Tertiary architecture of the Oceanobacillus iheyensis group II intron

RNA

Volumn 16, Issue 1, 2010, Pages 57-69

  Toor, Navtej ^a,d   Keating, Kevin S ^a   Fedorova, Olga ^a   Rajashankar, Kanagalaghatta ^b   Wang, Jimin ^a   Pyle, Anna Marie ^a,c  

^a YALE UNIVERSITY   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Group II intron; Ribozyme; RNA tertiary structure; X ray crystallography

Indexed keywords

RIBOSE; RIBOZYME; RNA; BACTERIAL RNA;

ARTICLE; BACILLUS; CRYSTAL STRUCTURE; GENETIC CONSERVATION; GENETIC VARIABILITY; INTRON; MOLECULAR STABILITY; NONHUMAN; OCEANOBACILLUS IHEYENSIS; PRIORITY JOURNAL; RNA STRUCTURE; SPLICEOSOME; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RNA SPLICING;

EUKARYOTA; OCEANOBACILLUS IHEYENSIS;

BACILLUS; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; INTRONS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA SPLICING; RNA, BACTERIAL; RNA, CATALYTIC;

EID: 75649084603     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1844010     Document Type: Article

References (75)

1. Abramovitz DL, Friedman RA, Pyle AM. 1996. Catalytic role of 2′-hydroxyl groups within a group II intron active site. Science 271: 1410-1413. (Pubitemid 26089475)
2. Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC. 2002. PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58: 1948-1954.
3. Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA. 2004. Crystal structure of a self-splicing group I intron with both exons. Nature 430: 45-50. (Pubitemid 38915218)
4. Bonen L, Vogel J. 2001. The ins and outs of group II introns. Trends Genet 17: 322-331.
5. Boudvillain M, Pyle AM. 1998.Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: A NAIM analysis. EMBO J 17: 7091-7104. (Pubitemid 28550302)
6. Boudvillain M, de Lencastre A, Pyle AM. 2000. A new RNA tertiary interaction that links active-site domains of a group II intron and anchors them at the site of catalysis. Nature 406: 315-318.
7. Brunger AT. 2007. Version 1.2 of the crystallography and NMR system. Nat Protoc 2: 2728-2733.
8. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, et al. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54: 905-921.
9. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. 1996. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273: 1678-1685. (Pubitemid 26317777)
10. Chanfreau G, Jacquier A. 1994. Catalytic site components common to both splicing steps of a group II intron. Science 266: 1383-1387.
11. Chu V-T, Liu Q, Podar M, Perlman PS, Pyle AM. 1998. More than one way to splice an RNA: Branching without a bulge and splicing without branching in group II introns. RNA 4: 1186-1202. (Pubitemid 28457850)
12. Costa M, Michel F. 1997. Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution. EMBO J 16: 3289-3302. (Pubitemid 27234966)
13. Costa M, Deme E, Jacquier A, Michel F. 1997. Multiple tertiary interactions involving domain II of group II self- splicing introns. J Mol Biol 267: 520-536. (Pubitemid 27170679)
14. Costa M, Christian EL, Michel F. 1998. Differential chemical probing of a group II self-splicing intron identifies bases involved in tertiary interactions and supports an alternative secondary structure model of domain V. RNA 4: 1055-1068. (Pubitemid 28413453)
15. Costa M, Michel F, Westhof E. 2000. A three-dimensional perspective on exon binding by a group II self-splicing intron. EMBO J 19: 5007-5018.
16. Dai L, Chai D, Gu SQ, Gabel J, Noskov SY, Blocker FJ, Lambowitz AM, Zimmerly S. 2008. A three-dimensional model of a group II intron RNA and its interaction with the intron-encoded reverse transcriptase. Mol Cell 30: 472-485.
17. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB III, Snoeyink J, Richardson JS, et al. 2007. MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35: W375-W383.
18. Dayie KT, Padgett RA. 2008. A glimpse into the active site of a group II intron and maybe the spliceosome, too. RNA 14: 1697-1703.
19. de Lencastre A, Hamill S, Pyle AM. 2005. A single active-site region for a group II intron. Nat Struct Mol Biol 12: 626-627. (Pubitemid 40980815)
20. Dib-Hajj SD, Boulanger SC, Hebbar SK, Peebles CL, Franzen JS, Perlman PS. 1993. Domain 5 interacts with domain 6 and influences the second transesterification reaction of group II intron self-splicing. Nucleic Acids Res 21: 1797-1804.
21. Dieckmann T, Suzuki E, Nakamura GK, Feigon J. 1996. Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA 2: 628-640. (Pubitemid 26374215)
22. Emsley P, Cowtan K. 2004. Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132. (Pubitemid 41742764)
23. England TE, Uhlenbeck OC. 1978. 3′-Terminal labelling of RNA with T4 RNA ligase. Nature 275: 560-561.
24. Fedorova O, Pyle AM. 2005. Linking the group II intron catalytic domains: Tertiary contacts and structural features of domain 3. EMBO J 24: 3906-3916. (Pubitemid 41637997)
25. Fedorova O, Pyle AM. 2008. A conserved element that stabilizes the group II intron active site. RNA 14: 1048-1056. (Pubitemid 351717486)
26. Fedorova O, Boudvillain M, Kawaoka J, Pyle AM. 2005. Nucleotide analog interference mapping and suppression: specific applications in studies of RNA tertiary structure, dynamic helicase mechanism and RNA-protein interactions. Wiley-VCH, Weinheim.
27. Ferré-D'Amaré AR, Zhou K, Doudna JA. 1998. Crystal structure of a hepatitis delta virus ribozyme. Nature 395: 567-574. (Pubitemid 28475703)
28. Franzen JS, Zhang M, Peebles CL. 1993. Kinetic analysis of the 5′-splice junction hydrolysis of a group II intron promoted by domain 5. Nucleic Acids Res 21: 627-634. (Pubitemid 23155554)
29. Gordon PM, Piccirilli JA. 2001. Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis. Nat Struct Biol 8: 893-898.
30. Gordon PM, Fong R, Piccirilli JA. 2007. A second divalent metal ion in the group II intron reaction center. Chem Biol 14: 607-612. (Pubitemid 46920986)
31. Granlund M, Michel F, Norgren M. 2001. Mutually exclusive distribution of IS1548 and GBSi1, an active group II intron identified in human isolates of group B streptococci. J Bacteriol 183: 2560-2569. (Pubitemid 32249765)
32. Hamill S, Pyle AM. 2006. The receptor for branch-site docking within a group II intron active site. Mol Cell 23: 831-840. (Pubitemid 44344513)
33. Harris-Kerr CL, Zhang M, Peebles CL. 1993. The phylogenetically predicted base-pairing interaction between a and α′ is required for group II splicing in vitro. Proc Natl Acad Sci 90: 10658-10662. (Pubitemid 23347101)
34. Jacquier A, Michel F. 1987. Multiple exon-binding sites in class II self-splicing introns. Cell 50: 17-29.
35. Jacquier A, Michel F. 1990. Base-pairing interactions involving the 5′ and 3′-terminal nucleotides of group II self-splicing introns. J Mol Biol 213: 437-447. (Pubitemid 20194524)
36. Jaeger L, Michel F, Westhof E. 1994. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J Mol Biol 236: 1271-1276. (Pubitemid 24147450)
37. Jaeger L, Verzemnieks EJ, Geary C. 2009. The UA-handle: A versatile submotif in stable RNA architectures. Nucleic Acids Res 37: 215-230.
38. Jarrell K, Dietrich R, Perlman P. 1988. Group II Intron domain 5 facilitates a trans-splicing reaction. Mol Cell Biol 8: 2361-2366.
39. Jestin J-L, Deme E, Jacquier A. 1997. Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron. EMBO 16: 2945-2954. (Pubitemid 27226230)
40. Keating KS, Toor N, Pyle AM. 2008. The GANC tetraloop: A novel motif in the group IIC intron structure. J Mol Biol 383: 475-481.
41. Koch JL, Boulanger SC, Dib-Hajj SD, Hebbar SK, Perlman PS. 1992. Group II Introns deleted for multiple substructures retain selfsplicing activity. Mol Cell Biol 12: 1950-1958.
42. Konforti BB, Abramovitz DL, Duarte CM, Karpeisky A, Beigelman L, Pyle AM. 1998. Ribozyme catalysis from the major groove of group II intron domain 5. Mol Cell 1: 433-441. (Pubitemid 128378891)
43. Krasilnikov AS, Mondragon A. 2003. On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA 9: 640-643. (Pubitemid 36618191)
44. Lambowitz AM, Zimmerly S. 2004. Mobile group II introns. Annu Rev Genet 38: 1-35.
45. Lee JC, Cannone JJ, Gutell RR. 2003. The lonepair triloop: A new motif in RNA structure. J Mol Biol 325: 65-83.
46. Lehmann K, Schmidt U. 2003. Group II introns: Structure and catalytic versatility of large natural ribozymes. Crit Rev Biochem Mol Biol 38: 249-303. (Pubitemid 36793893)
47. Leontis NB, Westhof E. 1998. A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs. J Mol Biol 283: 571-583. (Pubitemid 28486721)
48. Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512. (Pubitemid 32416808)
49. Mattick JS. 1994. Introns: Evolution and function. Curr Opin Genet Dev 4: 823-831.
50. Mattick JS. 2001. Noncoding RNAs: The architects of eukaryotic complexity. EMBO Rep 2: 986-991.
51. Michel F, Umesono K, Ozeki H. 1989. Comparative and functional anatomy of group II catalytic introns - A review. Gene 82: 5-30. (Pubitemid 19248654)
52. Michel F, Costa M, Massire C, Westhof E. 2000. Modeling RNA tertiary structure from patterns of sequence variation. Methods Enzymol 317: 491-510. (Pubitemid 30418102)
53. Michel F, Costa M, Westhof E. 2009. The ribozyme core of group II introns: A structure in want of partners. Trends Biochem Sci 34: 189-199.
54. Nagaswamy U, Fox GE. 2002. Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs. RNA 8: 1112-1119. (Pubitemid 35024567)
55. Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA. 2001. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc Natl Acad Sci 98: 4899-4903. (Pubitemid 32397054)
56. 2+ concentration on group II intron RNA folding investigated by UV cross-linking. Biochemistry 42: 12466-12480.
57. Pley HW, Flaherty KM, McKay DB. 1994. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372: 111-113.
58. 2+-dependent cross-link traps an active form of domain 3 of a self-splicing group II intron. RNA 1: 828-840.
59. Pyle AM, Green JB. 1994. Building a kinetic framework for group II intron ribozyme activity: Quantitation of interdomain binding and reaction rate. Biochemistry 33: 2716-2725.
60. Pyle AM, Lambowitz AM. 2006. Group II introns: Ribozymes that splice RNA and invade DNA. In The RNA world (ed. R Gesteland et al.), pp. 469-506. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
61. Pyle AM, Chu VT, Jankowsky E, Boudvillain M. 2000. Using DNAzymes to cut, process and map RNA molecules for structural studies or modification. Methods Enzymol 317: 140-146. (Pubitemid 30418083)
62. Pyle AM, Fedorova O, Waldsich C. 2007. Folding of group II introns: A model system for large, multidomain RNAs? Trends Biochem Sci 32: 138-145.
63. Rest JS, Mindell DP. 2003. Retroids in Archaea: Phylogeny and lateral origins. Mol Biol Evol 20: 1134-1142.
64. Ryder SP, Ortoleva-Donnelly L, Kosek AB, Strobel SA. 2000. Chemical probing of RNA by nucleotide analog interference mapping. Methods Enzymol 317: 92-109. (Pubitemid 30418079)
65. Sontheimer EJ, Gordon PM, Piccirilli JA. 1999. Metal ion catalysis during group II intron self-splicing: Parallels with the spliceosome. Genes & Dev 13: 1729-1741. (Pubitemid 29325877)
66. Su L, Qin P, Michels W, Pyle A. 2001. Guiding ribozyme cleavage through motif recognition: The mechanism of cleavage site selection by a Group II intron ribozyme. J Mol Biol 306: 665-668. (Pubitemid 33027690)
67. Swisher J, Duarte C, Su L, Pyle A. 2001. Visualizing the solvent-inaccessible core of a group II intron ribozyme. EMBO J 20: 2051-2061. (Pubitemid 32397406)
68. Toor N, Hausner G, Zimmerly S. 2001. Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7: 1142-1152. (Pubitemid 32726912)
69. Toor N, Robart AR, Christianson J, Zimmerly S. 2006. Self-splicing of a group IIC intron: 5′ exon recognition and alternative 5′ splicing events implicate the stem-loop motif of a transcriptional terminator. Nucleic Acids Res 34: 6461-6471. (Pubitemid 46017943)
70. Toor N, Keating KS, Taylor SD, Pyle AM. 2008a. Crystal structure of a self-spliced group II intron. Science 320: 77-82. (Pubitemid 351490756)
71. Toor N, Rajashankar K, Keating KS, Pyle AM. 2008b. Structural basis for exon recognition by a group II intron. Nat Struct Mol Biol 15: 1221-1222.
72. Toor N, Keating KS, Pyle AM. 2009. Structural insights into RNA splicing. Curr Opin Struct Biol 19: 260-266.
73. Vogel J, Borner T. 2002. Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing. EMBO J 21: 3794-3803. (Pubitemid 34787052)
74. Waldsich C, Masquida B, Westhof E, Schroeder R. 2002. Monitoring intermediate folding states of the td group I intron in vivo. EMBO J 21: 5281-5291.
75. Zimmerly S, Hausner G, Wu X. 2001. Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res 29: 1238-1250. (Pubitemid 32186211)