ライフサイエンスコーパス: riboswitch

1 7-aminomethyl-7-deazaguanine (preQ1)-sensing riboswitch.

2 is distinctly different from that in the apo riboswitch.

3 evealed new tertiary interactions in the TPP riboswitch.

4 n-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch.

5 d metabolite-bound closed state of the SAM-I riboswitch.

6 positive bacteria are regulated by the T box riboswitch.

7 edge, of translational regulation in a T box riboswitch.

8 expression is controlled by a type I c-diGMP riboswitch.

9 e folding free energy landscape of the SAM-I riboswitch.

10 31 expression by a c-diGMP-dependent type II riboswitch.

11 dscapes of the cyclic diguanylate (c-di-GMP) riboswitch.

12 uctural probes into an ES of the ligand-free riboswitch.

13 ultiple conformational states of the adenine riboswitch.

14 es making quasi-equivalent contacts with the riboswitch.

15 ngle adenosyl cobalamine (AdoCbl)-responsive riboswitch.

16 determined the co-crystal structure of this riboswitch.

17 us explicit-solvent simulations of the SAM-I riboswitch.

18 folding free energy landscape of the SAM-II riboswitch.

19 s strong co-transcriptional effects for this riboswitch.

20 and the P3 helix is a bottleneck in the apo riboswitch.

21 development of efficient cis-acting aptazyme riboswitches.

22 ersity of naturally occurring ligand-binding riboswitches.

23 h2 aptamer to ligand-binding domains of cdiA riboswitches.

24 nine synthase, can be converted into Spinach riboswitches.

25 lite sensor derived from naturally occurring riboswitches.

26 integral components of ribozymes, mRNA, and riboswitches.

27 egion (UTR) derives from bacterial and other riboswitches.

28 regulation implemented by a wide variety of riboswitches.

29 t in Archaea is controlled by FMN-responsive riboswitches.

30 strand-specific RNA sequencing to identify 4 riboswitches, 13 trans-acting (intergenic), and 22 cis-a

31 standard inducible promoters and orthogonal riboswitches, a multi-layered modular genetic control ci

32 Here we describe Spinach riboswitches, a new class of genetically encoded metabol

33 Riboswitches, a widespread group of regulatory RNAs, are

34 macromolecular crowding collectively control riboswitch activation.

35 cted toward the identification of artificial riboswitch activators by establishing high-throughput sc

36 A T-box regulator or riboswitch actively monitors the levels of charged/uncha

37 ding pocket have relatively little impact on riboswitch activity.

38 apped for the expression platform of various riboswitches, allowing metabolite binding to induce Spin

39 Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high se

40 ong evidence that translationally regulating riboswitches also regulate mRNA levels through an indire

41 A majority of riboswitches, an important class of small metabolite-sen

42 An artificial flavin mononucleotide riboswitch and a randomly generated RNA sequence are fou

43 structure upstream of the characterized HIV riboswitch and demonstrates the basal translation rate o

44 electivity similar to that of the endogenous riboswitch and enables the discovery of agonists and ant

45 t with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of

46 ession platform of the P3 helix in the bound riboswitch and the P3 helix is a bottleneck in the apo r

47 ed allosteric switching" is proposed to link riboswitch and translation regulation.

48 ional interactions-e.g., at switch points in riboswitches and at a complex nucleation site in HIV.

49 ross species, which correspond to many known riboswitches and further suggest novel putative regulato

50 ecent studies have identified new classes of riboswitches and have revealed new insights into the mol

51 ods that have been developed to engineer new riboswitches and highlight applications of natural and s

52 ble approach for pharmacologically targeting riboswitches and other structured RNA molecules.

53 esistance genes including metabolite-binding riboswitches and other transcription attenuators.

54 ting a screening assay platform suitable for riboswitches and potentially a wide range of RNA and oth

55 ble to modulate gene expression as shown for riboswitches and RNA thermometers.

56 n streamlines design of synthetic allosteric riboswitches and small molecule-nucleic acid complexes.

57 from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation

58 long-lost ligand sensed by the ykkC class of riboswitches, and identified that members of its regulon

59 of the streptomycin aptamer into functional riboswitches appears to be difficult.

60 y determining four structures of the adenine riboswitch aptamer domain during the course of a reactio

61 within a single folded domain, the preQ1-III riboswitch aptamer forms a HLout-type pseudoknot that do

62 ring ligand recognition of the preQ1 class-I riboswitch aptamer from Thermoanaerobacter tengcongensis

63 dent and specific to c-di-GMP binding to the riboswitch aptamer.

64 highly extended conformations of an adenine riboswitch aptamer.

65 yclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose st

66 structured RNAs including ribozyme domains, riboswitch aptamers, and viral RNA domains with a single

67 Riboswitches are a broadly distributed form of RNA-based

68 Riboswitches are a class of cis-acting regulatory RNAs n

69 Riboswitches are a class of metabolism control elements

70 Riboswitches are a widely distributed class of regulator

71 Riboswitches are cis-regulatory elements in mRNA, mostly

72 Riboswitches are common gene regulatory units mostly fou

73 The ligand recognition mechanisms of riboswitches are diverse, but we find that they share a

74 Flavin mononucleotide (FMN) riboswitches are genetic elements, which in many bacteri

75 Riboswitches are natural ligand-sensing RNAs typically t

76 PreQ1-III riboswitches are newly identified RNA elements that cont

77 Riboswitches are non-coding RNA structures located in me

78 Riboswitches are regulatory elements that control gene e

79 Riboswitches are RNA elements that act on the mRNA with

80 Prequeuosine (preQ1) riboswitches are RNA regulatory elements located in the

81 Riboswitches are RNAs that form complex, folded structur

82 Riboswitches are shape-changing regulatory RNAs that bin

83 Riboswitches are short sequences of messenger RNA that c

84 s, the ligand-mediated folding mechanisms of riboswitches are still poorly understood.

85 Riboswitches are structural genetic regulatory elements

86 Riboswitches are structural RNA elements that are genera

87 Synthetic riboswitches are versatile tools for the study and manip

88 Riboswitches are widespread RNA motifs that regulate gen

89 rize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON ribosw

90 ach for the design of synthetic theophylline riboswitches based on secondary structure prediction.

91 Our riboswitch-based biosensors required an alternate invert

92 The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three fa

93 These riboswitches bind metal cooperatively, and with affiniti

94 This TPP Spinach riboswitch binds TPP with affinity and selectivity simil

95 nucleotide Streptococcus pneumoniae preQ1-II riboswitch bound to preQ1.

96 h-fidelity co-transcriptional folding of the riboswitch but are only indirectly linked to regulatory

97 at the two alternate secondary structures of riboswitches can be accurately predicted once the 'switc

98 ption of essential genes controlled by T-box riboswitches can be directly modulated by commonly used

99 trate how the modular architecture of purine riboswitches can be exploited to develop orthogonal and

100 Computational prediction of putative riboswitches can provide direction to molecular biologis

101 f the ykkC motif RNA, the longest unresolved riboswitch candidate, naturally sense and respond to gua

102 NA-mediated regulators (e.g., thermosensors, riboswitches, cis- and trans-encoded RNAs) used for adap

103 iochemical data confirm that members of this riboswitch class selectively bind ZMP and ZTP with nanom

104 The wide distribution of this riboswitch class suggests that ZMP/ZTP signaling is impo

105 ein, we report the existence of a widespread riboswitch class that is most commonly associated with g

106 scoveries are unique variants of the guanine riboswitch class that most tightly bind the nucleoside 2

107 ition, we identified variants of the glycine riboswitch class that no longer recognize this amino aci

108 nesis are controlled by members of a variant riboswitch class that selectively bind c-AMP-GMP.

109 roups of protein enzymes and receptors, some riboswitch classes have evolved to change their ligand s

110 a procedure to systematically analyze known riboswitch classes to find additional variants that have

111 overing a large number of additional natural riboswitch classes.

112 ls in Gram--negative bacteria, translational riboswitches--commonly embedded in messenger RNAs (mRNAs

113 is required to couple ligand binding to the riboswitch conformational changes involved in regulating

114 Thus, Spinach riboswitches constitute a novel class of RNA-based fluor

115 ructures show that the Escherichia coli btuB riboswitch contains a kissing loop interaction that is i

116 uggesting that the majority of known E. coli riboswitches control transcription termination by using

117 A recently discovered c-di-AMP-responsive riboswitch controls the expression of genes in a variety

118 Bacterial riboswitches couple small-molecule ligand binding to RNA

119 Known primarily from bacteria, riboswitches couple specific ligand binding and changes

120 same RNA structural transitions related to a riboswitch decision-making process that we previously id

121 la Mg(2+) transporter mgtA locus in a Mg(2+) riboswitch-dependent manner.

122 Riboswitch descriptions are easily modifiable and new on

123 ertiary structural interactions in cobalamin riboswitches dictate ligand selectivity.

124 On the other hand, these two types of cation riboswitches do not share similarity at the primary or s

125 This riboswitch domain is also conserved in several Gram-nega

126 f the phylogenetically widespread classes of riboswitches, each specific to a particular metabolite o

127 This riboswitch-effector interplay produces a layer of gene r

128 namics of a hydroxocobalamin (HyCbl) binding riboswitch (env8HyCbl) with a known crystallographic str

129 The resulting tetracycline riboswitches exhibit robust regulatory properties in viv

130 he folding of the aptamer, kissing loop, and riboswitch expression platform, we established the confo

131 has been very successful in identifying new riboswitch families and defining their distributions, sm

132 9% sensitivity and >99.99% specificity on 13 riboswitch families.

133 The yybP-ykoY riboswitch family is quite widespread, yet its ligand an

134 Although numerous riboswitches fold as H-type or HLout-type pseudoknots th

135 We review how riboswitch folds adhere to this fundamental strategy and

136 which also measured a 3.7 nM affinity of the riboswitch for guanine.

137 e 71-nucleotide aptamer domain of an adenine riboswitch for nuclear magnetic resonance spectroscopy o

138 Here, we introduce these artificial riboswitches for regulation of DNA and RNA viruses.

139 t broadly distributed and numerous bacterial riboswitches for which the cognate ligand was unknown.

140 iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis(48 nt), and a frame-s

141 d approach was used to re-engineer the PreQ1 riboswitch from Bacillus subtilis into an orthogonal OFF

142 e show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of t

143 the crystal structure of the class III preQ1 riboswitch from Faecalibacterium prausnitzii at 2.75 A r

144 ide resolution for the I-A type 2'dG-sensing riboswitch from Mesoplasma florum by NMR spectroscopy.

145 transferase, and the S-adenosyl-methionine-I riboswitch from the B. subtilis yitJ gene encoding methi

146 case of the thiamine 5'-pyrophosphate (TPP) riboswitch from the Escherichia coli thiM gene encoding

147 iboswitch, including the guanine and adenine riboswitches from the Bacillus subtilis xpt gene encodin

148 ency make screening such large libraries for riboswitch function in intact cells impractical.

149 pling of synthesis and folding essential for riboswitch function, revealing the importance of metasta

150 ing RNA synthesis is important to understand riboswitch function.

151 Here we show that synthetic riboswitches function in an E. coli S30 extract in a man

152 oduces cAG and uses a subset of GEMM-I class riboswitches (GEMM-Ib, Genes for the Environment, Membra

153 tomic-resolution structural information, and riboswitch gene associations.

154 edicted once the 'switching sequence' of the riboswitch has been properly identified.

155 A typical class of riboswitch has its own unique structural and biological

156 epresentative members of the SAM-I family of riboswitches has been extensively analyzed using approac

157 While SAM-I riboswitches have 3b.3n sequences that would predispose

158 genic approach to demonstrate that cobalamin riboswitches have a broad spectrum of preference for the

159 These riboswitches have been constructed to regulate ligand-de

160 Numerous classes of riboswitches have been discovered, enabling mRNA to be r

161 alian gene expression with ligand-responsive riboswitches have been hindered by lack of a general met

162 Traditionally, riboswitches have been identified through comparative ge

163 ntal importance in bacteria gene regulation, riboswitches have been proposed as antibacterial drug ta

164 Although Bacillus subtilis riboswitches have been shown to control premature transc

165 Riboswitches have gained attention as tools for syntheti

166 al and biological complexity, making de novo riboswitch identification a formidable task.

167 uggests the need for alternative methods for riboswitch identification, possibly based on features in

168 ence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis,

169 g data for the Bacillus subtilis glyQS T-box riboswitch in complex with an uncharged tRNAGly.

170 g mechanism of an H-type pseudoknotted preQ1 riboswitch in dependence of Mg(2+) and three ligands of

171 Furthermore, expression of the TPP Spinach riboswitch in Escherichia coli enables live imaging of d

172 closed and open conformations of the SAM-II riboswitch in the absence of ligand.

173 ure of the eukaryotic thiamine pyrophosphate riboswitch in the context of a hexanucleotide loop seque

174 the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and

175 le to perform selections for novel synthetic riboswitches in an in vitro system.

176 MN-induced "turn-off" activities of both FMN riboswitches in Bacillus subtilis, allowing rib gene exp

177 hlight applications of natural and synthetic riboswitches in enzyme and strain engineering, in contro

178 tial explanation for the apparent absence of riboswitches in the human genome.

179 a reporter gene fused to representative ZTP riboswitches in vivo.

180 f new potential antibiotic drugs that target riboswitches in which dissimilarity is an important aspe

181 aptamer, which can be employed as synthetic riboswitch, in the range of physiological magnesium conc

182 o utilize highly selective metalloregulatory riboswitches, in addition to metalloregulatory proteins,

183 uctural mechanism similar to that of the TPP riboswitch, including the guanine and adenine riboswitch

184 Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA syn

185 The thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modi

186 The S-adenosylmethionine (SAM)-I riboswitch is a noncoding RNA that regulates the transcr

187 that the halide selectivity of the fluoride riboswitch is determined by the stronger Mg-F bond, whic

188 st that the correlation network in the bound riboswitch is distinctly different from that in the apo

189 We report that the AdoCbl-binding riboswitch is part of a small, trans-acting RNA, EutX, w

190 /water cluster at the center of the fluoride riboswitch is stable by its own and, once assembled, doe

191 te-dependent conformational switching in RNA riboswitches is now widely accepted as a critical regula

192 Gene regulation in cis by riboswitches is prevalent in bacteria.

193 The defining feature of riboswitches is that they directly recognize a physiolog

194 One of the most studied riboswitches is the Bacillus subtilis adenine-responsive

195 fficient ("high levels"), FMN binding to FMN riboswitches leads to a reduction of rib gene expression

196 binding and associated mobility shifts for a riboswitch-ligand interaction, thus demonstrating a scre

197 s led to the identification of an orthogonal riboswitch-ligand pairing that effectively repressed the

198 ene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of m

199 The aptamer portion of the riboswitch may adopt an open or closed state depending o

200 y implies that gene regulation by artificial riboswitches may be an appealing alternative to Tet- and

201 This work introduces riboswitch-mediated control of protein sequestration as

202 e direction to molecular biologists studying riboswitch-mediated gene expression.

203 T box riboswitch-mediated gene regulation was shown previously

204 Riboswitch-mediated mechanisms are ubiquitous across bac

205 al ligand, flavin mononucleotide, to repress riboswitch-mediated ribB gene expression and inhibit bac

206 control by the cyclic AMP receptor protein, riboswitch-mediated transcription attenuation in respons

207 h previously and newly discovered classes of riboswitches might reveal subgroups of RNAs that respond

208 tructured, cis-encoded RNA elements known as riboswitches modify gene expression upon binding a wide

209 es is essential for deeply understanding how riboswitches modulate gene expression.

210 esults support a mechanism by which the btuB riboswitch modulates the formation of a tertiary structu

211 n of just six synthetic compounds with seven riboswitch mutants led to the identification of an ortho

212 We show that TSS reveals riboswitches, non-coding RNA and novel transcription uni

213 on, ligand-jump experiments reveal imperfect riboswitching of single mRNA molecules.

214 The discovery, design and reengineering of riboswitches offer an alternative means by which to cont

215 yielding new information about how different riboswitches operate.

216 echanisms of action of a family of synthetic riboswitches, our experiments suggest that it may be pos

217 Although there are a handful of known riboswitches, our knowledge in this field has been great

218 vailable to support tasks like the design of riboswitches; our analysis of RS3 suggests strong co-tra

219 pilA1 is preceded by a putative c-di-GMP riboswitch, predicted to be transcriptionally active upo

220 to an upstream transcriptionally activating riboswitch, promoting cell aggregation in C. difficile.

221 oach, and its extension to a second class of riboswitches, provides a methodological platform for the

222 Our model-based approach for engineering riboswitches quantitatively confirms several physical me

223 y, it is less clear how the unbound, sensing riboswitch refolds into the ligand binding-induced outpu

224 GEMM-Ib riboswitches regulate genes associated with extracellula

225 The T box riboswitch regulates many amino acid-related genes in Gr

226 The preQ1 class II (preQ1-II) riboswitch regulates preQ1 biosynthesis at the translati

227 We discovered that, although this family of riboswitches regulates the initiation of protein transla

228 role of the kissing loop interaction in the riboswitch regulatory mechanism, we used RNase H cleavag

229 -binding properties, on the widespread T-box riboswitches, remain unknown.

230 ever, the regulation mechanism for the preQ1 riboswitch remains unclear.

231 igands, but their conversion into functional riboswitches remains difficult.

232 ions of these riboswitches with theophylline riboswitches represent logic gates responding to two dif

233 The riboswitch resembles a hairpin, with two coaxially stack

234 The majority of riboswitches respond to cellular metabolites, often in a

235 e folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activi

236 bolite, a Mg(2+) (0-0.5 mm)-bound apo SAM-II riboswitch RNA exists in a minor ( approximately 10 %) p

237 structural details of a widespread class of riboswitch RNAs, whose members selectively and tightly b

238 sing of changes in the environment by use of riboswitches (RNAs that change shape in response to envi

239 ures are functionally relevant in ribozymes, riboswitches, rRNA, and during replication.

240 rationally designed, artificial theophylline riboswitch RS3.

241 pproach can also be paired to homology-based riboswitch searches.

242 The riboswitch selectively binds c-di-AMP and discriminates

243 itching sequence inside a putative, complete riboswitch sequence, on the basis of pairing behaviors,

244 We used structural entropy of riboswitch sequences as a measure of their secondary str

245 As such, riboswitches serve as a novel, yet largely unexploited,

246 ether, characterization of Mn(2+)-responsive riboswitches should expand the scope of RNA regulatory e

247 range tertiary interactions stabilize global riboswitch structure and confer increased ligand specifi

248 be used as a general strategy in studies of riboswitch structure-function relationship.

249 eatly facilitated by studying all aspects of riboswitch structure/dynamics/function in the same model

250 Comparison of preQ1-I and preQ1-II riboswitch structures reveals that whereas both form H-t

251 t there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods

252 r how their sequence controls the physics of riboswitch switching and activation, particularly when c

253 Here, we present a riboswitch that contributes to transcriptional regulatio

254 don, termed the "Specifier Sequence," in the riboswitch that corresponds to the amino acid identity o

255 on-native, idiosyncratic conformation of the riboswitch that inhibits c-di-GMP binding.

256 mational change in a regulatory element of a riboswitch that results from ligand binding in the aptam

257 nal map of the Vibrio vulnificus add adenine riboswitch that reveals five classes of structures.

258 We conclude that UTR1 is a riboswitch that senses cytoplasmic Mn(2+) and therefore

259 tion relationship for translation-regulating riboswitches that activate gene expression, characterize

260 regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM).

261 ass, and also variants of c-di-GMP-I and -II riboswitches that might recognize different bacterial si

262 ulation is exemplified by metabolite-binding riboswitches that modulate gene expression through confo

263 Re-engineered riboswitches that no longer respond to cellular metaboli

264 Riboswitches that regulate gene expression at the transc

265 Additionally, we show that other riboswitches that use a structural mechanism similar to

266 tomated computational design of 62 synthetic riboswitches that used six different RNA aptamers to sen

267 For ribozymes and riboswitches, the RNA structure itself provides the biol

268 re employed to re-engineer a natural adenine riboswitch to create orthogonal ON-switches, enabling tr

269 cleotide) binds to and activates a conserved riboswitch to regulate expression of one-carbon metaboli

270 le longevity of this pause is required for a riboswitch to stimulate Rho-dependent termination in the

271 Ribo-attenuators allow riboswitches to be treated as truly modular and tunable

272 the specificity of TALEs with the ability of riboswitches to recognize exogenous signals and differen

273 different combinations of TALE proteins and riboswitches, to rapidly and reproducibly control the ex

274 gies developed for visualizing ribozymes and riboswitches, together with new approaches for mapping R

275 age assays to probe the structure of nascent riboswitch transcripts produced by the E. coli RNA polym

276 n, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expressio

277 Our studies show that the preQ1-II riboswitch uses an unusual mechanism to harness exquisit

278 overy of agonists and antagonists of the TPP riboswitch using simple fluorescence readouts.

279 ch by analyzing the fluorescence response of riboswitch variants, each with a single, strategically p

280 of the thiamin pyrophosphate-dependent thiM riboswitch, we find that Rho-dependent transcription ter

281 To overcome the associated difficulties with riboswitches, we have designed and introduced a novel ge

282 he structural switching mechanism of natural riboswitches, we show that Spinach can be swapped for th

283 Entropy values of a diverse set of riboswitches were compared to that of their mutants, the

284 n, we present a crystal structure for an RNA riboswitch where a stem C:G pair has been replaced by a

285 re of the same sequence located in the SAM-I riboswitch, where it adopts an N1 structure, showing the

286 e demonstrate these approaches on a fluoride riboswitch, where one-bond (13)C-(1)H RDCs from both bas

287 he Bacillus subtilis adenine-responsive pbuE riboswitch, which regulates gene expression at the trans

288 Riboswitches, which are embedded in untranslated regions

289 tory mechanisms employed by Escherichia coli riboswitches, which are predicted to regulate mostly at

290 convertible RNA conformations, as known from riboswitches, which might act as a flux sensor.

291 tory RNAs are classified as cis-acting, e.g. riboswitches, which modulate the transcription, translat

292 e chemical modulator of bacterial riboflavin riboswitches, which was identified in a phenotypic scree

293 t is able to model the switching behavior of riboswitches whose generated ensemble covers both altern

294 tional switching provides insight into how a riboswitch with bipartite architecture uses dynamics to

295 le hairpin, and a 112-nt three-state adenine riboswitch with its expression platform, molecules whose

296 (untranslated region), which is an indirect riboswitch with secondary and tertiary RNA structures th

297 itable targets for construction of synthetic riboswitches with design approaches based on equilibrium

298 switches that differ from metabolite-sensing riboswitches with regard to their small size, as well as

299 Tandem fusions of these riboswitches with theophylline riboswitches represent lo

300 witch as a Mn(2+)-dependent transcription-ON riboswitch, with a approximately 30-40 muM affinity for