ライフサイエンスコーパス: group II intron

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

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

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

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

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

6 proteins facilitate folding of the ai5gamma group II intron.

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

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

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

10 se domain with similarity to telomerases and 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 fold to form the conserved structures of two group II introns.

20 plicing of certain mitochondrial and plastid group II introns.

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

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

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

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

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

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

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

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

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

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

34 9 and Mss116p in splicing the yeast aI5gamma group II intron and less efficiently in splicing the bI1

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

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

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

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

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

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

41 verse transcriptases (RTs) encoded by mobile group II introns and other non-LTR retroelements differ

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 MarathonRT is encoded within a eubacterial group II intron, and it has been shown to efficiently co

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

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

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

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

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

53 ctions of the template-switching activity of group II intron- and other non-LTR retroelement-encoded

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

55 Group II introns are a class of retroelements that invad

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

57 Mobile group II introns are bacterial retrotransposons thought

58 Group II introns are commonly believed to be the progeni

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

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

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

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

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

64 Group II introns are hypothesized to share common ancest

65 Group II introns are large catalytic RNA molecules that

66 Group II introns are large catalytic RNAs that are ances

67 Group II introns are large, autocatalytic ribozymes that

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

69 Group II introns are mobile genetic elements that invade

70 Catalytic group II introns are mobile retroelements that invade co

71 Group II introns are mobile retroelements that invade th

72 Group II introns are ribozymes whose catalytic mechanism

73 Group II introns are self-splicing ribozymes and mobile

74 Group II introns are self-splicing ribozymes that cataly

75 Group II introns are self-splicing ribozymes that share

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

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

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

79 Group II introns are structurally complex catalytic RNAs

80 Group II introns are the putative progenitors of nuclear

81 Group II introns are ubiquitous self-splicing ribozymes

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

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

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

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

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

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

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

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

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

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

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

93 idence of the role the maturase plays during group II intron catalysis.

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

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

96 3 and the base of D2 are key elements of the group II intron core and they suggest a hierarchy for ac

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

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

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

100 Mobile group II introns encode proteins with both reverse trans

101 Mobile group II introns encode reverse transcriptases that also

102 Mobile group II introns encode reverse transcriptases that bind

103 Group II intron-encoded proteins promote both splicing a

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

129 Group II intron homing in yeast mitochondria is initiate

130 Many group II introns identified in bacteria reside on plasmi

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

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

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

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

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

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

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

138 play essential roles in splicing group I and group II introns in mitochondria and chloroplasts.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

157 tle is known about how splicing of bacterial group II introns is influenced by environmental conditio

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

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

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

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

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

163 the pRS01 plasmid-encoded Lactococcus lactis group II intron, Ll.LtrB, splicing enables expression of

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

182 Most group II introns require accessory factors to splice eff

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

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

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

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

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

188 Group II intron retrohoming occurs by a mechanism in whi

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

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

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

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

193 structures at 3.6- angstrom resolution of a group II intron reverse splicing into DNA.

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

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

196 Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-

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 Thermostable group II intron reverse transcriptases (TGIRTs) with hig

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

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

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

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

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

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

216 Although structures of spliced group II intron RNAs and RNP complexes have been charact

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 k-turn motif instances, conserved domains in group II intron RNAs, and the tRNA mimicry of IRES RNAs.

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

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

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

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

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

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

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

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

233 Group II intron RNPs are mobile genetic elements that at

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

235 cryo-EM structures of endogenously produced group II intron RNPs trapped in their pre-catalytic stat

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

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

238 cceptor RNAs or DNAs, we used a thermostable group II intron RT (TGIRT; GsI-IIC RT) that can template

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

240 inst mismatches and the high processivity of group II intron RTs enable synthesis of full-length DNA

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

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

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

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

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

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

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

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

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

250 s not only the intrinsic cold sensitivity of group II intron splicing and the role of the IEP for col

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

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

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

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

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

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

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

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

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

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

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

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

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

264 Our insights into the mechanism of group II intron splicing parallels functional data on th

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

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

267 tanding the structural basis of IEP-assisted group II intron splicing, but also provide parallels to

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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