The chemical repertoire of natural ribozymes (original) (raw)
Kruger, K. et al. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell31, 147–157 (1982). ArticleCASPubMed Google Scholar
Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell35, 849–857 (1983). ArticleCASPubMed Google Scholar
Lohse, P. A. & Szostak, J. W. Ribozyme-catalysed amino-acid transfer reactions. Nature381, 442–444 (1996). ArticleADSCASPubMed Google Scholar
Wiegand, T. W., Janssen, R. C. & Eaton, B. E. Selection of RNA amide synthases. Chem. Biol.4, 675–683 (1997). ArticleCASPubMed Google Scholar
Sengle, G., Eisenfuhr, A., Arora, P. S., Nowick, J. S. & Famulok, M. Novel RNA catalysts for the Michael reaction. Chem. Biol.8, 459–473 (2001). ArticleCASPubMed Google Scholar
Jadhav, V. R. & Yarus, M. Acyl-CoAs from coenzyme ribozymes. Biochemistry41, 723–729 (2002). ArticleCASPubMed Google Scholar
Wilson, D. S. & Szostak, J. W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem.68, 611–647 (1999). ArticleCASPubMed Google Scholar
Perrotta, A. T., Shih, I. & Been, M. D. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science286, 123–126 (1999). ArticleCASPubMed Google Scholar
Santoro, S. W., Joyce, G. F., Sakthivel, K., Gramatikova, S. & Barbas, C. F. III RNA cleavage by a DNA enzyme with extended chemical functionality. J. Am. Chem. Soc.122, 2433–2439 (2000). ArticleCASPubMed Google Scholar
Tang, J. & Breaker, R. R. Rational design of allosteric ribozymes. Chem. Biol.4, 453–459 (1997). ArticleCASPubMed Google Scholar
Salehi-Ashtiani, K. & Szostak, J. W. In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature414, 82–84 (2001). ArticleADSCASPubMed Google Scholar
Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M. & Scott, W. G. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol.5, 587–595 (1998). ArticleCASPubMed Google Scholar
Pley, H. W., Flaherty, K. M. & McKay, D. B. Three-dimensional structure of a hammerhead ribozyme. Nature372, 68–74 (1994). ArticleADSCASPubMed Google Scholar
Scott, W. G., Finch, J. T. & Klug, A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell81, 991–1002 (1995). ArticleCASPubMed Google Scholar
Scott, W. G., Murray, J. B., Arnold, J. R., Stoddard, B. L. & Klug, A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science274, 2065–2069 (1996). ArticleADSCASPubMed Google Scholar
Murray, J. B. et al. The structural basis of hammerhead ribozyme self-cleavage. Cell92, 665–673 (1998). ArticleCASPubMed Google Scholar
Murray, J. B., Szoke, H., Szoke, A. & Scott, W. G. Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction. Mol. Cell5, 279–287 (2000). ArticleCASPubMed Google Scholar
Murray, J. B., Dunham, C. M. & Scott, W. G. A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction. J. Mol. Biol.315, 121–130 (2002). ArticleCASPubMed Google Scholar
Scott, E. C. & Uhlenbeck, O. C. A re-investigation of the thio effect at the hammerhead cleavage site. Nucleic Acids Res.27, 479–484 (1999). ArticleCASPubMedPubMed Central Google Scholar
Peracchi, A., Beigelman, L., Scott, E. C., Uhlenbeck, O. C. & Herschlag, D. Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. J. Biol. Chem.272, 26822–26826 (1997). ArticleCASPubMed Google Scholar
Wang, S., Karbstein, K., Peracchi, A., Beigelman, L. & Herschlag, D. Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochemistry38, 14363–14378 (1999). ArticleCASPubMed Google Scholar
Murray, J. B. & Scott, W. G. Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure? J. Mol. Biol.296, 33–41 (2000). ArticleCASPubMed Google Scholar
O'Rear, J. L. et al. Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA7, 537–545 (2001). ArticleCASPubMedPubMed Central Google Scholar
Ferre-D'Amare, A. R., Zhou, K. & Doudna, J. A. Crystal structure of a hepatitis delta virus ribozyme. Nature395, 567–574 (1998). ArticleADSCASPubMed Google Scholar
Rupert, P. B. & Ferre-D'Amare, A. R. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature410, 780–786 (2001). ArticleADSCASPubMed Google Scholar
Rajagopal, P. & Feigon, J. Triple-strand formation in the homopurine:homopyrimidine DNA oligonucleotides d(G-A)4 and d(T-C)4. Nature339, 637–640 (1989). ArticleADSCASPubMed Google Scholar
Sklenar, V. & Feigon, J. Formation of a stable triplex from a single DNA strand. Nature345, 836–838 (1990). ArticleADSCASPubMed Google Scholar
Connell, G. J. & Yarus, M. RNAs with dual specificity and dual RNAs with similar specificity. Science264, 1137–1141 (1994). ArticleADSCASPubMed Google Scholar
Legault, P. & Pardi, A. In situ probing of adenine protonation in RNA by 13C NMR. J. Am. Chem. Soc.116, 8390–8391 (1994). ArticleCAS Google Scholar
Ravindranathan, S., Butcher, S. E. & Feigon, J. Adenine protonation in domain B of the hairpin ribozyme. Biochemistry39, 16026–16032 (2000). ArticleCASPubMed Google Scholar
Shih, I. H. & Been, M. D. Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage. Proc. Natl Acad. Sci. USA98, 1489–1494 (2001). ArticleADSCASPubMedPubMed Central Google Scholar
Nakano, S., Chadalavada, D. M. & Bevilacqua, P. C. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science287, 1493–1497 (2000). ArticleADSCASPubMed Google Scholar
Nakano, S. & Bevilacqua, P. C. Proton inventory of the genomic HDV ribozyme in Mg2+-containing solutions. J. Am. Chem. Soc.123, 11333–11334 (2001). ArticleCASPubMed Google Scholar
Luptak, A., Ferre-D'Amare, A. R., Zhou, K., Zilm, K. W. & Doudna, J. A. Direct pKa measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme. J. Am. Chem. Soc.123, 8447–8452 (2001). ArticleCASPubMed Google Scholar
Nakano, S., Proctor, D. J. & Bevilacqua, P. C. Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Biochemistry40, 12022–12038 (2001). ArticleCASPubMed Google Scholar
Ryder, S. P. et al. Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping. RNA7, 1454–1463 (2001). CASPubMedPubMed Central Google Scholar
Hampel, A. & Cowan, J. A. A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Chem. Biol.4, 513–517 (1997). ArticleCASPubMed Google Scholar
Nesbitt, S., Hegg, L. A. & Fedor, M. J. An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem. Biol.4, 619–630 (1997). ArticleCASPubMed Google Scholar
Walter, N. G. & Burke, J. M. The hairpin ribozyme: structure, assembly and catalysis. Curr. Opin. Chem. Biol.2, 303 (1998). ArticleCASPubMed Google Scholar
Cech, T. R. & Herschlag, D. (eds) Group I Ribozymes: Substrate Recognition, Catalytic Strategies and Comparative Mechanistic Analysis (Springer, Berlin, 1996). Google Scholar
Narlikar, G. J. & Herschlag, D. Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes. Annu. Rev. Biochem.66, 19–59 (1997). ArticleCASPubMed Google Scholar
Shan, S., Kravchuk, A. V., Piccirilli, J. A. & Herschlag, D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry40, 5161–5171 (2001). ArticleCASPubMed Google Scholar
Cate, J. H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science273, 1678–1685 (1996). ArticleADSCASPubMed Google Scholar
Juneau, K., Podell, E., Harrington, D. J. & Cech, T. R. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA–solvent interactions. Structure (Camb.)9, 221–231 (2001). ArticleCAS Google Scholar
Golden, B. L., Gooding, A. R., Podell, E. R. & Cech, T. R. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science282, 259–264 (1998). ArticleADSCASPubMed Google Scholar
Michel, F. & Westhof, E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol.216, 585–610 (1990). ArticleCASPubMed Google Scholar
Szewczak, A. A. et al. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site. Proc. Natl Acad. Sci. USA96, 11183–11188 (1999). ArticleADSCASPubMedPubMed Central Google Scholar
Gordon, P. M., Sontheimer, E. J. & Piccirilli, J. A. Kinetic characterization of the second step of group II intron splicing: role of metal ions and the cleavage site 2′-OH in catalysis. Biochemistry39, 12939–12952 (2000). ArticleCASPubMed Google Scholar
Sigel, R. K., Vaidya, A. & Pyle, A. M. Metal ion binding sites in a group II intron core. Nature Struct. Biol.7, 1111–1116 (2000). ArticleCASPubMed Google Scholar
Gordon, P. M. & Piccirilli, J. A. Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis. Nature Struct. Biol.8, 893–898 (2001). ArticleCASPubMed Google Scholar
Jestin, J. L., Deme, E. & Jacquier, A. Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron. EMBO J.16, 2945–2954 (1997). ArticleCASPubMedPubMed Central Google Scholar
Boudvillain, M., de Lencastre, A. & Pyle, A. M. A tertiary interaction that links active-site domains to the 5′ splice site of a group II intron. Nature406, 315–318 (2000). ArticleADSCASPubMed Google Scholar
Chu, V. T., Adamidi, C., Liu, Q., Perlman, P. S. & Pyle, A. M. Control of branch-site choice by a group II intron. EMBO J.20, 6866–6876 (2001). ArticleCASPubMedPubMed Central Google Scholar
Zhang, L. & Doudna, J. A. Structural insights into group II intron catalysis and branch-site selection. Science295, 2084–2088 (2002). ArticleADSCASPubMed Google Scholar
Costa, M., Michel, F. & Westhof, E. A three-dimensional perspective on exon binding by a group II self-splicing intron. EMBO J.19, 5007–5018 (2000). ArticleCASPubMedPubMed Central Google Scholar
Swisher, J., Duarte, C. M., Su, L. J. & Pyle, A. M. Visualizing the solvent-inaccessible core of a group II intron ribozyme. EMBO J.20, 2051–2061 (2001). ArticleCASPubMedPubMed Central Google Scholar
Yang, J., Zimmerly, S., Perlman, P. S. & Lambowitz, A. M. Efficient integration of an intron RNA into double-stranded DNA by reverse splicing. Nature381, 332–335 (1996). ArticleADSCASPubMed Google Scholar
Frank, D. N. & Pace, N. R. Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem.67, 153–180 (1998). ArticleCASPubMed Google Scholar
Warnecke, J. M., Held, R., Busch, S. & Hartmann, R. K. Role of metal ions in the hydrolysis reaction catalyzed by RNase P RNA from Bacillus subtilis. J. Mol. Biol.290, 433–445 (1999). ArticleCASPubMed Google Scholar
Warnecke, J. M., Sontheimer, E. J., Piccirilli, J. A. & Hartmann, R. K. Active site constraints in the hydrolysis reaction catalyzed by bacterial RNase P: analysis of precursor tRNAs with a single 3′-S-phosphorothiolate internucleotide linkage. Nucleic Acids Res.28, 720–727 (2000). ArticleCASPubMedPubMed Central Google Scholar
Westhof, E. & Altman, S. Three-dimensional working model of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli. Proc. Natl Acad. Sci. USA91, 5133–5137 (1994). ArticleADSCASPubMedPubMed Central Google Scholar
Harris, M. E., Kazantsev, A. V., Chen, J. L. & Pace, N. R. Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking. RNA3, 561–576 (1997). CASPubMedPubMed Central Google Scholar
Frank, D. N., Adamidi, C., Ehringer, M. A., Pitulle, C. & Pace, N. R. Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA. RNA6, 1895–1904 (2000). ArticleCASPubMedPubMed Central Google Scholar
Xiao, S., Houser-Scott, F. & Engelke, D. R. Eukaryotic ribonuclease P: increased complexity to cope with the nuclear pre-tRNA pathway. J. Cell. Physiol.187, 11–20 (2001). ArticleCASPubMedPubMed Central Google Scholar
Tesmer, J. J. et al. Two-metal-ion catalysis in adenylyl cyclase. Science285, 756–760 (1999). ArticleCASPubMed Google Scholar
Wyckoff, H. W. et al. The three-dimensional structure of ribonuclease-S. Interpretation of an electron density map at a nominal resolution of 2 Å. J. Biol. Chem.245, 305–328 (1970). CASPubMed Google Scholar
Drum, C. L. et al. Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin. Nature415, 396–402 (2002). ArticleADSCASPubMed Google Scholar
Treiber, D. K. & Williamson, J. R. Exposing the kinetic traps in RNA folding. Curr. Opin. Struct. Biol.9, 339–345 (1999). ArticleCASPubMed Google Scholar
Thirumalai, D., Lee, N., Woodson, S. A. & Klimov, D. Early events in RNA folding. Annu. Rev. Phys. Chem.52, 751–762 (2001). ArticleADSCASPubMed Google Scholar
Treiber, D. K. & Williamson, J. R. Beyond kinetic traps in RNA folding. Curr. Opin. Struct. Biol.11, 309–314 (2001). ArticleCASPubMed Google Scholar
Zhuang, X. et al. A single-molecule study of RNA catalysis and folding. Science288, 2048–2051 (2000). ArticleADSCASPubMed Google Scholar
Liphardt, J., Onoa, B., Smith, S. B., Tinoco, I. J. & Bustamante, C. Reversible unfolding of single RNA molecules by mechanical force. Science292, 733–737 (2001). ArticleADSCASPubMed Google Scholar
Russell, R. et al. Exploring the folding landscape of a structured RNA. Proc. Natl Acad. Sci. USA99, 155–160 (2002). ArticleADSCASPubMed Google Scholar
Caprara, M. G., Mohr, G. & Lambowitz, A. M. A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core. J. Mol. Biol.257, 512–531 (1996). ArticleCASPubMed Google Scholar
Weeks, K. M. & Cech, T. R. Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science271, 345–348 (1996). ArticleADSCASPubMed Google Scholar
Chanfreau, G. & Jacquier, A. An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J.15, 3466–3476 (1996). ArticleCASPubMedPubMed Central Google Scholar
Cohen, S. B. & Cech, T. R. Dynamics of thermal motions within a large catalytic RNA investigated by cross-linking with thiol-disulfide interchange. J. Am. Chem. Soc.119, 6259–6268 (1997). ArticleCAS Google Scholar
Profenno, L. A., Kierzek, R., Testa, S. M. & Turner, D. H. Guanosine binds to the Tetrahymena ribozyme in more than one step, and its 2′-OH and the nonbridging pro-Sp phosphoryl oxygen at the cleavage site are required for productive docking. Biochemistry36, 12477–12485 (1997). ArticleCASPubMed Google Scholar
Murchie, A. I., Thomson, J. B., Walter, F. & Lilley, D. M. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol. Cell1, 873–881 (1998). ArticleCASPubMed Google Scholar
Andersen, A. A. & Collins, R. A. Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis. Mol. Cell5, 469–478 (2000). ArticleCASPubMed Google Scholar
Noller, H. F., Hoffarth, V. & Zimniak, L. Unusual resistance of peptidyl transferase to protein extraction procedures. Science256, 1416–1419 (1992). ArticleADSCASPubMed Google Scholar
Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science289, 905–920 (2000). ArticleADSCASPubMed Google Scholar
Welch, M., Chastang, J. & Yarus, M. An inhibitor of ribosomal peptidyl transferase using transition-state analogy. Biochemistry34, 385–390 (1995). ArticleCASPubMed Google Scholar
Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. The structural basis of ribosome activity in peptide bond synthesis. Science289, 920–930 (2000). ArticleADSCASPubMed Google Scholar
Polacek, N., Gaynor, M., Yassin, A. & Mankin, A. S. Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature411, 498–501 (2001). ArticleADSCASPubMed Google Scholar
Thompson, J. et al. Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit. Proc. Natl Acad. Sci. USA98, 9002–9007 (2001). ArticleADSCASPubMedPubMed Central Google Scholar
Murray, J. M. & Doudna, J. A. Creative catalysis: pieces of the RNA world jigsaw. Trends Biochem. Sci.26, 699–701 (2001). ArticleCASPubMed Google Scholar
Kumar, R. K. & Yarus, M. RNA-catalyzed amino acid activation. Biochemistry40, 6998–7004 (2001). ArticleCASPubMed Google Scholar
Collins, C. A. & Guthrie, C. The question remains: is the spliceosome a ribozyme? Nature Struct. Biol.7, 850–854 (2000). ArticleCASPubMed Google Scholar
Yean, S. L., Wuenschell, G., Termini, J. & Lin, R. J. Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome. Nature408, 881–884 (2000). ArticleADSCASPubMedPubMed Central Google Scholar
Valadkhan, S. & Manley, J. L. Splicing-related catalysis by protein-free snRNAs. Nature413, 701–707 (2001). ArticleADSCASPubMed Google Scholar