleobase catalysis? Where is the catalytic power from?
    • Leclerc F, (2010) Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from? Molecules 15, 5389-5407.
    • (2010) Molecules , vol.15 , pp. 5389-5407
    • Leclerc, F.1
  • 16
    • 0043009734 scopus 로고    scopus 로고
    • Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity
    • DOI 10.1038/nsb959
    • Khvorova A, Lescoute A, Westhof E, &, Jayasena S, (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Mol Biol 10, 708-712. (Pubitemid 37052408)
    • (2003) Nature Structural Biology , vol.10 , Issue.9 , pp. 708-712
    • Khvorova, A.1    Lescoute, A.2    Westhof, E.3    Jayasena, S.D.4
  • 17
    • 0142105383 scopus 로고    scopus 로고
    • Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity
    • DOI 10.1093/emboj/cdg530
    • De la Pena M, Gago S, &, Flores R, (2003) Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J 22, 5561-5570. (Pubitemid 37279965)
    • (2003) EMBO Journal , vol.22 , Issue.20 , pp. 5561-5570
    • De La Pena, M.1    Gago, S.2    Flores, R.3
  • 19
    • 1942533453 scopus 로고    scopus 로고
    • Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements
    • DOI 10.1261/rna.5268404
    • Penedo JC, Wilson TJ, Jayasena SD, Khvorova A, &, Lilley DMJ, (2004) Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. RNA 10, 880-888. (Pubitemid 38529750)
    • (2004) RNA , vol.10 , Issue.5 , pp. 880-888
    • Penedo, J.C.1    Wilson, T.J.2    Jayasena, S.D.3    Khvorova, A.4    Lilley, D.M.J.5
  • 20
    • 33746938267 scopus 로고    scopus 로고
    • When to Believe What You See
    • DOI 10.1016/j.molcel.2006.08.001, PII S1097276506005302
    • Nelson JA, &, Uhlenbeck OC, (2006) When to believe what you see. Mol Cell 23, 447-450. (Pubitemid 44205497)
    • (2006) Molecular Cell , vol.23 , Issue.4 , pp. 447-450
    • Nelson, J.A.1    Uhlenbeck, O.C.2
  • 21
    • 33947645368 scopus 로고    scopus 로고
    • Efficient ligation of the Schistosoma hammerhead ribozyme
    • DOI 10.1021/bi062077r
    • Canny MD, Jucker FM, &, Pardi A, (2007) Efficient ligation of the Schistosoma hammerhead ribozyme. Biochemistry 46, 3826-3834. (Pubitemid 46493482)
    • (2007) Biochemistry , vol.46 , Issue.12 , pp. 3826-3834
    • Canny, M.D.1    Jucker, F.M.2    Pardi, A.3
  • 22
    • 33746228126 scopus 로고    scopus 로고
    • Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis
    • DOI 10.1016/j.cell.2006.06.036, PII S0092867406008567
    • Martick M, &, Scott W, (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126, 309-320. (Pubitemid 44092962)
    • (2006) Cell , vol.126 , Issue.2 , pp. 309-320
    • Martick, M.1    Scott, W.G.2
  • 23
    • 0030851810 scopus 로고    scopus 로고
    • Chrysanthemum chlorotic mottle viroid: Unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes
    • DOI 10.1073/pnas.94.21.11262
    • Navarro B, &, Flores R, (1997) Chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes. Proc Natl Acad Sci USA 94, 11262-11267. (Pubitemid 27450986)
    • (1997) Proceedings of the National Academy of Sciences of the United States of America , vol.94 , Issue.21 , pp. 11262-11267
    • Navarro, B.1    Flores, R.2
  • 24
    • 59649130342 scopus 로고    scopus 로고
    • Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: A loop-loop interaction motif conserved in most natural hammerheads
    • Dufour D, de la Pena M, Gago S, Flores R, &, Gallego J, (2009) Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads. Nucleic Acids Res 37, 368-381.
    • (2009) Nucleic Acids Res , vol.37 , pp. 368-381
    • Dufour, D.1    De La Pena, M.2    Gago, S.3    Flores, R.4    Gallego, J.5
  • 26
    • 0022459444 scopus 로고
    • Osmotic stress for the direct measurement of intermolecular forces
    • Parsegian VA, Rand RP, Fuller NL, &, Rau DC, (1986) Osmotic stress for the direct measurement of intermolecular forces. Methods Enzymol 127, 400-416.
    • (1986) Methods Enzymol , vol.127 , pp. 400-416
    • Parsegian, V.A.1    Rand, R.P.2    Fuller, N.L.3    Rau, D.C.4
  • 27
    • 18744411284 scopus 로고    scopus 로고
    • The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure
    • DOI 10.1093/nar/gki552
    • Tobe S, Heams T, Vergne J, Herve G, &, Maurel MC, (2005) The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure. Nucleic Acids Res 33, 2557-2564. (Pubitemid 41511275)
    • (2005) Nucleic Acids Research , vol.33 , Issue.8 , pp. 2557-2564
    • Tobe, S.1    Heams, T.2    Vergne, J.3    Herve, G.4    Maurel, M.-C.5
  • 29
    • 77953022124 scopus 로고    scopus 로고
    • Diversity of viruses of the hyperthermophilic archaeal genus Aeropyrum, and isolation of the Aeropyrum pernix bacilliform virus 1, APBV1, the first representative of the family Clavaviridae
    • Mochizuki T, Yoshida T, Tanaka R, Forterre P, Sako Y, &, Prangishvili D, (2010) Diversity of viruses of the hyperthermophilic archaeal genus Aeropyrum, and isolation of the Aeropyrum pernix bacilliform virus 1, APBV1, the first representative of the family Clavaviridae. Virology 402, 347-354.
    • (2010) Virology , vol.402 , pp. 347-354
    • Mochizuki, T.1    Yoshida, T.2    Tanaka, R.3    Forterre, P.4    Sako, Y.5    Prangishvili, D.6
  • 32
    • 12844269766 scopus 로고    scopus 로고
    • Characterization of a native hammerhead ribozyme derived from schistosomes
    • DOI 10.1261/rna.7950605
    • Osborne EM, Schaak JE, &, Derose VJ, (2005) Characterization of a native hammerhead ribozyme derived from schistosomes. RNA 11, 187-196. (Pubitemid 40165633)
    • (2005) RNA , vol.11 , Issue.2 , pp. 187-196
    • Osborne, E.M.1    Schaak, J.E.2    Derose, V.J.3
  • 33
    • 0028906353 scopus 로고
    • The internal equilibrium of the hammerhead ribozyme reaction
    • Hertel KJ, &, Uhlenbeck OC, (1995) The internal equilibrium of the hammerhead ribozyme reaction. Biochemistry 34, 1744-1749.
    • (1995) Biochemistry , vol.34 , pp. 1744-1749
    • Hertel, K.J.1    Uhlenbeck, O.C.2
  • 34
    • 0031828144 scopus 로고    scopus 로고
    • Hammerhead ribozyme kinetics
    • DOI 10.1017/S1355838298980876
    • Stage-Zimmermann TK, &, Uhlenbeck OC, (1998) Hammerhead ribozyme kinetics. RNA 4, 875-889. (Pubitemid 28359759)
    • (1998) RNA , vol.4 , Issue.8 , pp. 875-889
    • Stage-Zimmermann, T.K.1    Uhlenbeck, O.C.2
  • 35
    • 0036293201 scopus 로고    scopus 로고
    • A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction
    • DOI 10.1006/jmbi.2001.5145
    • Murray JB, Dunham CM, &, Scott WG, (2002) A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction1. J Mol Biol 315, 121-130. (Pubitemid 34722116)
    • (2002) Journal of Molecular Biology , vol.315 , Issue.2 , pp. 121-130
    • Murray, J.B.1    Dunham, C.M.2    Scott, W.G.3
  • 36
    • 38049029204 scopus 로고    scopus 로고
    • Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis
    • Nelson JA, &, Uhlenbeck OC, (2008) Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis. RNA 14, 43-54.
    • (2008) RNA , vol.14 , pp. 43-54
    • Nelson, J.A.1    Uhlenbeck, O.C.2
  • 37
    • 33645960997 scopus 로고    scopus 로고
    • Protein stability and dynamics in the pressure-temperature plane
    • Meersman F, Smeller L, &, Heremans K, (2006) Protein stability and dynamics in the pressure-temperature plane. Biochim Biophys Acta 1764, 346-354.
    • (2006) Biochim Biophys Acta , vol.1764 , pp. 346-354
    • Meersman, F.1    Smeller, L.2    Heremans, K.3
  • 39
    • 27644432146 scopus 로고    scopus 로고
    • Hammerheads derived from sTRSV show enhanced cleavage and ligation rate constants
    • DOI 10.1021/bi051130t
    • Nelson JA, Shepotinovskaya I, &, Uhlenbeck OC, (2005) Hammerheads derived from sTRSV show enhanced cleavage and ligation rate constants. Biochemistry 44, 14577-14585. (Pubitemid 41567465)
    • (2005) Biochemistry , vol.44 , Issue.44 , pp. 14577-14585
    • Nelson, J.A.1    Shepotinovskaya, I.2    Uhlenbeck, O.C.3
  • 40
    • 52949104434 scopus 로고    scopus 로고
    • Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme
    • Boots JL, Canny MD, Azimi E, &, Pardi A, (2008) Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme. RNA 14, 2212-2222.
    • (2008) RNA , vol.14 , pp. 2212-2222
    • Boots, J.L.1    Canny, M.D.2    Azimi, E.3    Pardi, A.4
  • 41
    • 78649677325 scopus 로고    scopus 로고
    • Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations
    • McDowell SE, Jun JM, &, Walter NG, (2010) Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations. RNA 16, 2414-2426.
    • (2010) RNA , vol.16 , pp. 2414-2426
    • McDowell, S.E.1    Jun, J.M.2    Walter, N.G.3
  • 42
    • 56449119364 scopus 로고    scopus 로고
    • Probing general base catalysis in the hammerhead ribozyme
    • Thomas JM, &, Perrin DM, (2008) Probing general base catalysis in the hammerhead ribozyme. J Am Chem Soc 130, 15467-15475.
    • (2008) J Am Chem Soc , vol.130 , pp. 15467-15475
    • Thomas, J.M.1    Perrin, D.M.2
  • 43
    • 33749267488 scopus 로고    scopus 로고
    • Extraordinary rates of transition metal ion-mediated ribozyme catalysis
    • DOI 10.1261/rna.128906
    • Roychowdhury-Saha M, &, Burke DH, (2006) Extraordinary rates of transition metal ion-mediated ribozyme catalysis. RNA 12, 1846-1852. (Pubitemid 44484258)
    • (2006) RNA , vol.12 , Issue.10 , pp. 1846-1852
    • Roychowdhury-Saha, M.1    Burke, D.H.2
  • 44
    • 63649098099 scopus 로고    scopus 로고
    • Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation
    • Lee TS, Giambasu GM, Sosa CP, Martick M, Scott WG, &, York DM, (2009) Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation. J Mol Biol 388, 195-206.
    • (2009) J Mol Biol , vol.388 , pp. 195-206
    • Lee, T.S.1    Giambasu, G.M.2    Sosa, C.P.3    Martick, M.4    Scott, W.G.5    York, D.M.6
  • 45
    • 0033325108 scopus 로고    scopus 로고
    • Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme
    • DOI 10.1017/S003358350000353X
    • Scott WG, (1999) Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme. Q Rev Biophys 32, 241-284. (Pubitemid 30598969)
    • (1999) Quarterly Reviews of Biophysics , vol.32 , Issue.3 , pp. 241-284
    • Scott, W.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.