ライフサイエンスコーパス: group I intron

1 onformational change in P9.0 of the Azoarcus group I intron.

2 DeltaC209 P4-P6 domain from the Tetrahymena group I intron.

3 that compromise RNA self-splicing in the bI5 group I intron.

4 with the bI4 maturase to aid excision of the group I intron.

5 erized ribozyme derived from the Tetrahymena group I intron.

6 n a 659-nucleotide RNA containing the Cr.LSU group I intron.

7 the P4-P6 ribozyme domain of the Tetrahymena group I intron.

8 ted to that of larger ribozymes, such as the group I intron.

9 mega-homing endonuclease gene and associated group I intron.

10 lize the folded structure of the Tetrahymena group I intron.

11 tif originally discovered in the Tetrahymena group I intron.

12 the P5c helix of the Tetrahymena thermophila group I intron.

13 t, might have been derived from a degenerate group I intron.

14 the role of Suv3p in splicing of the aI5beta group I intron.

15 na thermophila large subunit rRNA-DeltaP5abc group I intron.

16 sibility along the length of the Tetrahymena group I intron.

17 function for many structured RNAs, including group I introns.

18 encoded within intervening sequences such as group I introns.

19 (CYT-18 protein) that functions in splicing group I introns.

20 But this ribozyme has unexpected relatives: group I introns.

21 an support the insertion and/or retention of group I introns.

22 but often evolutionarily distantly related, group I introns.

23 ase, including at structures conserved among group I introns.

24 glucose) present in T-even phages, and lacks group I introns.

25 eophile with an affinity comparable to other group I introns.

26 articularly rich in nuclear ribosomal [r]DNA group I introns.

27 s similar to GIY-YIG homing endonucleases of group I introns.

28 raloop receptor and P1 helix docking site in group I introns.

29 ain and CTD that enabled specific binding of group I introns.

30 ifferent sets of interactions with different group I introns.

31 ve drug target because humans do not contain group I introns.

32 structure-stabilizing splicing cofactors for group I introns.

33 in decreased splicing of the aI5beta and bI3 group I introns.

34 cripts, unprocessed transcripts, and excised group I introns.

35 act as splicing cofactors for autocatalytic group I introns.

36 structure-stabilizing splicing cofactor for group I introns.

37 to promote the splicing of a wide variety of group I introns.

38 ) and promotes the splicing of mitochondrial group I introns.

39 to establish the conserved chemical basis of group I intron activity.

40 cing of some Neurospora crassa mitochondrial group I introns additionally requires a DEAD-box protein

41 The sporadic distribution of nuclear group I introns among different fungal lineages can be e

42 The group I intron (AnCOB) of the mitochondrial apocytochrom

43 P4-P6 domain of the Tetrahymena thermophila group I intron and a 58-nt fragment of the Escherichia c

44 l-length tRNA synthetase, in binding the bI4 group I intron and facilitating its self-splicing activi

45 ith efficient inheritance of the phage T4 td group I intron and its endonuclease, I-TevI, for which t

46 to the evolution of splicing activity, binds group I intron and other RNAs non-specifically via its C

47 seedlings with impaired splicing of the trnL group I intron and the ndhA, ycf3-int1, and clpP-int2 gr

48 res of the Pezizomycotina enzymes related to group I intron and tRNA interactions.

49 leted regions are not highly conserved among group I introns and are often dispensable for catalytic

50 We used phylogenetic analyses of group I introns and lichen-fungal host cells to address

51 of molecular examples, with primary focus on group I introns and RNase P RNA.

52 e P456 domain of the Tetrahymena thermophila group I intron, and a 58 nt 23s rRNA from Escherichia co

53 mismatches, similar to the P5abc region of a group I intron, and is closed by a GAAA tetraloop.

54 It consists of the trnL intron, a group I intron, and the trnT-trnL and trnL-trnF intergen

55 nd our knowledge of substrate recognition by group I introns, and also provide a basis for rational d

56 Many homing endonucleases are encoded within group I introns, and such enzymes promote the mobility r

57 n of aberrant RNA species, including excised group I introns; and loss of mitochondrial DNA (mtDNA).

58 Many group I introns appear to have originated in the common

59 and site-directed mutagenesis indicate that group I introns are composed of a catalytic core that is

60 Group I introns are inserted into genes of a wide variet

61 Group I introns are mobile RNA enzymes (ribozymes) that

62 Mobile group I introns are RNA splicing elements that have been

63 he self-splicing and mobility of a few model group I introns are well understood.

64 Group I introns are widely distributed in protists, bact

65 Using the P4-P6 domain of the Tetrahymena group I intron as the test system, we identified pairs o

66 model to the evolution of HEGs found in the group I intron at position S943 of the nuclear ribosomal

67 yrRS showed that the overall topology of the group I intron binding surface is conserved but with var

68 at the catalytic domain uses a newly evolved group I intron binding surface that includes an N-termin

69 ture and amino acids potentially involved in group I intron binding than do neighboring protein core

70 one C-terminal domain insertion functions in group I intron binding, and that some C-terminal domain

71 structural adaptations that form a distinct group I intron-binding site in the N-terminal catalytic

72 howed that CYT-18 has distinct tRNA(Tyr) and group I intron-binding sites, with the latter formed by

73 The group I intron-binding surface includes three small inse

74 mena ribozyme derived from the self-splicing group I intron binds a 5'-splice site analog (S) and gua

75 The structure shows that the group I intron binds across the two subunits of the homo

76 droxyl radical cleavage assays show that the group I intron binds at a site formed in part by the thr

77 lent metal ions are required for splicing of group I introns, but their role in maintaining the struc

78 oming endonuclease initiates mobility of its group I intron by recognizing DNA both upstream and down

79 4-P6 domain from the Tetrahymena thermophila group I intron by single molecule fluorescence resonance

80 onucleotide-based therapeutics for targeting group I introns by binding enhancement by tertiary inter

81 ndonucleases initiate mobility of their host group I introns by binding to and cleaving lengthy recog

82 se (CYT-18 protein) promotes the splicing of group I introns by helping the intron RNA fold into the

83 rosyl-tRNA synthetase, functions in splicing group I introns by inducing formation of the catalytical

84 etase (CYT-18 protein) functions in splicing group I introns by promoting the formation of the cataly

85 etase (CYT-18 protein) functions in splicing group I introns by promoting the formation of the cataly

86 her aminoacyl-tRNA synthetases interact with group I introns by recognizing conserved tRNA-like struc

87 se proteins, Neurospora crassa CYT-18, binds group I introns by using both its N-terminal catalytic a

88 Previous studies showed: (i) CYT-18 binds group I introns by using both its N-terminal catalytic d

89 Here we show that a group I intron can move to degenerate sites under oxidiz

90 emical data, shows that conserved regions of group I introns can be superimposed over interacting reg

91 The extent of horizontal transfer of group I introns can potentially be determined by examini

92 bozymes, derived from a Pneumocystis carinii group I intron, can catalyze the excision of targeted se

93 ibozyme, derived from a Pneumocystis carinii group I intron, can replace the 5' end of a targeted exo

94 This chemical phylogeny for group I intron catalysis helps to refine structural mode

95 Our findings continue an emerging theme in group I intron catalysis: the oxygen atoms at the reacti

96 and that may be common chemical features of group I intron catalysts.

97 nizes a conserved tRNA-like structure of the group I intron catalytic core.

98 nserved tRNA-like structural features of the group I intron catalytic core.

99 ing, but partially overlapping, sides of the group I intron catalytic core.

100 its binding site in the P4-P6 domain of the group I intron catalytic core.

101 re in this region, leading to folding of the group I intron catalytic core.

102 ScaI ribozyme derived from the self-splicing group I intron catalyzes a reversible reaction analogous

103 r of selfish genetic elements, including two group I introns (Cbu.L1917 and Cbu.L1951) and an interve

104 The two group I introns, Cbu.L1917 and Cbu.L1951, are inserted a

105 Here, we show that, unlike all other group I introns, Cbu.L1917 utilizes a different cofactor

106 Modeling onto a CYT-18/group I intron cocrystal structure indicates that the C-

107 domains of CYT-18 interact with the expected group I intron cognates of the aminoacyl-acceptor stem a

108 Self-splicing group I introns come in two flavours - those with a homi

109 f an RNA hairpin modelling the P5 helix of a group I intron, complexed with Co(NH3)63+, has been dete

110 pecifically promotes formation of the native group I intron core from this misfolded conformation.

111 l hybridization data for three model RNAs: a group I intron, CsrB and a tRNA.

112 on-splicing reaction, a Pneumocystis carinii group I intron-derived ribozyme binds an RNA substrate,

113 We previously reported that a group I intron-derived ribozyme can catalyze the excisio

114 A group I intron-derived ribozyme from Pneumocystis carini

115 We demonstrate that a group I intron-derived ribozyme from the opportunistic p

116 Nevertheless, our results demonstrate that group I intron-derived ribozymes are inherently able to

117 ese results are a further demonstration that group I intron-derived ribozymes are quite malleable in

118 The implications of group I intron-derived ribozymes being able to catalyze

119 Group I intron-derived ribozymes can catalyze a variety

120 Group I intron-derived ribozymes can perform a variety o

121 med OmegaG, found in Cbu.L1951 and all other group I introns described to date.

122 d crystallographic model of a portion of the group I intron, despite the presence of J8/7 and P3 in t

123 served G.U base pair at the cleavage site of group I introns destabilizes the P1 extension >100-fold

124 However, the coral and sea anemone cox1 group I introns differed in several aspects, such as the

125 A large number of group I introns encode a family of homologous proteins t

126 Many group I introns encode endonucleases that promote intron

127 The Aspergillus nidulans mitochondrial COB group I intron encodes a bi-functional protein, I-AniI,

128 the first example of a chromosomally encoded group I intron endonuclease in bacteria.

129 side the catalytic core imply that different group I introns, even within the same subclass, use dist

130 the use of comparative methods to understand group I intron evolution in a broader context and to gen

131 l host cells to address four questions about group I intron evolution in lichens, and generally in al

132 PpLSU3, a mobile group I intron found in the ribo-somal RNA genes of Phys

133 tinct processes in the evolution of the 1500 group I introns found thus far in nature (e.g. in algae

134 ose zipper, originally observed in the P4-P6 group I intron fragment.

135 Group I introns frequently provide protection against se

136 activity and structure in the small (249 nt) group I intron from Anabaena, we used two independent as

137 The AnCOB group I intron from Aspergillus nidulans encodes a homin

138 and hydroxyl radical footprinting of a small group I intron from Azoarcus pre-tRNA(Ile) showed that t

139 Despite its small size, the 205 nt group I intron from Azoarcus tRNA(Ile) is an exceptional

140 The ODMiR method is demonstrated with the group I intron from Candida albicans, a human pathogen.

141 reverse cyclization reactions catalyzed by a group I intron from the opportunistic pathogen Pneumocys

142 The group I intron from this isolate is the first to be repo

143 we evaluate the self-splicing efficiency of group I introns from transcripts expressed by RNA polyme

144 ctivities of three classes of catalytic RNA: group I introns, group II introns, and 23S rRNA.

145 The group I intron has a rich history of biochemical efforts

146 A group I intron has been found to interrupt the anticodon

147 lished, the function of Suv3p in splicing of group I introns has remained elusive.

148 The J4/5 loop of group I introns has tertiary interactions with the P1 he

149 egarding the cleavage mechanisms of the four group I intron homing endonuclease families: LAGLIDADG,

150 full-length SegF and is likely analogous to group I intron homing, in which repair of a DSB results

151 e by the intron-encoded endonuclease, as for group I intron homing.

152 nterference set collected on the Tetrahymena group I intron (IC1 class), these data define a "chemica

153 ions from the conserved core sequences of 93 Group I introns, identified 17 introns similar to that o

154 crystal structure of the Azoarcus bacterial group I intron in complex with its 5' and 3' exons.

155 alian pathogen that contains a self-splicing group I intron in its large subunit rRNA precursor.

156 ea mays) chloroplasts is associated with the group I intron in pre-trnL-UAA and group II introns in t

157 en the IC-UTS and the 43B cistron; and (c) a group I intron in the 43B cistron.

158 e we report the insertion of a self-splicing group I intron in the coding sequence of the DNA polymer

159 of the COX3 mRNA and splicing of the aI5beta group I intron in the COX1 pre-mRNA in Saccharomyces cer

160 ndrial sequences revealed the existence of a group I intron in the cytochrome oxidase subunit 1 (cox1

161 Here we describe the discovery of a group I intron in the DNA polymerase gene of Bacillus th

162 Here we show that the group I intron in the DNA polymerase gene of T7-like bac

163 DNA (rDNA) focuses on a naturally occurring group I intron in the I-CpaI target site of 23S rDNA fro

164 A target in C. albicans is the self-splicing group I intron in the LSU rRNA precursor.

165 The J4/5 loop of the group I intron in the mouse-derived fungal pathogen Pneu

166 A striking example of this is a homing group I intron in the mt cox1 gene.

167 a LAGLI-DADG motif as reported for the cox1 group I intron in the sea anemone Metridium senile.

168 labeled with GTP indicates the existence of group I introns in genes of at least three transcription

169 ng surface diverged to accommodate different group I introns in other Pezizomycotina fungi, we determ

170 that there is no barrier for maintenance of group I introns in phages of proteobacteria.

171 The wide but sporadic distribution of group I introns in protists, plants, and fungi, as well

172 primary sequence and secondary structure of group I introns in subgroup IA2, which includes the intr

173 se genes play a role in splicing of multiple group I introns in the chloroplast.

174 Our analyses show that group I introns in the lichen-fungi and in the lichen-al

175 e up the lichen thallus? 2) Are the multiple group I introns in the lichen-fungi of independent origi

176 ns the evidence for an elevated abundance of group I introns in the mitochondria of anthozoans.

177 nce and characteristics of two self-splicing group I introns in the sole 23S rRNA gene of Coxiella bu

178 n CYT-19 functions in the folding of several group I introns in vivo and a diverse set of group I and

179 are magnesium ion binding sites, in diverse group I introns, including those from Azoarcus and Tetra

180 Certain group I introns insert into intronless DNA via an endonu

181 A endonucleases, which are each encoded by a group I intron inserted into homologous sites within the

182 We have recently described three group I introns inserted into a single gene, orf142, of

183 An in vitro form of the self-splicing group-I intron interrupting the Azoarcus tRNA(Ile) was s

184 A group I intron interrupts the tRNA(Arg)CCU gene of the a

185 uclease I-Ssp6803I causes the insertion of a group I intron into a bacterial tRNA gene-the only examp

186 of the intron-bearing 43B site; and (c) the group I intron is a self-splicing RNA.

187 e evolutionary history of most lichen-fungal group I introns is characterized by rare gains followed

188 Although the active site of group I introns is phylogenetically conserved, subclasse

189 though CYT-18's C-terminal domain also binds group I introns, it has been intractable to X-ray crysta

190 g of how specific structural features of the group I intron lead to catalysis.

191 In this way, a group I intron located in tRNA(Leu), which has been used

192 most closely resemble the mitochondrial cox1 group I introns of a sponge species, which also has the

193 contrast, a pre-mRNA bearing the Tetrahymena group I intron or the yeast spliceosomal ACT1 intron at

194 r by disruption of the recognition site by a group I intron (or intein) into which the endonuclease O

195 Folding of the 160-nucleotide Tetrahymena group I intron P4-P6 domain was used as a test system.

196 tif of the recently crystallized Tetrahymena group I intron P4-P6 domain.

197 rm species" N. commune characterized through group I intron phylogeny.

198 A group I intron precursor and ribozyme were cloned from t

199 Cbu.L1917, a group I intron present in the 23S rRNA gene of Coxiella

200 maturase thus represents a rare example of a group I intron protein cofactor whose binding is adequat

201 The discovery of the RNA self-splicing group I intron provided the first demonstration that not

202 rf142) is interrupted by three self-splicing group I introns, providing the first example of a phage

203 The Tetrahymena group I intron recognizes its oligonucleotide substrate

204 cular ruler is conserved among a subclass of group I introns related to the Tetrahymena intron.

205 s the native conformation of the Tetrahymena group I intron relative to a globally similar misfolded

206 sults suggest that it stabilizes its cognate group I introns relative to analogous misfolded intermed

207 Like most cellular RNA enzymes, the bI5 group I intron requires binding by a protein cofactor to

208 nal intron of yeast cytochrome b pre-mRNA (a group I intron) requires a protein encoded by the nuclea

209 3p result in accumulation of stable, excised group I intron ribonucleoproteins, which result in seque

210 co-crystal structure of the Twort orf142-I2 group I intron ribozyme bound to splicing-active, carbox

211 cleotide RNA) of the Tetrahymena thermophila group I intron ribozyme changes when its tertiary struct

212 that observed in the crystal structure of a group I intron ribozyme domain.

213 The Tetrahymena group I intron ribozyme folds in vitro to a long-lived m

214 Like many structured RNAs, the Tetrahymena group I intron ribozyme folds through multiple pathways

215 tions on tertiary interactions, binding to a group I intron ribozyme from mouse-derived Pneumocystis

216 o, here we measure native folding of a small group I intron ribozyme from the bacterium Azoarcus by m

217 ns enhance binding of specific hexamers to a group I intron ribozyme from the opportunistic pathogen

218 of the self-splicing Tetrahymena thermophila group I intron ribozyme that is inserted into the ORF of

219 tertiary contact mutants of the Tetrahymena group I intron ribozyme to demonstrate that the efficien

220 As model system, a trans-splicing group I intron ribozyme was evolved in Escherichia coli

221 e of the earliest folding transitions in the group I intron ribozyme, and that it leads to a metastab

222 emble into covalent versions of the Azoarcus group I intron ribozyme.

223 of the P5abc subdomain of the 'Tetrahymena' group I intron ribozyme.

224 RNA, and the P4-P6 domain of the tetrahymena Group I intron ribozyme.

225 Modified Tetrahymena group I intron ribozymes have been used to mediate trans

226 blished crystal and NMR structures of tRNAs, group I introns, ribozymes, RNA aptamers and synthetic o

227 y determined cocrystal structure of a CYT-18/group I intron RNA complex, we identify conserved featur

228 A two-piece version of the group I intron RNA from Tetrahymena is used here to show

229 e Saccharomyces cerevisiae mitochondrial bI3 group I intron RNA in vitro is shown to require both an

230 e Saccharomyces cerevisiae mitochondrial bI5 group I intron RNA is facilitated by both the S. cerevis

231 used to prepare by ligation the Tetrahymena group I intron RNA P4-P6 domain, a representative struct

232 the near-native collapsed state for the bI5 group I intron RNA plays an obligatory role in self-chap

233 The yeast mitochondrial bI3 group I intron RNA splices in vitro as a six-component r

234 ase (LeuRS) performs dual essential roles in group I intron RNA splicing as well as protein synthesis

235 The LeuRS CP1 domain can also support group I intron RNA splicing in the yeast mitochondria, a

236 es/KCl buffer, the catalytic core of the bI5 group I intron RNA undergoes a conformational collapse c

237 environment at adenosine residues in the bI5 group I intron RNA was monitored as a function of Mg(2+)

238 The P4-P6 domain of the Tetrahymena group I intron RNA was systematically modified at multip

239 0-nucleotide P4-P6 domain of the Tetrahymena group I intron RNA, using stopped-flow fluorescence with

240 , but move inward to bind opposite ends of a group I intron RNA.

241 lding of the P4-P6 domain of the Tetrahymena group I intron RNA.

242 CYT-19 does not bind specifically to group I intron RNAs and instead functions as an ATP-depe

243 cing factor by acquiring the ability to bind group I intron RNAs and stabilize their catalytically ac

244 nthetase that also promotes self-splicing of group I intron RNAs by stabilizing the functional struct

245 Group I intron RNAs contain a core of highly conserved h

246 minal domain regions bind both tRNA(Tyr) and group I intron RNAs.

247 bility for nearly all nucleotides in the bI3 group I intron RNP in four assembly states: the free RNA

248 The transition state of the group I intron self-splicing reaction is stabilized by t

249 n (CTD); and (ii) the catalytic domain binds group I introns specifically via multiple structural ada

250 mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity evolved during or after

251 zizomycotina, and biochemical assays confirm group I intron splicing activity for the enzymes from se

252 The unique group I intron splicing activity of these fungal enzymes

253 a mitochondrial RNA chaperone that promotes group I intron splicing and has been shown to resolve mi

254 e (ymLeuRS) performs dual essential roles in group I intron splicing and protein synthesis.

255 ined the crystal structure of a bifunctional group I intron splicing factor and homing endonuclease,

256 CYT-18 protein) evolved a new function as a group I intron splicing factor by acquiring the ability

257 s from those of two other well-characterized group I intron splicing factors, CYT-18 and Cpb2.

258 locked nucleic acid residue, inhibit 50% of group I intron splicing in a transcription mixture at ab

259 functions in concert with CYT-18 to promote group I intron splicing in vivo and vitro.

260 crystal structure of a catalytically active group I intron splicing intermediate containing the comp

261 e the development of a new protein-dependent group I intron splicing system that requires such an ATP

262 ly challenging to determine if Suv3p effects group I intron splicing through RNA degradation as part

263 re provides insight into how CYT-18 promotes group I intron splicing, how it evolved to have this fun

264 TD, but lacks further adaptations needed for group I intron splicing.

265 In the case of the yeast bI3 group I intron, splicing requires binding by two protein

266 andscape of the L-21 Tetrahymena thermophila group I intron structurally and kinetically from its ear

267 further understand the role of metal ions in group I intron structure and function.

268 multiple metal ion core that is critical to group I intron structure and function.

269 the RNA and yielded the catalytically active group I intron structure.

270 cing and has been shown to resolve misfolded group I intron structures, allowing them to refold.

271 Comparative sequence analysis of this group I intron subclass suggests that the A29 interactio

272 ved, selfish genetic elements, including two group I introns, termed Cbu.L1917 (L1917) and Cbu.L1951

273 ons grossly disrupt the catalytically-active group I intron tertiary structure, and that CYT-18 bindi

274 ntially important, high scoring sites in the group I intron that are not currently annotated as Mg2+

275 I-BmoI is encoded by a group I intron that interrupts the thymidylate synthase

276 The group I intron that interrupts the tRNA-Leu gene in cyan

277 precursor of P. carinii contains a conserved group I intron that is an attractive drug target because

278 less active in facilitating the folding of a group I intron that requires CYT-19 in vivo.

279 One such protein is encoded within a group I intron that resides in the recA gene of the Baci

280 Group I introns that encode homing endonuclease genes (H

281 include the signal recognition particle RNA, group I intron, the GlmS ribozyme, RNAseP RNA, and ribos

282 Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a

283 ng of two phylogenetically related catalytic group I introns, the Twort and Azoarcus group I ribozyme

284 , and the first instance of a tRNA(Leu)(UAA) group I intron to be found in a group of bacteria other

285 The unspliced 658-nt intron is the first group I intron to be found in bacterial rDNA or rRNA, an

286 (including 62 novel large subunit [LSU] rRNA group I introns) to study intron movement within the mon

287 exity, the P4-P6 domain from the Tetrahymena group I intron, to address basic questions in RNA foldin

288 RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly.

289 Similarly, group I introns use RNA-catalysed splicing reactions, bu

290 tein CYT-19 disrupts tertiary structure in a group I intron using a helix capture mechanism.

291 iated folding of the Tetrahymena thermophila group I intron using this combined experimental and comp

292 In the first step of self-splicing, group I introns utilize an exogenous guanosine nucleophi

293 ancestral fungal mtTyrRS and a self-splicing group I intron was "fixed" by an intron RNA mutation tha

294 es (hairpins and the Tetrahymena thermophila group I intron), we compute the quasiequilibrium fluctua

295 ed for splicing of the mitochondrial aI5beta group I intron, we show that efficient in vitro splicing

296 rk with Physciaceae small subunit (SSU) rDNA group I introns where strong support was found for multi

297 e of a free-standing endonuclease gene and a group I intron, which we denote "collaborative homing,"

298 e within the P4-P6 domain of the Tetrahymena group I intron, while site 2 is unique among known ion b

299 i, the psbA gene contains four self-splicing group I introns whose rates of splicing in vivo are incr

300 Phage T4 has three group I introns, within the td, nrdB and nrdD genes.