ライフサイエンスコーパス: group II intron

1 romotes the splicing of the chloroplast atpF group II intron.

2 ner to a divalent cation binding site of the group II intron.

3 ron and less efficiently in splicing the bI1 group II intron.

4 ce ribozyme constructs based on the ai5gamma group II intron.

5 proteins facilitate folding of the ai5gamma group II intron.

6 lasts, even after the loss of its co-evolved group II intron.

7 n genes, 3 rRNA genes, 17 tRNA genes, and 30 group II introns.

8 nomes in land plants harbor approximately 20 group II introns.

9 se domain with similarity to telomerases and group II introns.

10 fold to form the conserved structures of two group II introns.

11 at are much smaller than the spliceosome and group II introns.

12 ural sequences of spliceosome substrates and group II introns.

13 tion sites of the E.c.I4 family of bacterial group II introns.

14 echanisms shared by organellar and bacterial group II introns.

15 stal structures of domain 5 of self-splicing group II introns.

16 s that regulate translation, and group I and group II introns.

17 snRNAs and their resemblance to elements of group II introns.

18 at appear to govern branch-site selection by group II introns.

19 perone in splicing mitochondrial group I and group II introns.

20 ctions in splicing mitochondrial group I and group II introns.

21 s at the heart of the catalytic apparatus in group II introns.

22 is among the most conserved elements in the group II intron active site.

23 site" strategy, we show that the yeast mtDNA group II intron aI1 retrotransposes by reverse splicing

24 e Saccharomyces cerevisiae mitochondrial DNA group II intron aI2 depends on the intron-encoded 62-kDa

25 ntains circles, indicating that at least one group II intron (aI2) forms circles in vivo.

26 The group II intron ai5gamma from S. cerevisiae requires hig

27 The autocatalytic group II intron ai5gamma from Saccharomyces cerevisiae s

28 t that the rate-limiting step for folding of group II intron ai5gamma occurs early along the reaction

29 long the backbone of a ribozyme derived from group II intron ai5gamma.

30 protein Mss116 on its natural substrate, the group II intron ai5gamma.

31 en suggested to assist in the folding of one group II intron (aI5gamma) primarily by stabilizing a fo

32 te themselves via reverse transcription, the group II introns, also known as retrointrons.

33 somal introns, consistent with the bacterial group II intron ancestry hypothesis.

34 omplex formed between the Lactococcus lactis group II intron and its self-encoded LtrA protein is ess

35 9 and Mss116p in splicing the yeast aI5gamma group II intron and less efficiently in splicing the bI1

36 ses of retargeted Lactococcus lactis Ll.LtrB group II introns and a compilation of nucleotide frequen

37 g, and the evolutionary relationship between group II introns and both eukaryotic spliceosomal intron

38 ritical Mg(2+)-dependent RNA folding step in group II introns and demonstrate the feasibility of sele

39 s of proteins that assemble with chloroplast group II introns and facilitate splicing.

40 fficient in vivo splicing of all group I and group II introns and for activation of mRNA translation.

41 nction in splicing mitochondrial group I and group II introns and in translational activation.

42 idence that RH3 functions in the splicing of group II introns and possibly also contributes to the as

43 eedlings with defects in splicing of several group II introns and rRNA maturation as well as reduced

44 tional analogies support the hypothesis that group II introns and the spliceosome share a common ance

45 These findings indicate that group II introns and the spliceosome share common cataly

46 leotide, which is almost always adenosine in group II introns and the spliceosome.

47 e classes of catalytic RNA: group I introns, group II introns, and 23S rRNA.

48 mulates the in vitro splicing of group I and group II introns, and functions indistinguishably from C

49 timulate the splicing of diverse group I and group II introns, and that Ded1p also has an RNA chapero

50 The distinguishing feature of group II introns, and the property that links them with

51 splicing of structurally diverse group I and group II introns, and uses the energy of ATP binding or

52 The chloroplast gene trnK and its associated group II intron appear to be absent in a large and ancie

53 Although group II introns are active in bacteria, their natural h

54 Mobile group II introns are bacterial retrotransposons thought

55 Group II introns are catalytic RNAs that have been propo

56 Group II introns are commonly believed to be the progeni

57 Most chloroplast group II introns are degenerate, requiring interaction w

58 is no doubt that prokaryotic and organellar group II introns are evolutionary related, there are rem

59 Group II introns are found in all three domains of life

60 Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, an

61 Group II introns are found in fungal and land plant mito

62 Group II introns are hypothesized to share common ancest

63 Group II introns are large catalytic RNA molecules that

64 Group II introns are large catalytic RNAs that are ances

65 Group II introns are large, autocatalytic ribozymes that

66 Group II introns are Mg(2+)-dependent ribozymes that are

67 Group II introns are mobile genetic elements that invade

68 Catalytic group II introns are mobile retroelements that invade co

69 Group II introns are mobile retroelements that invade th

70 Group II introns are ribozymes whose catalytic mechanism

71 Group II introns are self-splicing ribozymes that cataly

72 Group II introns are self-splicing ribozymes that share

73 Group II introns are self-splicing RNA molecules that al

74 Group II introns are self-splicing RNAs found in eubacte

75 Mobile group II introns are site-specific retroelements that us

76 Group II introns are structurally complex catalytic RNAs

77 Group II introns are usually removed from precursor RNAs

78 Group II introns are well recognized for their remarkabl

79 y structure and tertiary interactions of the group II intron, as well as the derived maturase primary

80 cific set of plastid RNAs, including several group II introns, as well as pre23S and 23S ribosomal RN

81 Here we report 14 crystal structures of a group II intron at different stages of catalysis.

82 g body of information on the folded state of group II introns at equilibrium, there is currently no i

83 Thus, a group II intron can splice from a nuclear transcript, bu

84 We find that group II introns can also be excised as complete circles

85 Consequently, group II introns can be reprogrammed to insert into spec

86 he human CCR5 gene as examples, we show that group II introns can be retargeted to insert efficiently

87 Mobile group II introns can be retargeted to insert into virtua

88 Here we show that retargeted group II introns can be used for highly specific chromos

89 sm for linear group II intron RNAs, show how group II introns can co-opt different DNA repair pathway

90 The duality of group II introns, capable of carrying out both self-spli

91 ss about branching than any other feature of group II intron catalysis, largely because the receptor

92 Despite its importance for group II intron catalytic activity, structural informati

93 three-dimensional structural modeling of the group II intron catalytic core.

94 The mechanism by which group II introns cleave the correct phosphodiester linka

95 3 and the base of D2 are key elements of the group II intron core and they suggest a hierarchy for ac

96 Thus, during evolution, group II introns could have spliced and transposed by re

97 conjugative element suggests a mechanism for group II intron dispersal among bacteria.

98 les at 5 mM Mg(2+), suggests models in which group II intron domains I and II are either coaxially st

99 Mobile group II introns encode proteins with both reverse trans

100 Mobile group II introns encode reverse transcriptases that also

101 Mobile group II introns encode reverse transcriptases that bind

102 Group II intron-encoded proteins promote both splicing a

103 nuclease domains characteristic of canonical group II intron-encoded proteins, while the two nMat-2 p

104 reading frames encoding proteins related to group II intron-encoded reverse transcriptase/maturases.

105 The Lactococcus lactis Ll.LtrB group II intron encodes a reverse transcriptase (LtrA pr

106 The Lactococcus lactis Ll.LtrB group II intron encodes a reverse transcriptase/maturase

107 nteraction of the Lactococcus lactis Ll.LtrB group II intron endonuclease with its DNA target site by

108 first detailed view of the interaction of a group II intron endonuclease with its DNA target site.

109 The group II intron endonuclease, which mediates this proces

110 ility and DNA replication, new insights into group II intron evolution arising from bacterial genome

111 y, we selected a member of the self-splicing group II intron family, which is hypothesized to be the

112 its biological role in the stabilization of group II intron folding intermediates.

113 We propose that Mss116 stimulates group II intron folding through a multi-step process tha

114 that can be selectively lost, and a designed group II intron for efficient, targeted chromosomal inse

115 Mobile group II introns, found in bacterial and organellar geno

116 rizontal transfer of a self-splicing, homing group II intron from a cyanobacteria to the chloroplast

117 first example of a self-splicing chloroplast group II intron from any organism.

118 crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 ang

119 g, and mechanistic characterization of a new group II intron from the bacterium Azotobacter vinelandi

120 step to understanding the transition of the group II intron from the precursor to a species fully ac

121 ed that ISE2 is required for the splicing of group II introns from chloroplast transcripts.

122 of the host gene contributed to expulsion of group II introns from nuclear genomes and drove the evol

123 Barriers to group II intron function in nuclear genomes therefore be

124 RNA folding models and to better understand group II intron function, we have examined the tertiary

125 oan nuclear spliceosomal introns; therefore, group II introns have been invoked as the progenitors of

126 Mobile group II introns have been used to develop a novel class

127 Many group II introns have lost the ability to splice autonom

128 Group II introns have played a major role in genome evol

129 The structure and catalytic mechanism of group II introns have recently been elucidated through a

130 Group II intron homing in yeast mitochondria is initiate

131 Many group II introns identified in bacteria reside on plasmi

132 Among the 22 group II introns identified, 7 are trans-spliced.

133 nucleotide D5 from the Pylaiella littoralis group II intron in the presence and absence of magnesium

134 us study showed that nuclear expression of a group II intron in yeast results in nonsense-mediated de

135 , which is required for the splicing of nine group II introns in chloroplasts.

136 protein, Zm-mTERF4, promotes the splicing of group II introns in chloroplasts.

137 to promote the splicing of specific sets of group II introns in maize chloroplasts.

138 ed protein required for the splicing of nine group II introns in maize chloroplasts.

139 ncoded proteins required for the splicing of group II introns in maize chloroplasts.

140 mechanistic rationales for the prevalence of group II introns in natural plasmid populations and unde

141 o have a generalist function, splicing other group II introns in the chloroplast genome.

142 with the group I intron in pre-trnL-UAA and group II introns in the ndhA and ycf3 pre-mRNAs.

143 -CAF complexes bind tightly to their cognate group II introns in vivo, with the CAF subunit determini

144 promotes the splicing of several chloroplast group II introns: in Arabidopsis apo1 mutants, ycf3-intr

145 Results for the aI2 group II intron indicate that Mss116p is needed after bi

146 nd reveals a previously unsuspected bias for group II intron insertion near the chromosome replicatio

147 The mobile Lactococcus lactis Ll.LtrB group II intron integrates into DNA target sites by a me

148 iosis through fragmentation of self-splicing group II introns into a dynamic, protein-rich RNP machin

149 the protein, it has been possible to develop group II introns into a new type of gene targeting vecto

150 and may have contributed to the dispersal of group II introns into different genes.

151 nally, we describe the development of mobile group II introns into gene-targeting vectors, "targetron

152 ay reflect a step in the evolution of mobile group II introns into spliceosomal introns.

153 ay (NMD), and the mature mRNA from which the group II intron is spliced is poorly translated.

154 However, a pre-mRNA harboring a group II intron is spliced predominantly in the cytoplas

155 ere, we show that retrohoming of the Ll.LtrB group II intron is strongly inhibited in an Escherichia

156 NA binding motifs to those of telomerase and group II introns is discussed.

157 The RNA-catalyzed splicing of group I and group II introns is facilitated by proteins that stabili

158 The branch site of group II introns is typically a bulged adenosine near th

159 s in plants and green algae contain numerous group II introns, large ribozymes that splice via the sa

160 The TP retrotransposons considered here are group II introns, LINEs and SINEs, whereas the EP elemen

161 The lactococcal group II intron Ll.ltrB interrupts the ltrB relaxase gen

162 e ltrB gene is interrupted by the functional group II intron Ll.ltrB.

163 coli, retrotransposition of the lactococcal group II intron, Ll.LtrB, occurs preferentially within t

164 d support the putative function of MATK as a group II intron maturase.

165 unts, in part, for the intron specificity of group II intron maturases and has parallels in template-

166 Our results suggest that the folding of some group II introns may be limited by kinetic traps and tha

167 Self-splicing group II introns may be the evolutionary progenitors of

168 so discuss recently discovered links between group II intron mobility and DNA replication, new insigh

169 ental basis for our current understanding of group II intron mobility mechanisms, beginning with gene

170 Group II intron mobility occurs by a target DNA-primed r

171 in these regions, and could potentially link group II intron mobility to the host DNA replication and

172 ing metabolic stress, cAMP and ppGpp control group II intron movement in concert with the cell's glob

173 . trans-splicing status of the mitochondrial group II intron nad1i728 in 439 species (427 genera) of

174 ry contacts that have been identified within group II introns, none has included D3 residues.

175 Among land plants, mitochondrial and plastid group II introns occasionally encode proteins called mat

176 Retrohoming of group II introns occurs by a mechanism in which the intr

177 Splicing by group II introns plays a major role in the metabolism of

178 nce of the introns within cox1 is similar to Group II introns previously identified, suggesting that

179 recruited to promote the splicing of plastid group II introns prior to the divergence of monocot and

180 activity and constitute a natural barrier to group II intron proliferation within nuclear genomes.

181 omain that are conserved in LtrA and related group II intron proteins, and their functional importanc

182 Chlamydomonas reinhardtii, two discontinuous group II introns, psaA-i1 and psaA-i2, splice in trans,

183 D3 stimulates the chemical rate constant of group II intron reactions, and that it behaves as a form

184 Most group II introns require accessory factors to splice eff

185 The ai5gamma group II intron requires a protein cofactor to facilitat

186 Furthermore, many bacterial group II introns reside on the lagging-strand template,

187 ding indicates not only that retrotransposed group II introns retain mobility properties, but also th

188 Mobile group II introns retrohome by an RNP-based mechanism in

189 The Lactococcus lactis Ll.LtrB group II intron retrohomes by reverse-splicing into one

190 Group II intron retrohoming occurs by a mechanism in whi

191 of global regulators cAMP and ppGpp inhibits group II intron retromobility.

192 nd origins of replication is consistent with group II intron retrotransposition into single-stranded

193 results suggest that bipolar localization of group II intron retrotransposition results from the resi

194 e C-terminal DNA endonuclease domain and for group II intron retrotransposition to ectopic sites.

195 iated domains of Prp8 resembling a bacterial group II intron reverse transcriptase and a type II rest

196 ar ligands for IFIT5 by using a thermostable group II intron reverse transcriptase for RNA sequencing

197 present our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-

198 lations and a highly processive thermostable group II intron reverse transcriptase to overcome these

199 fications as mismatches using a thermostable group II intron reverse transcriptase.

200 Bacterial group II intron reverse transcriptases (RTs) function in

201 template-switching activity of thermostable group II intron reverse transcriptases (TGIRTs) for DNA-

202 own function 860" (DUF860) as a component of group II intron ribonucleoprotein particles in maize chl

203 data demonstrate that the cleavage site of a group II intron ribozyme can be tuned at will by manipul

204 rotections that are distributed throughout a group II intron ribozyme derived from intron ai5gamma.

205 The D135 group II intron ribozyme follows a unique folding pathwa

206 The D135 group II intron ribozyme is unusual in that it can fold

207 Group II intron ribozymes catalyze the cleavage of (and

208 The folding of group II intron ribozymes has been studied extensively u

209 at natively prepared 160 and 175 kDa minimal group II intron ribozymes have enhanced catalytic activi

210 ., the cleavage of the 5'-exon) catalyzed by group II intron ribozymes.

211 CRS2 co-sediments with group II intron RNA during centrifugation of stroma thro

212 Folding of group II intron RNA is often guided by an intron-encoded

213 at-2), neither of which is associated with a group II intron RNA structure.

214 ides a first example of a thermally tolerant group II intron RNA.

215 , divalent metals in crystal structures of a group II intron RNA.

216 enough to accommodate the catalytic core of group II intron RNA.

217 Group II intron RNAs fold into catalytically active stru

218 The secondary structure of group II intron RNAs is typically described as a series

219 ays for retrohoming, and suggest that linear group II intron RNAs might be used for site-specific DNA

220 In contrast, DbpA binds group I and group II intron RNAs nonspecifically, but its ATPase act

221 Group II intron RNAs self-splice in vitro but only at hi

222 , this correlation holds for all group I and group II intron RNAs tested, implying a fundamentally si

223 o weaker non-specific binding of group I and group II intron RNAs, and surprisingly, also impairs RNA

224 omotes in vitro splicing of both group I and group II intron RNAs, as well as RNA cleavage by the aI5

225 investigated cellular dynamics of processed group II intron RNAs, from transcription to cellular loc

226 noprecipitates from chloroplast extract with group II intron RNAs, is required for the splicing of th

227 dings reveal a mobility mechanism for linear group II intron RNAs, show how group II introns can co-o

228 rs ago, after the discovery of self-splicing group II intron RNAs, the snRNAs were proposed to cataly

229 However, linear group II intron RNAs, which can arise by either hydrolyt

230 e have trapped the native Lactococcus lactis group II intron RNP complex in its precursor form, by de

231 odynamic and structural properties of active group II intron RNP particles (+A) isolated from its nat

232 Group II intron RNPs are mobile genetic elements that at

233 rosophila melanogaster embryos, to show that group II intron RNPs containing linear intron RNA can re

234 her that AtCAF1 promotes the splicing of two group II introns, rpoC1 and clpP-intron 1, that are foun

235 ion comparable to well-folded RNAs, like the group II intron, rRNA, or lncRNA steroid receptor activa

236 stal structure of a full-length thermostable group II intron RT in complex with an RNA template-DNA p

237 ute to distinctive biochemical properties of group II intron RTs, and it provides a prototype for man

238 Because of their wide host range, mobile group II introns should be useful for genetic engineerin

239 Studies of a bacterial group II intron showed that the DIVa substructure of int

240 ity to target DNA replication may be used by group II intron species that encode proteins lacking the

241 ion to providing a mechanistic rationale for group II intron-specific repression, our data support th

242 and that these roadblocks to expression are group II intron-specific.

243 tion capabilities in four additional RNAs: a group II intron, Spinach II, 2-MS2 binding domain and gl

244 we show that the Lactococcus lactis Ll.LtrB group II intron splices accurately and efficiently from

245 decreasing duplex length and correlates with group II intron splicing activity in quantitative assays

246 al repertoire of the mTERF family to include group II intron splicing and suggest that a conserved ro

247 ion in mitochondria to stimulate group I and group II intron splicing and to activate mRNA translatio

248 y be imported into organelles to function in group II intron splicing and/or they may have assumed ot

249 ypothesis that DEAD-box proteins function in group II intron splicing as in other processes by using

250 f DEAD-box proteins to stimulate group I and group II intron splicing correlates primarily with their

251 ts mitochondrial translation and group I and group II intron splicing defects in mss116Delta strains,

252 CAF1, CAF2 and the previously described group II intron splicing factor CRS1 are characterized b

253 recognized RNA binding domain found in three group II intron splicing factors in chloroplasts, in a b

254 ere, we describe two additional host-encoded group II intron splicing factors, CRS2-associated factor

255 in some organisms could evolve into general group II intron splicing factors, potentially mirroring

256 he notion that nuclear pre-mRNA splicing and group II intron splicing have a common origin.

257 box protein SrmB also stimulates group I and group II intron splicing in vitro, while the E. coli DEA

258 clear DEAD-box protein Ded1p could stimulate group II intron splicing in vitro.

259 The DEAD-box protein Mss116p promotes group II intron splicing in vivo and in vitro.

260 additional protein that promotes chloroplast group II intron splicing in vivo.

261 otein NPH-II gave little, if any, group I or group II intron splicing stimulation in vitro or in vivo

262 DEAD-box proteins that stimulate group I and group II intron splicing unwind RNA duplexes by local st

263 ic 2',5'-branched RNAs for investigations of group II intron splicing, debranching enzyme (Dbr) activ

264 aspects of chloroplast RNA processing beyond group II intron splicing.

265 ts, suggesting that MTL1 is also involved in group II intron splicing.

266 with peptidyl-tRNAs to acquire a function in group II intron splicing.

267 lore two hypotheses for how Mss116p promotes group II intron splicing: by using its RNA unwinding act

268 which sheds new light on D3 function in the group II intron structure and mechanism.

269 in PTH, suggesting that CRS2 interacts with group II intron substrates via this surface.

270 rast, mostly linear RNA is obtained with the group II intron substrates.

271 nsertion sites provides further insight into group II intron target site recognition rules.

272 utational analysis provides new insight into group II intron target site recognition, and the set of

273 ion in ribozyme and substrate sequences near group II intron target sites.

274 ific probes, AW-10, encodes part of GBSi1, a group II intron that is inserted at two sites within the

275 irst intron of the plastid rps12 pre-mRNA, a group II intron that is transcribed in segments and spli

276 nd in complexes with a subset of chloroplast group II introns that includes but is not limited to CAF

277 Gnetum has two copies of intron 2, a group II intron, that differ in their exons, nucleotide

278 Group II introns, the presumed ancestors of nuclear pre-

279 he conjugative transposon Tn5397 including a group II intron, thus highlighting a potential decrease

280 Furthermore, an evolutionary relationship of group II introns to eukaryotic retroelements, including

281 However, the ability of group II introns to function outside of the bacteria-der

282 " to unoccupied sites in intronless alleles, group II introns transpose at low frequency to ectopic s

283 These experiments provide new insights to group II intron transposition and homing mechanisms in y

284 wo general mechanisms have been proposed for group II intron transposition, one involving reverse spl

285 lasses of introns: self-splicing group I and group II introns, tRNA and/or archaeal introns and splic

286 verse splicing of the yeast aI5gamma and bI1 group II introns under near-physiological conditions by

287 The Lactococcus lactis Ll.LtrB group II intron uses a major retrohoming mechanism in wh

288 ify yeast and phage RNA-binding proteins and group II intron, viral and bacterial noncoding RNA (ncRN

289 Using a retargeted group II intron, we generated a C. difficile mutation in

290 ues into oligonucleotides for studies of the group II intron, we synthesized six new phosphoramidite

291 ntron and the ndhA, ycf3-int1, and clpP-int2 group II introns (weak alleles).

292 tle is known about the tertiary structure of group II introns, which are among the largest natural ri

293 Splicing is necessary to remove the group II introns, which interrupt the coding sequences o

294 sely is domain 5 (D5) from the self-splicing group II introns, which is at the heart of its catalytic

295 a situation that may resemble most bacterial group II introns, which lack the endonuclease.

296 Group II introns, widely believed to be the ancestors of

297 dracea was found to contain a single 2566 nt group II intron with a gene in domain 4 for a 575 amino

298 perties, it has been of interest to find new group II introns with novel properties.

299 iceosomal introns are thought to derive from group II introns, with which they show mechanistic and s

300 e host defenses, the infrequent mutations of group II introns would ensure intron spread through rete