Evolution of group II introns

Mobile DNA

Volumn 6, Issue 1, 2015, Pages

  Zimmerly, Steven ^a   Semper, Cameron ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

Mobile DNA; Molecular evolution; Retroelement; Ribozyme; Spliceosome

Indexed keywords

RIBONUCLEOPROTEIN; RIBOZYME; RNA;

ALTERNATIVE RNA SPLICING; ARCHAEON; BACTERIUM; BINDING SITE; CHLOROPLAST; EXON; GENE LOCUS; GENE STRUCTURE; GROUP II INTRON; HOUSEKEEPING GENE; INTRON; MITOCHONDRION; MOLECULAR PHYLOGENY; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; REVIEW; RNA SPLICING; SPLICEOSOME; TRANS SPLICING;

EUKARYOTA;

EID: 84928892707     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/s13100-015-0037-5     Document Type: Review

References (203)

1. L Bonen J Vogel 2001 The ins and outs of group II introns Trends Genet 17 322 31 1:CAS:528:DC%2BD3MXjslSiu7g%3D 11377794
2. Belfort M, Derbyshire V, Parker MM, Cousineau B, Lambowitz AM. Mobile introns: pathways and proteins. In: Craig NL, Craigie R, Gellert M, Lambowitz AM, editors. Mobile DNA II. Washington, DC: ASM Press Publishers; 2002. p. 761-83.
3. K Lehmann U Schmidt 2003 Group II introns: structure and catalytic versatility of large natural ribozymes Crit Rev Biochem Mol Biol 38 249 303 1:CAS:528:DC%2BD3sXlvFelsr4%3D 12870716
4. Zimmerly S. Mobile introns and retroelements in bacteria. In: Mullany P, editor. The dynamic bacterial genome. Cambridge University Press; 2005. p. 121-150.
5. N Toro JI Jimenez-Zurdo FM Garcia-Rodriguez 2007 Bacterial group II introns: not just splicing FEMS Microbiol Rev 31 342 58 1:CAS:528:DC%2BD2sXks1Grtrc%3D 17374133
6. AM Lambowitz S Zimmerly 2011 Group II introns: mobile ribozymes that invade DNA Cold Spring Harb Perspect Biol 3 a003616 3140690 20463000
7. V Knoop A Brennicke 1994 Promiscuous mitochondrial group II intron sequences in plant nuclear genomes J Mol Evol 39 144 50 1:CAS:528:DyaK2cXlsFShtro%3D 7932778
8. X Lin S Kaul S Rounsley TP Shea MI Benito CD Town, et al. 1999 Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana Nature 402 761 8 1:STN:280:DC%2BD3c%2FotlCrtQ%3D%3D 10617197
9. F Michel JL Ferat 1995 Structure and activities of group II introns Annu Rev Biochem 64 435 61 1:CAS:528:DyaK2MXmsl2qsbk%3D 7574489
10. AM Lambowitz S Zimmerly 2004 Mobile group II introns Annu Rev Genet 38 1 35 1:CAS:528:DC%2BD2MXltlOruw%3D%3D 15568970
11. O Fedorova N Zingler 2007 Group II introns: structure, folding and splicing mechanism Biol Chem 388 665 78 1:CAS:528:DC%2BD2sXnvVWktLo%3D 17570818
12. F Michel M Costa E Westhof 2009 The ribozyme core of group II introns: a structure in want of partners Trends Biochem Sci 34 189 99 1:CAS:528:DC%2BD1MXksVSkt7Y%3D 19299141
13. AM Pyle 2010 The tertiary structure of group II introns: implications for biological function and evolution Crit Rev Biochem Mol Biol 45 215 32 4408542 1:CAS:528:DC%2BC3cXmtlSjsrg%3D 20446804
14. M Marcia S Somarowthu AM Pyle 2013 Now on display: a gallery of group II intron structures at different stages of catalysis Mob DNA 4 14 3669008 1:CAS:528:DC%2BC3sXhtVSkur%2FF 23634971
15. F Michel K Umesono H Ozeki 1989 Comparative and functional anatomy of group II catalytic introns - a review Gene 82 5 30 1:CAS:528:DyaL1MXmtV2kurs%3D 2684776
16. Pyle AM, Lambowitz AM. Group II introns: ribozymes that splice RNA and invade DNA. In: Gesteland RF, Cech TR, Atkins JF, editors. The RNA world. Cold Springs Harbor, New York: Cold Springs Harbor Laboratory Press; 2006. p. 469-505.
17. N Toor K Rajashankar KS Keating AM Pyle 2008 Structural basis for exon recognition by a group II intron Nat Struct Mol Biol 15 1221 2 2735234 1:CAS:528:DC%2BD1cXhtlalsLzI 18953333
18. AR Robart RT Chan JK Peters KR Rajashankar N Toor 2014 Crystal structure of a eukaryotic group II intron lariat Nature 514 193 7 4197185 1:CAS:528:DC%2BC2cXhslaqs7jL 25252982
19. F Michel A Jacquier 1987 Long-range intron-exon and intron-intron pairings involved in self-splicing of class II catalytic introns Cold Spring Harb Symp Quant Biol 52 201 12 1:CAS:528:DyaL1cXlsVeqsbc%3D 2841064
20. A Jacquier F Michel 1990 Base-pairing interactions involving the 5′ and 3′-terminal nucleotides of group II self-splicing introns J Mol Biol 213 437 47 1:CAS:528:DyaK3cXkslagtr8%3D 2191139
21. M Costa F Michel E Westhof 2000 A three-dimensional perspective on exon binding by a group II self-splicing intron EMBO J 19 5007 18 314214 1:CAS:528:DC%2BD3cXntVartLg%3D 10990464
22. BB Konforti DL Abramovitz CM Duarte A Karpeisky L Beigelman AM Pyle 1998 Ribozyme catalysis from the major groove of group II intron domain 5 Mol Cell 1 433 41 1:CAS:528:DyaK1cXhtlyhur0%3D 9660927
23. PM Gordon JA Piccirilli 2001 Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis Nat Struct Biol 8 893 8 1:CAS:528:DC%2BD3MXnsVentbk%3D 11573097
24. C Schmelzer RJ Schweyen 1986 Self-splicing of group II introns in vitro: mapping of the branch point and mutational inhibition of lariat formation Cell 46 557 65 1:CAS:528:DyaL28Xlt12mtLg%3D 3524857
25. R van der Veen AC Arnberg G van der Horst L Bonen HF Tabak LA Grivell 1986 Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro Cell 44 225 34 2417726
26. F Michel BF Lang 1985 Mitochondrial class II introns encode proteins related to the reverse transcriptases of retroviruses Nature 316 641 3 1:CAS:528:DyaL2MXltlKhsL8%3D 2412125
27. G Mohr PS Perlman AM Lambowitz 1993 Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function Nucleic Acids Res 21 4991 7 310608 1:CAS:528:DyaK2cXisFykuw%3D%3D 8255751
28. S Zimmerly G Hausner X Wu 2001 Phylogenetic relationships among group II intron ORFs Nucleic Acids Res 29 1238 50 29734 1:CAS:528:DC%2BD3MXhvFGgsbk%3D 11222775
29. FJ Blocker G Mohr LH Conlan L Qi M Belfort AM Lambowitz 2005 Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase RNA 11 14 28 1370687 1:CAS:528:DC%2BD2MXhvFaksg%3D%3D 15574519
30. AE Gorbalenya 1994 Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family Protein Sci 3 1117 20 2142905 1:CAS:528:DyaK2MXit1yhtQ%3D%3D 7920259
31. S Zimmerly H Guo PS Perlman AM Lambowitz 1995 Group II intron mobility occurs by target DNA-primed reverse transcription Cell 82 545 54 1:CAS:528:DyaK2MXnvVWmtLw%3D 7664334
32. J San Filippo AM Lambowitz 2002 Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded protein J Mol Biol 324 933 51 1:CAS:528:DC%2BD38XpsF2kurc%3D 12470950
33. JI Jimenez-Zurdo FM Garcia-Rodriguez A Barrientos-Duran N Toro 2003 DNA target site requirements for homing in vivo of a bacterial group II intron encoding a protein lacking the DNA endonuclease domain J Mol Biol 326 413 23 1:CAS:528:DC%2BD3sXmt1Wlsg%3D%3D 12559910
34. JV Moran KL Mecklenburg P Sass SM Belcher D Mahnke A Lewin, et al. 1994 Splicing defective mutants of the COXI gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron aI2 Nucleic Acids Res 22 2057 64 308121 1:CAS:528:DyaK2cXltVWisbg%3D 8029012
35. H Wank J SanFilippo RN Singh M Matsuura AM Lambowitz 1999 A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA Mol Cell 4 239 50 1:CAS:528:DyaK1MXmtVajs7o%3D 10488339
36. M Matsuura JW Noah AM Lambowitz 2001 Mechanism of maturase-promoted group II intron splicing EMBO J 20 7259 70 125332 1:CAS:528:DC%2BD38XpsF2h 11743002
37. JW Noah AM Lambowitz 2003 Effects of maturase binding and Mg2+ concentration on group II intron RNA folding investigated by UV cross-linking Biochemistry 42 12466 80 1:CAS:528:DC%2BD3sXnvFOitr8%3D 14580192
38. X Cui M Matsuura Q Wang H Ma AM Lambowitz 2004 A group II intron-encoded maturase functions preferentially in cis and requires both the reverse transcriptase and X domains to promote RNA splicing J Mol Biol 340 211 31 1:CAS:528:DC%2BD2cXkvVKmurs%3D 15201048
39. R Saldanha B Chen H Wank M Matsuura J Edwards AM Lambowitz 1999 RNA and protein catalysis in group II intron splicing and mobility reactions using purified components Biochemistry 38 9069 83 1:CAS:528:DyaK1MXjvVCqtro%3D 10413481
40. H Guo S Zimmerly PS Perlman AM Lambowitz 1997 Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA EMBO J 16 6835 48 1170287 1:CAS:528:DyaK1cXisVWlug%3D%3D 9362497
41. B Cousineau D Smith S Lawrence-Cavanagh JE Mueller J Yang D Mills, et al. 1998 Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination Cell 94 451 62 1:CAS:528:DyaK1cXlslOktb8%3D 9727488
42. G Mohr D Smith M Belfort AM Lambowitz 2000 Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences Genes Dev 14 559 73 316424 1:CAS:528:DC%2BD3cXitFWrsrs%3D 10716944
43. NN Singh AM Lambowitz 2001 Interaction of a group II intron ribonucleoprotein endonuclease with its DNA target site investigated by DNA footprinting and modification interference J Mol Biol 309 361 86 1:CAS:528:DC%2BD3MXjslansrg%3D 11371159
44. AR Robart S Zimmerly 2005 Group II intron retroelements: function and diversity Cytogenet Genome Res 110 589 97 1:CAS:528:DC%2BD2MXnvFygsLY%3D 16093712
45. M Matsuura R Saldanha H Ma H Wank J Yang G Mohr, et al. 1997 A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron Genes Dev 11 2910 24 316661 1:CAS:528:DyaK2sXntlOiurs%3D 9353259
46. R Eskes J Yang AM Lambowitz PS Perlman 1997 Mobility of yeast mitochondrial group II introns: engineering a new site specificity and retrohoming via full reverse splicing Cell 88 865 74 1:STN:280:DyaK2s3js1GjtA%3D%3D 9118229
47. D Smith J Zhong M Matsuura AM Lambowitz M Belfort 2005 Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming Genes Dev 19 2477 87 1257402 1:CAS:528:DC%2BD2MXhtFOntLvN 16230535
48. LM Contreras T Huang CL Piazza D Smith G Qu G Gelderman, et al. 2013 Group II intron-ribosome association protects intron RNA from degradation RNA 19 1497 509 3851717 1:CAS:528:DC%2BC3sXhslSqtrfI 24046482
49. L Dai S Zimmerly 2002 Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior Nucleic Acids Res 30 1091 102 101233 1:CAS:528:DC%2BD38XitVOisb8%3D 11861899
50. DM Simon NA Clarke BA McNeil I Johnson D Pantuso L Dai, et al. 2008 Group II introns in eubacteria and archaea: ORF-less introns and new varieties RNA 14 1704 13 2525955 1:CAS:528:DC%2BD1cXhtFSnu7vP 18676618
51. MA Candales A Duong KS Hood T Li RA Neufeld R Sun, et al. 2012 Database for bacterial group II introns Nucleic Acids Res 40 D187 90 3245105 1:CAS:528:DC%2BC3MXhs12hurjP 22080509
52. M Granlund F Michel M Norgren 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 9 95173 1:CAS:528:DC%2BD3MXis1art7o%3D 11274116
53. N Toor G Hausner S Zimmerly 2001 Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases RNA 7 1142 52 1370161 1:CAS:528:DC%2BD3MXlvVGmt7c%3D 11497432
54. F Martinez-Abarca N Toro 2000 Group II introns in the bacterial world Mol Microbiol 38 917 26 1:CAS:528:DC%2BD3MXis1Gmtw%3D%3D 11123668
55. N Toro 2003 Bacteria and archaea group II introns: additional mobile genetic elements in the environment Environ Microbiol 5 143 51 1:CAS:528:DC%2BD3sXitlehsr0%3D 12588294
56. N Toro MD Molina-Sanchez M Fernandez-Lopez 2002 Identification and characterization of bacterial class E group II introns Gene 299 245 50 1:CAS:528:DC%2BD38XovFSksL8%3D 12459272
57. DM Simon SA Kelchner S Zimmerly 2009 A broadscale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases Mol Biol Evol 26 2795 808 1:CAS:528:DC%2BD1MXhsVajs7fN 19713327
58. DA Shub H Goodrich-Blair SR Eddy 1994 Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns Trends Biochem Sci 19 402 4 1:CAS:528:DyaK2MXhvFWnt7g%3D 7817395
59. K Ichiyanagi A Beauregard S Lawrence D Smith B Cousineau M Belfort 2002 Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets Mol Microbiol 46 1259 72 1:CAS:528:DC%2BD38XpsFGisL0%3D 12453213
60. J Zhong AM Lambowitz 2003 Group II intron mobility using nascent strands at DNA replication forks to prime reverse transcription EMBO J 22 4555 65 202375 1:CAS:528:DC%2BD3sXmvVWku7g%3D 12941706
61. K Ichiyanagi A Beauregard M Belfort 2003 A bacterial group II intron favors retrotransposition into plasmid targets Proc Natl Acad Sci U S A 100 15742 7 307638 1:CAS:528:DC%2BD2cXhtVCntQ%3D%3D 14673083
62. E Munoz-Adelantado J San Filippo F Martinez-Abarca FM Garcia-Rodriguez AM Lambowitz N Toro 2003 Mobility of the Sinorhizobium meliloti group II intron RmInt1 occurs by reverse splicing into DNA, but requires an unknown reverse transcriptase priming mechanism J Mol Biol 327 931 43 1:CAS:528:DC%2BD3sXitlWgsb8%3D 12662921
63. M Sunde 2005 Class I, integron with a group II intron detected in an Escherichia coli strain from a free-range reindeer Antimicrob Agents Chemother 49 2512 4 1140521 1:CAS:528:DC%2BD2MXkvFCgsbk%3D 15917559
64. AR Robart W Seo S Zimmerly 2007 Insertion of group II intron retroelements after intrinsic transcriptional terminators Proc Natl Acad Sci U S A 104 6620 5 1871835 1:CAS:528:DC%2BD2sXkvFSqu7Y%3D 17420455
65. C Quiroga PH Roy D Centron 2008 The S.ma.I2 class C group II intron inserts at integron attC sites Microbiology 154 1341 53 1:CAS:528:DC%2BD1cXmsFOiur4%3D 18451043
66. C Quiroga D Centron 2009 Using genomic data to determine the diversity and distribution of target site motifs recognized by class C-attC group II introns J Mol Evol 68 539 49 1:CAS:528:DC%2BD1MXmsVClt70%3D 19449055
67. G Leon PH Roy 2009 Potential role of group IIC-attC introns in integron cassette formation J Bacteriol 191 6040 51 2747902 1:CAS:528:DC%2BD1MXht1Oktr7E 19633079
68. G Leon PH Roy 2009 Group IIC intron mobility into attC sites involves a bulged DNA stem-loop motif RNA 15 1543 53 2714756 1:CAS:528:DC%2BD1MXpsFOlu7o%3D 19509303
69. G Leon C Quiroga D Centron PH Roy 2010 Diversity and strength of internal outward-oriented promoters in group IIC-attC introns Nucleic Acids Res 38 8196 207 3001079 1:CAS:528:DC%2BC3cXhsFGrs7zO 20716518
70. R Zoschke M Nakamura K Liere M Sugiura T Borner C Schmitz-Linneweber 2010 An organellar maturase associates with multiple group II introns Proc Natl Acad Sci U S A 107 3245 50 2840290 1:CAS:528:DC%2BC3cXis1Cgtbc%3D 20133623
71. GG Brown C Colas Des Francs-Small O Ostersetzer-Biran 2014 Group II intron splicing factors in plant mitochondria Front Plant Sci 5 35 3927076 24600456
72. J Vogel T Hubschmann T Borner WR Hess 1997 Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: support for MatK as an essential splice factor J Mol Biol 270 179 87 1:CAS:528:DyaK2sXkvVWls7c%3D 9236120
73. N Toor S Zimmerly 2002 Identification of a family of group II introns encoding LAGLIDADG ORFs typical of group I introns RNA 8 1373 7 1370344 1:CAS:528:DC%2BD38Xpt1Sjsro%3D 12458791
74. CF Li M Costa G Bassi YK Lai F Michel 2011 Recurrent insertion of 5′-terminal nucleotides and loss of the branchpoint motif in lineages of group II introns inserted in mitochondrial preribosomal RNAs RNA 17 1321 35 3138568 1:CAS:528:DC%2BC3MXos1OqsL8%3D 21613530
75. CB Monteiro-Vitorello G Hausner DB Searles EA Gibb DW Fulbright H Bertrand 2009 The Cryphonectria parasitica mitochondrial rns gene: plasmid-like elements, introns and homing endonucleases Fungal Genet Biol 46 837 48 1:CAS:528:DC%2BD1MXhtFGnsLvO 19607930
76. V Salman R Amann DA Shub HN Schulz-Vogt 2012 Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria Proc Natl Acad Sci U S A 109 4203 8 3306719 1:CAS:528:DC%2BC38XkvVWgt7w%3D 22371583
77. ST Mullineux M Costa GS Bassi F Michel G Hausner 2010 A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions RNA 16 1818 31 2924541 1:CAS:528:DC%2BC3cXhtFajtb%2FL 20656798
78. A Pfeifer B Martin J Kamper CW Basse 2012 The mitochondrial LSU rRNA group II intron of Ustilago maydis encodes an active homing endonuclease likely involved in intron mobility PLoS One 7 e49551 3498182 1:CAS:528:DC%2BC38XhslyisL3O 23166709
79. R Saldanha G Mohr M Belfort AM Lambowitz 1993 Group I and group II introns FASEB J 7 15 24 1:CAS:528:DyaK3sXhs1eltbg%3D 8422962
80. ST Mullineux K Willows G Hausner 2011 Evolutionary dynamics of the mS952 intron: a novel mitochondrial group II intron encoding a LAGLIDADG homing endonuclease gene J Mol Evol 72 433 49 1:CAS:528:DC%2BC3MXptlyqtL4%3D 21479820
81. M Unseld JR Marienfeld P Brandt A Brennicke 1997 The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides Nat Genet 15 57 61 1:CAS:528:DyaK2sXjsFSiuw%3D%3D 8988169
82. S Sato Y Nakamura T Kaneko E Asamizu S Tabata 1999 Complete structure of the chloroplast genome of Arabidopsis thaliana DNA Res 6 283 90 1:CAS:528:DyaK1MXnt1ajsbs%3D 10574454
83. M Turmel C Otis C Lemieux 2003 The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants Plant Cell 15 1888 903 167177 1:CAS:528:DC%2BD3sXms1Wlsbg%3D 12897260
84. LF Yin MJ Hu F Wang H Kuang Y Zhang G Schnabel, et al. 2012 Frequent gain and loss of introns in fungal cytochrome b genes PLoS One 7 e49096 3492308 1:CAS:528:DC%2BC38XhslehsLjO 23145081
85. W Guo JP Mower 2013 Evolution of plant mitochondrial intron-encoded maturases: frequent lineage-specific loss and recurrent intracellular transfer to the nucleus J Mol Evol 77 43 54 1:CAS:528:DC%2BC3sXhtlCnsrbP 23979261
86. M Hafez A Majer J Sethuraman SM Rudski F Michel G Hausner 2013 The mtDNA rns gene landscape in the Ophiostomatales and other fungal taxa: twintrons, introns, and intron-encoded proteins Fungal Genet Biol 53 71 83 1:CAS:528:DC%2BC3sXjsFOqtbY%3D 23403360
87. Q Meng Y Wang XQ Liu 2005 An intron-encoded protein assists RNA splicing of multiple similar introns of different bacterial genes J Biol Chem 280 35085 8 1:CAS:528:DC%2BD2MXhtFWmtb3J 16150738
88. BA McNeil DM Simon S Zimmerly 2014 Alternative splicing of a group II intron in a surface layer protein gene in Clostridium tetani Nucleic Acids Res 42 1959 69 3919590 1:CAS:528:DC%2BC2cXisFKkt7o%3D 24214997
89. BA McNeil S Zimmerly 2014 Novel RNA structural features of an alternatively splicing group II intron from Clostridium tetani RNA 20 855 66 1:CAS:528:DC%2BC2cXhtVSkt7jN 24751650
90. M Abebe MA Candales A Duong KS Hood T Li RA Neufeld, et al. 2013 A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank Mob DNA 4 28 4028801 24359548
91. C Carrillo Y Chapdelaine L Bonen 2001 Variation in sequence and RNA editing within core domains of mitochondrial group II introns among plants Mol Gen Genet 264 595 603 1:CAS:528:DC%2BD3MXhs1Onsbk%3D 11212914
92. J Li-Pook-Than L Bonen 2006 Multiple physical forms of excised group II intron RNAs in wheat mitochondria Nucleic Acids Res 34 2782 90 1464410 1:CAS:528:DC%2BD28XmsVeit7c%3D 16717283
93. Barkan A. Intron splicing in plant organelles. In: Daniell H, Chase C, editors. Molecular biology and biotechnology of plant organelles. Dordrecht, The Netherlands: Kluwer Academic Publishers; 2004. p. 281-308.
94. A Germain AM Hotto A Barkan DB Stern 2013 RNA processing and decay in plastids Wiley Interdiscip Rev RNA 4 295 316 1:CAS:528:DC%2BC3sXmt1OhtLY%3D 23536311
95. I Niemer C Schmelzer GV Borner 1995 Overexpression of DEAD box protein pMSS116 promotes ATP-dependent splicing of a yeast group II intron in vitro Nucleic Acids Res 23 2966 72 307137 1:CAS:528:DyaK2MXnvVektbY%3D
96. K Hammani A Barkan 2014 An mTERF domain protein functions in group II intron splicing in maize chloroplasts Nucleic Acids Res 42 5033 42 4005652 1:CAS:528:DC%2BC2cXntlyksbg%3D 24500208
97. BD Jenkins DJ Kulhanek A Barkan 1997 Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors Plant Cell 9 283 96 156918 1:CAS:528:DyaK2sXitFWktLc%3D 9090875
98. O Ostersetzer AM Cooke KP Watkins A Barkan 2005 CRS1, a chloroplast group II intron splicing factor, promotes intron folding through specific interactions with two intron domains Plant Cell 17 241 55 544502 1:CAS:528:DC%2BD2MXotlantQ%3D%3D 15598799
99. Y Asakura A Barkan 2006 Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns Plant Physiol 142 1656 63 1676066 1:CAS:528:DC%2BD28XhtlCns7jO 17071648
100. Y Asakura OA Bayraktar A Barkan 2008 Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts RNA 14 2319 32 2578863 1:CAS:528:DC%2BD1cXhtlCgsL3F 18799595
101. M Zmudjak C Colas Des Francs-Small I Keren F Shaya E Belausov I Small, et al. 2013 mCSF1, a nucleus-encoded CRM protein required for the processing of many mitochondrial introns, is involved in the biogenesis of respiratory complexes I and IV in Arabidopsis New Phytol 199 379 94 1:CAS:528:DC%2BC3sXpvFarsL4%3D 23646912
102. G Mohr AM Lambowitz 2003 Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants Nucleic Acids Res 31 647 52 140517 1:CAS:528:DC%2BD3sXitlCgu7o%3D 12527773
103. N Nakagawa N Sakurai 2006 A mutation in At-nMat1a, which encodes a nuclear gene having high similarity to group II intron maturase, causes impaired splicing of mitochondrial NAD4 transcript and altered carbon metabolism in Arabidopsis thaliana Plant Cell Physiol 47 772 83 1:CAS:528:DC%2BD28XmvVCgsr0%3D 16621844
104. I Keren A Bezawork-Geleta M Kolton I Maayan E Belausov M Levy, et al. 2009 AtnMat2, a nuclear-encoded maturase required for splicing of group-II introns in Arabidopsis mitochondria RNA 15 2299 311 2779688 1:CAS:528:DC%2BD1MXhsFGhtrvL 19946041
105. I Keren L Tal C Colas Des Francs-Small WL Araujo S Shevtsov F Shaya 2012 nMAT1, a nuclear-encoded maturase involved in the trans-splicing of nad1 intron 1, is essential for mitochondrial complex I assembly and function Plant J 71 413 26 1:CAS:528:DC%2BC38XhtFCkurbO 22429648
106. DW Copertino RB Hallick 1993 Group II and group III introns of twintrons: potential relationships with nuclear pre-mRNA introns Trends Biochem Sci 18 467 71 1:CAS:528:DyaK2cXntVaqsA%3D%3D 8108859
107. L Bonen 1993 Trans-splicing of pre-mRNA in plants, animals, and protists FASEB J 7 40 6 1:CAS:528:DyaK3sXhs1egs7k%3D 8422973
108. L Bonen 2008 Cis- and trans-splicing of group II introns in plant mitochondria Mitochondrion 8 26 34 1:CAS:528:DC%2BD2sXhsVOlt77P 18006386
109. V Knoop M Altwasser A Brennicke 1997 A tripartite group II intron in mitochondria of an angiosperm plant Mol Gen Genet 255 269 76 1:CAS:528:DyaK2sXlsFers78%3D 9268017
110. Y Choquet M Goldschmidt-Clermont J Girard-Bascou U Kuck P Bennoun JD Rochaix 1988 Mutant phenotypes support a trans-splicing mechanism for the expression of the tripartite psaA gene in the C reinhardtii chloroplast Cell 52 903 13 1:CAS:528:DyaL1cXhvF2gsb4%3D 3280139
111. M Goldschmidt-Clermont Y Choquet J Girard-Bascou F Michel M Schirmer-Rahire JD Rochaix 1991 A small chloroplast RNA may be required for trans-splicing in Chlamydomonas reinhardtii Cell 65 135 43 1:CAS:528:DyaK3MXks1GrsL8%3D 1707343
112. O Malek V Knoop 1998 Trans-splicing group II introns in plant mitochondria: the complete set of cis-arranged homologs in ferns, fern allies, and a hornwort RNA 4 1599 609 1369728 1:CAS:528:DyaK1cXnvFOgs7s%3D 9848656
113. YL Qiu JD Palmer 2004 Many independent origins of trans splicing of a plant mitochondrial group II intron J Mol Evol 59 80 9 1:CAS:528:DC%2BD2cXlsleisbg%3D 15383910
114. FB Stabell NJ Tourasse S Ravnum AB Kolsto 2007 Group II intron in Bacillus cereus has an unusual 3′ extension and splices 56 nucleotides downstream of the predicted site Nucleic Acids Res 35 1612 23 1865049 1:CAS:528:DC%2BD2sXktlSqurc%3D 17301069
115. FB Stabell NJ Tourasse AB Kolsto 2009 A conserved 3′ extension in unusual group II introns is important for efficient second-step splicing Nucleic Acids Res 37 3202 14 2691827 1:CAS:528:DC%2BD1MXntVSqs70%3D 19304998
116. NJ Tourasse FB Stabell AB Kolsto 2010 Structural and functional evolution of group II intron ribozymes: insights from unusual elements carrying a 3′ extension N Biotechnol 27 204 11 1:CAS:528:DC%2BC3cXntVeku7w%3D 20219707
117. KP Jenkins L Hong RB Hallick 1995 Alternative splicing of the Euglena gracilis chloroplast roaA transcript RNA 1 624 33 1369306 1:CAS:528:DyaK2MXot1Wqsbg%3D 7489521
118. DW Copertino RB Hallick 1991 Group II twintron: an intron within an intron in a chloroplast cytochrome b-559 gene EMBO J 10 433 42 452664 1:CAS:528:DyaK3MXhtFKhsLo%3D 1899376
119. AR Robart NK Montgomery KL Smith S Zimmerly 2004 Principles of 3′ splice site selection and alternative splicing for an unusual group II intron from Bacillus anthracis RNA 10 854 62 1370575 1:CAS:528:DC%2BD2cXjs1Gnt7c%3D 15100440
120. DW Copertino DA Christopher RB Hallick 1991 A mixed group II/group III twintron in the Euglena gracilis chloroplast ribosomal protein S3 gene: evidence for intron insertion during gene evolution Nucleic Acids Res 19 6491 7 329205 1:CAS:528:DyaK38Xlt1Omsw%3D%3D 1721702
121. L Hong RB Hallick 1994 A group III intron is formed from domains of two individual group II introns Genes Dev 8 1589 99 1:CAS:528:DyaK2cXltVWjsrk%3D 7958842
122. Y Nakamura T Kaneko S Sato M Ikeuchi H Katoh S Sasamoto, et al. 2002 Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 DNA Res 9 123 30 1:CAS:528:DC%2BD38XntVSisLk%3D 12240834
123. L Dai S Zimmerly 2003 ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs RNA 9 14 9 1370365 1:CAS:528:DC%2BD3sXhtFahsrY%3D 12554871
124. EV Sheveleva RB Hallick 2004 Recent horizontal intron transfer to a chloroplast genome Nucleic Acids Res 32 803 10 373349 1:CAS:528:DC%2BD2cXhtVKrsLg%3D 14762207
125. OW Odom DL Shenkenberg JA Garcia DL Herrin 2004 A horizontally acquired group II intron in the chloroplast psbA gene of a psychrophilic Chlamydomonas: in vitro self-splicing and genetic evidence for maturase activity RNA 10 1097 107 1370600 1:CAS:528:DC%2BD2cXltlKmu7w%3D 15208445
126. H Khan JM Archibald 2008 Lateral transfer of introns in the cryptophyte plastid genome Nucleic Acids Res 36 3043 53 2396441 1:CAS:528:DC%2BD1cXmtleqsLs%3D 18397952
127. R Kamikawa I Masuda M Demura K Oyama S Yoshimatsu M Kawachi, et al. 2009 Mitochondrial group II introns in the raphidophycean flagellate Chattonella spp suggest a diatom-to-Chattonella lateral group II intron transfer Protist 160 364 75 1:CAS:528:DC%2BD1MXhtVGisbvL 19346162
128. CM Hardy GD Clark-Walker 1991 Nucleotide sequence of the COX1 gene in Kluyveromyces lactis mitochondrial DNA: evidence for recent horizontal transfer of a group II intron Curr Genet 20 99 114 1:CAS:528:DyaK38XisV2ltbw%3D 1657415
129. S Leclercq I Giraud R Cordaux 2011 Remarkable abundance and evolution of mobile group II introns in Wolbachia bacterial endosymbionts Mol Biol Evol 28 685 97 1:CAS:528:DC%2BC3cXhsF2rsLzJ 20819906
130. L Dai S Zimmerly 2002 The dispersal of five group II introns among natural populations of Escherichia coli RNA 8 1294 307 1370338 1:CAS:528:DC%2BD38Xot1Kjt7o%3D 12403467
131. NJ Tourasse AB Kolsto 2008 Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution Nucleic Acids Res 36 4529 48 2504315 1:CAS:528:DC%2BD1cXpslWnu70%3D 18587153
132. N Toro F Martinez-Abarca 2013 Comprehensive phylogenetic analysis of bacterial group II intron-encoded ORFs lacking the DNA endonuclease domain reveals new varieties PLoS One 8 e55102 3552965 1:CAS:528:DC%2BC3sXitVylt7Y%3D 23355907
133. JM Fontaine D Goux B Kloareg GS Loiseaux-de 1997 The reverse-transcriptase-like proteins encoded by group II introns in the mitochondrial genome of the brown alga Pylaiella littoralis belong to two different lineages which apparently coevolved with the group II ribosyme lineages J Mol Evol 44 33 42 1:CAS:528:DyaK2sXlt1Wlsg%3D%3D 9010134
134. MR Goddard A Burt 1999 Recurrent invasion and extinction of a selfish gene Proc Natl Acad Sci U S A 96 13880 5 24159 1:CAS:528:DyaK1MXns1OqtLY%3D 10570167
135. A Burt V Koufopanou 2004 Homing endonuclease genes: the rise and fall and rise again of a selfish element Curr Opin Genet Dev 14 609 15 1:CAS:528:DC%2BD2cXpsVOrt70%3D 15531154
136. P Haugen DM Simon D Bhattacharya 2005 The natural history of group I introns Trends Genet 21 111 9 1:CAS:528:DC%2BD2MXmslKgtA%3D%3D 15661357
137. P Haugen OG Wikmark A Vader DH Coucheron E Sjottem SD Johansen 2005 The recent transfer of a homing endonuclease gene Nucleic Acids Res 33 2734 41 1110740 1:CAS:528:DC%2BD2MXktF2nsLg%3D 15891115
138. C Adamidi O Fedorova AM Pyle 2003 A group II intron inserted into a bacterial heat-shock operon shows autocatalytic activity and unusual thermostability Biochemistry 42 3409 18 1:CAS:528:DC%2BD3sXhvVygsb0%3D 12653544
139. GJ Chee H Takami 2005 Housekeeping recA gene interrupted by group II intron in the thermophilic Geobacillus kaustophilus Gene 363 211 20 1:CAS:528:DC%2BD2MXht1Klu7%2FF 16242272
140. JF Pombert ER James J Janouskovec PJ Keeling 2012 Evidence for transitional stages in the evolution of euglenid group II introns and twintrons in the Monomorphina aenigmatica plastid genome PLoS One 7 e53433 3534033 1:CAS:528:DC%2BC3sXptVSltg%3D%3D 23300929
141. KE Wiegert MS Bennett RE Triemer 2013 Tracing patterns of chloroplast evolution in euglenoids: contributions from Colacium vesiculosum and Strombomonas acuminata (Euglenophyta) J Eukaryot Microbiol 60 214 21 1:CAS:528:DC%2BC3sXlsFSiu7Y%3D 23351081
142. MJ Curcio M Belfort 1996 Retrohoming: cDNA-mediated mobility of group II introns requires a catalytic RNA Cell 84 9 12 1:CAS:528:DyaK28XltFSqsw%3D%3D 8548830
143. DM Simon S Zimmerly 2008 A diversity of uncharacterized reverse transcriptases in bacteria Nucleic Acids Res 36 7219 29 2602772 1:CAS:528:DC%2BD1cXhsV2rsrjJ 19004871
144. Z Weinberg J Perreault MM Meyer RR Breaker 2009 Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis Nature 462 656 9 4140389 1:CAS:528:DC%2BD1MXhsFWjtLzO 19956260
145. Z Weinberg JX Wang J Bogue J Yang K Corbino RH Moy, et al. 2010 Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes Genome Biol 11 R31 2864571 20230605
146. G Storz J Vogel KM Wassarman 2011 Regulation by small RNAs in bacteria: expanding frontiers Mol Cell 43 880 91 3176440 1:CAS:528:DC%2BC3MXhtFymsLjN 21925377
147. N Toor KS Keating SD Taylor AM Pyle 2008 Crystal structure of a self-spliced group II intron Science 320 77 82 4406475 1:CAS:528:DC%2BD1cXktVKhtL8%3D 18388288
148. JS Rest DP Mindell 2003 Retroids in archaea: phylogeny and lateral origins Mol Biol Evol 20 1134 42 1:CAS:528:DC%2BD3sXltlemsrw%3D 12777534
149. PA Sharp 1985 On the origin of RNA splicing and introns Cell 42 397 400 1:CAS:528:DyaL2MXlslensrg%3D 2411416
150. TR Cech 1986 The generality of self-splicing RNA: relationship to nuclear mRNA splicing Cell 44 207 10 1:CAS:528:DyaL28XhsVeitrg%3D 2417724
151. PA Sharp 1991 Five easy pieces Science 254 663 1:CAS:528:DyaK38Xhs1aj 1948046
152. AM Weiner 1993 mRNA splicing and autocatalytic introns: distant cousins or the products of chemical determinism? Cell 72 161 4 1:CAS:528:DyaK3sXhtF2jtrg%3D 8425215
153. MJ Moore PA Sharp 1993 Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing Nature 365 364 8 1:CAS:528:DyaK3sXmtF2kt7o%3D 8397340
154. KL Maschhoff RA Padgett 1993 The stereochemical course of the first step of pre-mRNA splicing Nucleic Acids Res 21 5456 62 310585 1:CAS:528:DyaK2cXkvValug%3D%3D 8265362
155. RA Padgett M Podar SC Boulanger PS Perlman 1994 The stereochemical course of group II intron self-splicing Science 266 1685 8 1:CAS:528:DyaK2MXis12rsbg%3D 7527587
156. M Podar PS Perlman RA Padgett 1998 The two steps of group II intron self-splicing are mechanistically distinguishable RNA 4 890 900 1369667 1:CAS:528:DyaK1cXltFyktrs%3D 9701281
157. J Rajagopal JA Doudna JW Szostak 1989 Stereochemical course of catalysis by the Tetrahymena ribozyme Science 244 692 4 1:CAS:528:DyaL1MXkvFaktL8%3D 2470151
158. JA McSwiggen TR Cech 1989 Stereochemistry of RNA cleavage by the Tetrahymena ribozyme and evidence that the chemical step is not rate-limiting Science 244 679 83 1:CAS:528:DyaL1MXksFeisb0%3D 2470150
159. S Valadkhan 2013 The role of snRNAs in spliceosomal catalysis Prog Mol Biol Transl Sci 120 195 228 1:CAS:528:DC%2BC2cXkt1ynsrw%3D 24156945
160. G Chanfreau A Jacquier 1993 Interaction of intronic boundaries is required for the second splicing step efficiency of a group II intron EMBO J 12 5173 80 413780 1:CAS:528:DyaK2cXntFOluw%3D%3D 8262060
161. R Parker PG Siliciano 1993 Evidence for an essential non-Watson-Crick interaction between the first and last nucleotides of a nuclear pre-mRNA intron Nature 361 660 2 1:CAS:528:DyaK3sXhvVGqtbc%3D 8437627
162. BL Ruis WJ Kivens PG Siliciano 1994 The interaction between the first and last intron nucleotides in the second step of pre-mRNA splicing is independent of other conserved intron nucleotides Nucleic Acids Res 22 5190 5 332059 1:CAS:528:DyaK2MXivFKmtbs%3D 7816605
163. GC Shukla RA Padgett 2002 A catalytically active group II intron domain 5 can function in the U12-dependent spliceosome Mol Cell 9 1145 50 1:CAS:528:DC%2BD38XksFKjtbc%3D 12049749
164. SM Fica N Tuttle T Novak NS Li J Lu P Koodathingal, et al. 2013 RNA catalyses nuclear pre-mRNA splicing Nature 503 229 34 1:CAS:528:DC%2BC3sXhslOlsb7P 24196718
165. SM Fica MA Mefford JA Piccirilli JP Staley 2014 Evidence for a group II intron-like catalytic triplex in the spliceosome Nat Struct Mol Biol 21 464 71 4257784 1:CAS:528:DC%2BC2cXmsVKlsrw%3D 24747940
166. WP Galej C Oubridge AJ Newman K Nagai 2013 Crystal structure of Prp8 reveals active site cavity of the spliceosome Nature 493 638 43 3672837 1:CAS:528:DC%2BC3sXhsVygsLs%3D 23354046
167. M Dlakic A Mushegian 2011 Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase RNA 17 799 808 3078730 1:CAS:528:DC%2BC3MXls1Ojtrg%3D 21441348
168. AJ Newman C Norman 1992 U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites Cell 68 743 54 1:CAS:528:DyaK38Xhs12rur8%3D 1739979
169. M Hetzer G Wurzer RJ Schweyen MW Mueller 1997 Trans-activation of group II intron splicing by nuclear U5 snRNA Nature 386 417 20 1:CAS:528:DyaK2sXit1WrtLg%3D 9121561
170. RT O'Keefe C Norman AJ Newman 1996 The invariant U5 snRNA loop 1 sequence is dispensable for the first catalytic step of pre-mRNA splicing in yeast Cell 86 679 89 8752221
171. CF Lesser C Guthrie 1993 Mutations in U6 snRNA that alter splice site specificity: implications for the active site Science 262 1982 8 1:CAS:528:DyaK2cXht1Knt7c%3D 8266093
172. S Kandels-Lewis B Seraphin 1993 Involvement of U6 snRNA in 5′ splice site selection Science 262 2035 9 1:CAS:528:DyaK2cXht1KktLw%3D 8266100
173. M Boudvillain A de Lencastre AM Pyle 2000 A tertiary interaction that links active-site domains to the 5′ splice site of a group II intron Nature 406 315 8 1:CAS:528:DC%2BD3cXlsFKgsbs%3D 10917534
174. BM Rhode K Hartmuth E Westhof R Luhrmann 2006 Proximity of conserved U6 and U2 snRNA elements to the 5′ splice site region in activated spliceosomes EMBO J 25 2475 86 1478171 1:CAS:528:DC%2BD28XltlGlu7g%3D 16688215
175. M Anokhina S Bessonov Z Miao E Westhof K Hartmuth R Luhrmann 2013 RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core EMBO J 32 2804 18 3817461 1:CAS:528:DC%2BC3sXhtlKru7vP 24002212
176. JP Staley C Guthrie 1998 Mechanical devices of the spliceosome: motors, clocks, springs, and things Cell 92 315 26 1:CAS:528:DyaK1cXhtFGisLo%3D 9476892
177. HD Madhani C Guthrie 1992 A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome Cell 71 803 17 1:CAS:528:DyaK3sXit1ygsbk%3D 1423631
178. R Reddy D Henning P Epstein H Busch 1981 Primary and secondary structure of U2 snRNA Nucleic Acids Res 9 5645 58 327549 1:CAS:528:DyaL38XmsVenug%3D%3D 6796940
179. C Guthrie B Patterson 1988 Spliceosomal snRNAs Annu Rev Genet 22 387 419 1:CAS:528:DyaL1MXhsV2rt74%3D 2977088
180. DG Sashital G Cornilescu CJ McManus DA Brow SE Butcher 2004 U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction Nat Struct Mol Biol 11 1237 42 1:CAS:528:DC%2BD2cXhtVens7jI 15543154
181. EA Dunn SD Rader 2010 Secondary structure of U6 small nuclear RNA: implications for spliceosome assembly Biochem Soc Trans 38 1099 104 1:CAS:528:DC%2BC3cXptlylsbo%3D 20659011
182. CL Will R Luhrmann 2011 Spliceosome structure and function Cold Spring Harb Perspect Biol 3 7 a003707 3119917 1:CAS:528:DC%2BC3MXhtVCgu7%2FJ 21441581 doi:10.1101/cshperspect.a003707
183. MA Mefford JP Staley 2009 Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps RNA 15 1386 97 2704075 1:CAS:528:DC%2BD1MXotlWqsLg%3D 19458033
184. M Irimia SW Roy 2014 Origin of spliceosomal introns and alternative splicing Cold Spring Harb Perspect Biol 6 6 a016071 24890509 doi:10.1101/cshperspect.a016071
185. JO Andersson AM Sjogren DS Horner CA Murphy PL Dyal SG Svard, et al. 2007 A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution BMC Genomics 8 51 1805757 17298675
186. CE Lane K van den Heuvel C Kozera BA Curtis BJ Parsons S Bowman, et al. 2007 Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function Proc Natl Acad Sci U S A 104 19908 13 2148396 1:CAS:528:DC%2BD1cXhs1Wntw%3D%3D 18077423
187. EV Koonin 2009 Intron-dominated genomes of early ancestors of eukaryotes J Hered 100 618 23 2877545 1:CAS:528:DC%2BD1MXhtVGrsbnN 19617525
188. W Martin EV Koonin 2006 Introns and the origin of nucleus-cytosol compartmentalization Nature 440 41 5 1:CAS:528:DC%2BD28XhvFajtL8%3D 16511485
189. K Belhocine AB Mak B Cousineau 2007 Trans-splicing of the Ll.LtrB group II intron in Lactococcus lactis Nucleic Acids Res 35 2257 68 1874635 1:CAS:528:DC%2BD2sXmsVWgt70%3D 17389638
190. VR Chalamcharla MJ Curcio M Belfort 2010 Nuclear expression of a group II intron is consistent with spliceosomal intron ancestry Genes Dev 24 827 36 2854396 1:CAS:528:DC%2BC3cXlsVahsr0%3D 20351053
191. Y Xiong TH Eickbush 1990 Origin and evolution of retroelements based upon their reverse transcriptase sequences EMBO J 9 3353 62 552073 1:CAS:528:DyaK3cXmt1Ghsbk%3D 1698615
192. RJ Grainger JD Beggs 2005 Prp8 protein: at the heart of the spliceosome RNA 11 533 57 1370742 1:CAS:528:DC%2BD2MXktFejs7o%3D 15840809
193. EV Koonin 2006 The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol Direct 1 22 1570339 16907971
194. K Belhocine AB Mak B Cousineau 2008 Trans-splicing versatility of the Ll.LtrB group II intron RNA 14 1782 90 2525943 1:CAS:528:DC%2BD1cXhtFSnu7jN 18648072
195. C Ritlop C Monat B Cousineau 2012 Isolation and characterization of functional tripartite group II introns using a Tn5-based genetic screen PLoS One 7 e41589 3410883 1:CAS:528:DC%2BC38XhtFKht7nE 22876289
196. G Qu X Dong CL Piazza VR Chalamcharla S Lutz MJ Curcio, et al. 2014 RNA-RNA interactions and pre-mRNA mislocalization as drivers of group II intron loss from nuclear genomes Proc Natl Acad Sci U S A 111 6612 7 4020058 1:CAS:528:DC%2BC2cXmtlWnt7Y%3D 24722636
197. WF Doolittle 2014 The trouble with (group II) introns Proc Natl Acad Sci U S A 111 6536 7 4020116 1:CAS:528:DC%2BC2cXnsFWltLY%3D 24757059
198. Eickbush TH. Origin and evolutionary relationships of retroelements. In: Morse SS, editor. Evolutionary biology of viruses. New York: Raven; 1994. p. 121-57.
199. HS Malik WD Burke TH Eickbush 1999 The age and evolution of non-LTR retrotransposable elements Mol Biol Evol 16 793 805 1:CAS:528:DyaK1MXjslGitbs%3D 10368957
200. DD Luan MH Korman JL Jakubczak TH Eickbush 1993 Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition Cell 72 595 605 1:CAS:528:DyaK3sXhs1ansrc%3D 7679954
201. KK Kojima M Kanehisa 2008 Systematic survey for novel types of prokaryotic retroelements based on gene neighborhood and protein architecture Mol Biol Evol 25 1395 404 1:CAS:528:DC%2BD1cXotlKgtro%3D 18391066
202. J van der Oost ER Westra RN Jackson B Wiedenheft 2014 Unravelling the structural and mechanistic basis of CRISPR-Cas systems Nat Rev Microbiol 12 479 92 24909109
203. SW Burge J Daub R Eberhardt J Tate L Barquist EP Nawrocki, et al. 2013 Rfam 11.0: 10 years of RNA families Nucleic Acids Res 41 D226 32 3531072 1:CAS:528:DC%2BC38XhvV2ktrrF 23125362