Now on display: A gallery of group II intron structures at different stages of catalysis

Mobile DNA

Volumn 4, Issue 1, 2013, Pages

  Marcia, Marco ^a   Somarowthu, Srinivas ^a   Pyle, Anna Marie ^a,b  

^a YALE UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Metal ions; Retrotransposition; RNA catalysis; Spliceosome; X ray structures

Indexed keywords

ADENOSINE; CALCIUM ION; GUANOSINE; MAGNESIUM ION; OXYGEN; PHOSPHODIESTERASE; PHOSPHORUS; SODIUM ION;

AMINO ACID SUBSTITUTION; BINDING SITE; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTALLOGRAPHY; EXON; GENE REARRANGEMENT; GENE SEQUENCE; HYDROLYSIS; INTRON; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; REVIEW; RNA SPLICING; SITE DIRECTED MUTAGENESIS; SPLICEOSOME; TRANSESTERIFICATION;

EUKARYOTA;

EID: 84878580948     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/1759-8753-4-14     Document Type: Review

References (81)

1. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Michel F, Jacquier A, Dujon B, Biochimie 1982 64 867 881 10.1016/S0300-9084(82)80349-0 6817818
2. Introns: evolution and function. Mattick JS, Curr Opin Genet Dev 1994 4 823 831 10.1016/0959-437X(94)90066-3 7888751
3. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Koonin EV, Biol Direct 2006 1 22 10.1186/1745-6150-1-22 16907971
4. Group II introns: ribozymes that splice RNA and invade DNA. Pyle AM, Lambowitz AM, The RNA World Cold Spring Harbor: Cold Spring Harbor Press, Gesteland RF, Cech TR, Atkins JF, 3 2006 469 505
5. Splicing of the Sinorhizobium meliloti RmInt1 group II intron provides evidence of retroelement behavior. Chillon I, Martinez-Abarca F, Toro N, Nucleic Acids Res 2011 39 1095 1104 10.1093/nar/gkq847 20876688
6. The generality of self-splicing RNA: relationship to nuclear mRNA splicing. Cech TR, Cell 1986 44 207 210 10.1016/0092-8674(86)90751-8 2417724
7. Retroids in archaea: phylogeny and lateral origins. Rest JS, Mindell DP, Mol Biol Evol 2003 20 1134 1142 10.1093/molbev/msg135 12777534
8. Five easy pieces. Sharp PA, Science 1991 254 663 10.1126/science.1948046 1948046
9. Use of RmInt1, a group IIB intron lacking the intron-encoded protein endonuclease domain, in gene targeting. Garcia-Rodriguez FM, Barrientos-Duran A, Diaz-Prado V, Fernandez-Lopez M, Toro N, Applied and Environmental Microbiology 2011 77 854 861 10.1128/AEM.02319-10 21115708
10. Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Guo H, Karberg M, Long M, Jones JP 3rd, Sullenger B, Lambowitz AM, Science 2000 289 452 457 10.1126/science.289.5478.452 10903206
11. Group II intron-based gene targeting reactions in eukaryotes. Mastroianni M, Watanabe K, White TB, Zhuang F, Vernon J, Matsuura M, Wallingford J, Lambowitz AM, PLoS One 2008 3 3121 10.1371/journal.pone.0003121 18769669
12. A glimpse into the active site of a group II intron and maybe the spliceosome, too. Dayie KT, Padgett RA, RNA 2008 14 1697 1703 10.1261/rna.1154408 18658120
13. Group II intron self-splicing. Alternative reaction conditions yield novel products. Jarrell KA, Peebles CL, Dietrich RC, Romiti SL, Perlman PS, J Biol Chem 1988 263 3432 3439 2830285
14. Deletion of a conserved dinucleotide inhibits the second step of group II intron splicing. Mikheeva S, Murray HL, Zhou H, Turczyk BM, Jarrell KA, RNA 2000 6 1509 1515 10.1017/S1355838200000972 11105751
15. Stereochemical selectivity of group II intron splicing, reverse splicing, and hydrolysis reactions. Podar M, Perlman PS, Padgett RA, Mol Cell Biol 1995 15 4466 4478 7542746
16. Group II introns in eubacteria and archaea: ORF-less introns and new varieties. Simon DM, Clarke NA, McNeil BA, Johnson I, Pantuso D, Dai L, Chai D, Zimmerly S, RNA 2008 14 1704 1713 10.1261/rna.1056108 18676618
17. Phylogenetic relationships among group II intron ORFs. Zimmerly S, Hausner G, Wu X, Nucleic Acids Res 2001 29 1238 1250 10.1093/nar/29.5.1238 11222775
18. Comparative and functional anatomy of group II catalytic introns-a review. Michel F, Umesono K, Ozeki H, Gene 1989 82 5 30 10.1016/0378-1119(89) 90026-7 2684776
19. The architectural organization and mechanistic function of group II intron structural elements. Qin PZ, Pyle AM, Curr Opin Struct Biol 1998 8 301 308 10.1016/S0959-440X(98)80062-6 9666325
20. Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. Toor N, Hausner G, Zimmerly S, RNA 2001 7 1142 1152 10.1017/S1355838201010251 11497432
21. The tertiary structure of group II introns: implications for biological function and evolution. Pyle AM, Crit Rev Biochem Mol Biol 2010 45 215 232 10.3109/10409231003796523 20446804
22. A group II self-splicing intron from the brown alga Pylaiella littoralis is active at unusually low magnesium concentrations and forms populations of molecules with a uniform conformation. Costa M, Fontaine JM, Loiseaux-de Goer S, Michel F, J Mol Biol 1997 274 353 364 10.1006/jmbi.1997.1416 9405145
23. A three-dimensional model of a group II intron RNA and its interaction with the intron-encoded reverse transcriptase. Dai L, Chai D, Gu SQ, Gabel J, Noskov SY, Blocker FJ, Lambowitz AM, Zimmerly S, Mol Cell 2008 30 472 485 10.1016/j.molcel.2008.04.001 18424209
24. A single active-site region for a group II intron. de Lencastre A, Hamill S, Pyle AM, Nat Struct Mol Biol 2005 12 626 627 10.1038/nsmb957 15980867
25. The receptor for branch-site docking within a group II intron active site. Hamill S, Pyle AM, Mol Cell 2006 23 831 840 10.1016/j.molcel.2006.07.017 16973435
26. Crystal structure of a self-spliced group II intron. Toor N, Keating KS, Taylor SD, Pyle AM, Science 2008 320 77 82 10.1126/science.1153803 18388288
27. Tertiary architecture of the Oceanobacillus iheyensis group II intron. Toor N, Keating KS, Fedorova O, Rajashankar K, Wang J, Pyle AM, RNA 2010 16 57 69 10.1261/rna.1844010 19952115
28. Linking the branchpoint helix to a newly found receptor allows lariat formation by a group II intron. Li CF, Costa M, Michel F, Embo J 2011 30 3040 3051 10.1038/emboj.2011.214 21712813
29. Crystal structure of a group II intron in the pre-catalytic state. Chan RT, Robart AR, Rajashankar KR, Pyle AM, Toor N, Nat Struct Mol Biol 2012 19 555 557 10.1038/nsmb.2270 22484319
30. Visualizing group II intron catalysis through the stages of splicing. Marcia M, Pyle AM, Cell 2012 151 497 507 10.1016/j.cell.2012.09.033 23101623
31. Structural basis for exon recognition by a group II intron. Toor N, Rajashankar K, Keating KS, Pyle AM, Nat Struct Mol Biol 2008 15 1221 1222 10.1038/nsmb.1509 18953333
32. Catalytic role of 2′-hydroxyl groups within a group II intron active site. Abramovitz DL, Friedman RA, Pyle AM, Science 1996 271 1410 1413 10.1126/science.271.5254.1410 8596912
33. Studies of point mutants define three essential paired nucleotides in the domain 5 substructure of a group II intron. Boulanger SC, Belcher SM, Schmidt U, Dib-Hajj SD, Schmidt T, Perlman PS, Mol Cell Biol 1995 15 4479 4488 7623838
34. Catalytic site components common to both splicing steps of a group II intron. Chanfreau G, Jacquier A, Science 1994 266 1383 1387 10.1126/science. 7973729 7973729
35. Catalytically critical nucleotide in domain 5 of a group II intron. Peebles CL, Zhang M, Perlman PS, Franzen JS, Proc Natl Acad Sci USA 1995 92 4422 4426 10.1073/pnas.92.10.4422 7538669
36. Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: phenotypes and suppressor mutations. Schmidt U, Podar M, Stahl U, Perlman PS, RNA 1996 2 1161 1172 8903346
37. Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases. Vipond IB, Baldwin GS, Halford SE, Biochemistry 1995 34 697 704 10.1021/bi00002a037 7819265
38. Divalent metal ions tune the self-splicing reaction of the yeast mitochondrial group II intron Sc.ai5γ Erat MC, Sigel RK, J Biol Inorg Chem 2008 13 1025 1036 10.1007/s00775-008-0390-7 18528718
39. PvuII endonuclease contains two calcium ions in active sites. Horton JR, Cheng X, J Mol Biol 2000 300 1049 1056 10.1006/jmbi.2000.3938 10903853
40. Effects of divalent metal ions on individual steps of the Tetrahymena ribozyme reaction. McConnell TS, Herschlag D, Cech TR, Biochemistry 1997 36 8293 8303 10.1021/bi9700678 9204875
41. Three metal ions participate in the reaction catalyzed by T5 flap endonuclease. Syson K, Tomlinson C, Chapados BR, Sayers JR, Tainer JA, Williams NH, Grasby JA, J Biol Chem 2008 283 28741 28746 10.1074/jbc.M801264200 18697748
42. The role of metals in catalysis by the restriction endonuclease BamHI. Viadiu H, Aggarwal AK, Nat Struct Biol 1998 5 910 916 10.1038/2352 9783752
43. Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease. Martin AM, Horton NC, Lusetti S, Reich NO, Perona JJ, Biochemistry 1999 38 8430 8439 10.1021/bi9905359 10387089
44. Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions. Vipond IB, Halford SE, Biochemistry 1995 34 1113 1119 10.1021/bi00004a002 7827059
45. Symmetry and structure. Cotton AF, Wilkinson G, Advanced Organic Chemistry:A comprehensive text New York, USA: John Wiley and Sons, Inc 4 1980 58 59
46. More mistakes by T7 RNA polymerase at the 5′ ends of in vitro-transcribed RNAs. Helm M, Brule H, Giege R, Florentz C, RNA 1999 5 618 621 10.1017/S1355838299982328 10334331
47. T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates. Pleiss JA, Derrick ML, Uhlenbeck OC, RNA 1998 4 1313 1317 10.1017/S135583829800106X 9769105
48. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Sampson JR, Uhlenbeck OC, Proc Natl Acad Sci USA 1988 85 1033 1037 10.1073/pnas.85.4.1033 3277187
49. Multiple exon-binding sites in class II self-splicing introns. Jacquier A, Michel F, Cell 1987 50 17 29 10.1016/0092-8674(87)90658-1 3297351
50. Two competing pathways for self-splicing by group II introns: a quantitative analysis of in vitro reaction rates and products. Daniels DL, Michels WJ Jr, Pyle AM, J Mol Biol 1996 256 31 49 10.1006/jmbi.1996.0066 8609612
51. Control of branch-site choice by a group II intron. Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM, Embo J 2001 20 6866 6876 10.1093/emboj/20.23.6866 11726522
52. Branch nucleophile selection in pre-mRNA splicing: evidence for the bulged duplex model. Query CC, Moore MJ, Sharp PA, Genes Dev 1994 8 587 597 10.1101/gad.8.5.587 7926752
53. Three recognition events at the branch-site adenine. Query CC, Strobel SA, Sharp PA, Embo J 1996 15 1392 1402 8635472
54. Conformation of the Group II intron branch site in solution. Schlatterer JC, Crayton SH, Greenbaum NL, J Am Chem Soc 2006 128 3866 3867 10.1021/ja0578754 16551067
55. More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns. Chu VT, Liu Q, Podar M, Perlman PS, Pyle AM, RNA 1998 4 1186 1202 10.1017/S1355838298980724 9769094
56. Internal bulge and tetraloop of the catalytic domain 5 of a group II intron ribozyme are flexible: implications for catalysis. Eldho NV, Dayie KT, J Mol Biol 2007 365 930 944 10.1016/j.jmb.2006.10.037 17098254
57. Multiple tertiary interactions involving domain II of group II self-splicing introns. Costa M, Deme E, Jacquier A, Michel F, J Mol Biol 1997 267 520 536 10.1006/jmbi.1996.0882 9126835
58. Ho Faix P, Conserved Nucleotides in the Joining Segment Between Domains 2 and 3 are Important for Group II Intron Splicing: University of Pittsburgh 1998
59. An RNA conformational change between the two chemical steps of group II self-splicing. Chanfreau G, Jacquier A, Embo J 1996 15 3466 3476 8670849
60. A three-dimensional perspective on exon binding by a group II self-splicing intron. Costa M, Michel F, Westhof E, Embo J 2000 19 5007 5018 10.1093/emboj/19.18.5007 10990464
61. Base-pairing interactions involving the 5′ and 3′-terminal nucleotides of group-II self-splicing introns. Jacquier A, Michel F, J Mol Biol 1990 213 437 447 10.1016/S0022-2836(05)80206-2 2191139
62. Interaction of intronic boundaries is required for the 2nd splicing step efficiency of a group-II intron. Chanfreau G, Jacquier A, Embo J 1993 12 5173 5180 8262060
63. The stereochemical course of group II intron self-splicing. Padgett RA, Podar M, Boulanger SC, Perlman PS, Science 1994 266 1685 1688 10.1126/science.7527587 7527587
64. Structural metals in the group I intron: a ribozyme with a multiple metal ion core. Stahley MR, Adams PL, Wang J, Strobel SA, J Mol Biol 2007 372 89 102 10.1016/j.jmb.2007.06.026 17612557
65. Solid-state 87Rb NMR signatures for rubidium cations bound to a G-quadruplex. Ida R, Wu G, 2005 Sep 14 2005 34 4294 4296 Epub 2005 Aug 2 10.1039/B505674H
66. Thallium-205 nuclear magnetic resonance study of the thallium(I)- gramicidin A association in trifluoroethanol. Turner GL, Hinton JF, Millett FS, Biochemistry 1982 21 646 651 10.1021/bi00533a008 6176261
67. The role of metal ions in RNA biochemistry. Feig AL, Uhlenbeck OC, The RNA World New York: Cold Spring Harbor Laboratory Press, Gesteland RF, Cech TR, Atkins JF, 2 1999 287 320
68. Retrotransposition of a bacterial group II intron. Cousineau B, Lawrence S, Smith D, Belfort M, Nature 2000 404 1018 1021 10.1038/35010029 10801134
69. The two steps of group II intron self-splicing are mechanistically distinguishable. Podar M, Perlman PS, Padgett RA, RNA 1998 4 890 900 10.1017/S1355838298971643 9701281
70. A general two-metal-ion mechanism for catalytic RNA. Steitz TA, Steitz JA, Proc Natl Acad Sci USA 1993 90 6498 6502 10.1073/pnas.90.14.6498 8341661
71. A structural analysis of the group II intron active site and implications for the spliceosome. Keating KS, Toor N, Perlman PS, Pyle AM, RNA 2010 16 1 9 10.1261/rna.1791310 19948765
72. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Madhani HD, Guthrie C, Cell 1992 71 803 817 10.1016/0092-8674(92)90556-R 1423631
73. Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome. Yean SL, Wuenschell G, Termini J, Lin RJ, Nature 2000 408 881 884 10.1038/35048617 11130730
74. Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps. Mefford MA, Staley JP, RNA 2009 15 1386 1397 10.1261/rna.1582609 19458033
75. Two domains of yeast U6 small nuclear RNA required for both steps of nuclear precursor messenger RNA splicing. Fabrizio P, Abelson J, Science 1990 250 404 409 10.1126/science.2145630 2145630
76. Splicing function of mammalian U6 small nuclear RNA: conserved positions in central domain and helix I are essential during the first and second step of pre-mRNA splicing. Wolff T, Menssen R, Hammel J, Bindereif A, Proc Natl Acad Sci USA 1994 91 903 907 10.1073/pnas.91.3.903 8302864
77. U6 snRNA function in nuclear pre-mRNA splicing: a phosphorothioate interference analysis of the U6 phosphate backbone. Yu YT, Maroney PA, Darzynkiwicz E, Nilsen TW, RNA 1995 1 46 54 7489488
78. Spliceosomal snRNAs: Mg§ssup§2+§esup§-dependent chemistry at the catalytic core? Villa T, Pleiss JA, Guthrie C, Cell 2002 109 149 152 10.1016/S0092-8674(02)00726-2 12007401
79. Both catalytic steps of nuclear pre-mRNA splicing are reversible. Tseng CK, Cheng SC, Science 2008 320 1782 1784 10.1126/science.1158993 18583613
80. Mechanistic insights from reversible splicing catalysis. Smith DJ, Konarska MM, RNA 2008 14 1975 1978 10.1261/rna.1289808 18755832
81. Crystal structure of Prp8 reveals active site cavity of the spliceosome. Galej WP, Oubridge C, Newman AJ, Nagai K, Nature 2013 advance online publication