ライフサイエンスコーパス: tRNA(Phe)

1 e crystal structure of the full-length yeast tRNAPhe.

2 om those seen for other tRNAs exemplified by tRNAPhe.

3 unit known to interact with the anticodon of tRNAPhe.

4 editing pathway that targets non-cognate Tyr-tRNAPhe.

5 on/peroxidation at position 37 of eukaryotic tRNAPhe.

6 n of HIV-1 with a PBS complementary to yeast tRNAPhe.

7 eit at a level less than that with wild-type tRNA(Phe).

8 bind observably to the nonsubstrate E. coli tRNA(Phe).

9 rystal structure of the fully modified yeast tRNA(Phe).

10 e show that ThiI binds to unmodified E. coli tRNA(Phe).

11 on for understanding Mg(2+) binding to yeast tRNA(Phe).

12 e X-ray crystallographic structures of yeast tRNA(Phe).

13 he cognate tRNA(His) but not with noncognate tRNA(Phe).

14 a U-turn found within the anticodon loop of tRNA(Phe).

15 d adjacent to the anticodon in undermodified tRNA(Phe).

16 transferred alanine, serine, and glycine to tRNA(Phe).

17 slow phases similar to those for natural Phe-tRNA(Phe).

18 tRNA, but still 2-fold less than natural Phe-tRNA(Phe).

19 the side chain of the esterified Phe of Phe-tRNA(Phe).

20 etases (PheRS) that hydrolyze mischarged Tyr-tRNA(Phe).

21 maritima RNase P holoenzyme in complex with tRNA(Phe).

22 zed canonical counterpart, yeast cytoplasmic tRNA(Phe).

23 ne 37 in both mitochondrial tRNA(Met)(f) and tRNA(Phe).

24 for hydrolysis of the noncognate product Tyr-tRNA(Phe).

25 editing of the misaminoacylated species Tyr-tRNA(Phe).

26 psi32 on the anticodon stem-loop from E.coli tRNA(Phe).

27 abolished both cis and trans editing of Tyr-tRNA(Phe).

28 ough hydrolysis of tyrosyl-adenylate and Tyr-tRNA(Phe).

29 has a reduced affinity for mitochondrial Phe-tRNA(Phe).

30 l-modified anticodon stem-loops from E. coli tRNA(Phe).

31 erved base pairs in the tertiary core of Phe-tRNA(Phe), 18-55 and 19-56, on rate and equilibrium cons

32 of PheRS editing caused accumulation of Tyr-tRNAPhe (5%), but not deacylated tRNAPhe during amino ac

33 arger than the corresponding angle for yeast tRNAPhe (70-80 degrees) under the same ionic conditions.

34 t position 73 of YFA2, a derivative of yeast tRNA(Phe), a single tRNA body was misacylated with 13 di

35 Na+] buffer at low temperature, native yeast tRNAPhe adopts tertiary structure in the absence of Mg2+

36 this modification into the scaffold of yeast tRNA(Phe) also resulted in blocked immunostimulation.

37 s and trans editing and could synthesize Tyr-tRNA(Phe), an activity enhanced in active site variants

38 Binding of N-acetylated Phe-tRNA(Phe), an analog of the initiator fMet-tRNA(Met), en

39 r which crystallographic data are available: tRNA(phe) and 5S rRNA from Escherichia coli, the P4-P6 d

40 We explore two systems, yeast tRNA(Phe) and a 58-nucleotide rRNA fragment, with differ

41 Michaelis constants for tRNA(Phe) and DMAPP are 96 +/- 11 nM and 3.2 +/- 0.5 mic

42 ide wyosine characteristic of position 37 in tRNA(Phe) and known previously only in eukarya, plus two

43 ach other and to that of an unmodified yeast tRNA(Phe) and native yeast tRNA(Phe), as determined by l

44 We find that both a T7 transcript of yeast tRNA(Phe) and natively extracted total bovine liver mt-t

45 fied anticodon stem-loop of Escherichia coli tRNA(Phe) and suggests that this hairpin has a 3 nt loop

46 hydrogen bonds in a co-crystal structure of tRNA(Phe) and T. aquaticus EF-Tu, while the fifth 2' hyd

47 NAs at 37 degrees C: the 76 nucleotide yeast tRNA(Phe) and the 255 nucleotide catalytic domain of the

48 For two RNAs, tRNA(Phe) and the adenine riboswitch, secondary structur

49 ylpyridyl)porphine were used to characterize tRNA(Phe) and the human immunodeficiency virus type-I Re

50 y, crystal structures of DusC complexes with tRNA(Phe) and tRNA(Trp) show that Dus subfamilies that s

51 for 30 in vitro synthesized T-arm mutants of tRNAPhe and 37 mutants of the 17-mer analog of the T-arm

52 show that NC destabilizes the folded form of tRNAPhe and by extension, other complex RNAs, in tertiar

53 Using misacylated Pro-tRNAPhe and Phe-tRNAPro, we show that the imino acid pro

54 ups in the crystal structure of native yeast tRNAPhe and that the modifications do not significantly

55 The recognition and cleavage of tRNAPhe and the TAR RNA of HIV-1 by metallopeptides of t

56 scale, the fluctuations calculated for yeast tRNAPhe and tRNAAsp in the free state, and for tRNAGln c

57 alpha-subunit monomer that does not edit Tyr-tRNA(Phe), and a comparable transacting activity does no

58 re force as compared to the complex with Phe-tRNA(Phe), and the resultant force was the same for both

59 bstrate tRNA species, like, tRNA (Thr)(GGT), tRNA(Phe), and tRNA (Ala)(TGC), bind the enzyme with sim

60 USD4 binds 16S mt-rRNA, mt-tRNA(Met), and mt-tRNA(Phe), and we demonstrate that it is responsible for

61 RNAPhe, the anticodon stem-loop (ACSLPhe) of tRNAPhe, and bulk tRNA isolated from a miaA mutant.

62 the stability of the anticodon arm of yeast-tRNAphe, and to the magnesium core of the Tetrahymena gr

63 ucleotide loop by the purine-rich unmodified tRNA(Phe) anticodon arm suggests that other anticodon se

64 ational flexibility, structures of the yeast tRNA(Phe) anticodon stem and loop (ASL(Phe)) with natura

65 ant guanosine situated on the 3'-side of the tRNA(Phe) anticodon.

66 ata demonstrate that only mt-tRNA(Val) or mt-tRNA(Phe) are found in the mitoribosomes of five differe

67 uncertain, the m values for the duplexes and tRNA(Phe) are proportional to the amount of the surface

68 bosomes with TMR-Met-tRNAMetf or TMR-Met-Phe-tRNAPhe are immobilized on mica and observed by fluoresc

69 (psHIV-Phe), which relies on exogenous yeast tRNA(Phe) as reverse transcription primer, was used to i

70 ide corresponding to the stem-loop region of tRNA(Phe) as substrates.

71 onformational properties of unmodified yeast tRNAPhe as a function of ionic strength, [Mg2+], and tem

72 unmodified yeast tRNA(Phe) and native yeast tRNA(Phe), as determined by lead cleavage patterns at U1

73 ngly with the L1 stalk compared to elongator tRNA(Phe), as seen in previous single-molecule experimen

74 rally well-characterized transfer RNA, yeast tRNAPhe, as a model for the natural primer.

75 r than unmodified, anticodon domain of yeast tRNA(Phe) (ASL(Phe)).

76 slation, we synthesized the unmodified yeast tRNA(Phe)ASL and ASLs with various derivatives of U(39)a

77 tely inhibit the Pb2(+)-ribozyme activity of tRNAPhe at 25 degrees C, pH 7.0 and 15 mM MgCl2, Zn2 HIV

78 namic description of Mg(2+) binding to yeast tRNA(Phe) based on the NLPB equation.

79 nylalanine-specific transfer RNA from yeast (tRNAPhe) because the unfolding rates and the correspondi

80 oss-link is in the central D region of yeast tRNAPhe between C11 and C25 and the third cross-link bri

81 The effects of P/P- and P/E-site tRNA(Phe) binding on the 16S rRNA structure in the Esche

82 as native MiaA and was completely active for tRNAPhe binding.

83 Irradiation of E. coli tmRNA and yeast tRNA(Phe) bound to a single SmpB molecule with UV light

84 re is very similar in shape to that of yeast tRNA(Phe) but is slightly smaller in size.

85 ld of the anticodon loop of Escherichia coli tRNA(Phe), but these elements do not result in this sign

86 alteration enhances the k(cat)/K(M) for ppp-tRNA(Phe) by nearly 100-fold relative to that of wild-ty

87 The folding of the unmodified yeast tRNA(Phe) can be described by two Mg(2+)-dependent trans

88 ynthesized for every approximately 7,300 Phe-tRNA(Phe), compatible with an error rate in translation

89 tRNAPhe conformational states that interchange much more

90 the anticodon and acceptor stems of a yeast tRNA(Phe) construct.

91 near-UV light, various derivatives of yeast tRNA(Phe) containing 2-azidoadenosine at the 3' terminus

92 lent adduct with 5-fluorouracil (FUra)-tRNA (tRNA(Phe) containing FUra in place of Ura) to form a put

93 examine the overall flexibility of the yeast tRNAPhe core (as unmodified transcript).

94 S) catalyzed aminoacylation of cognate yeast tRNA(Phe) corroborated the peptide's binding to the anti

95 has a U-turn structure similar to the yeast tRNA(Phe) crystal structure, unlike previously proposed

96 er degree of similarity to that of the yeast tRNA(Phe) crystal structure.

97 MuLV; however, infectivity was restored when tRNA(Phe)D(-) was directly transfected into the cytoplas

98 In contrast, tRNA(Phe) without the D loop (tRNA(Phe)D(-)) was retained within the nucleus and did n

99 I consider conformational spaces of tRNA(phe) defined by sets of suboptimal structures from

100 Our unmodified tRNA(Phe) derivative adaptor charged with a large unnatu

101 finities of the mutant proteins to yeast Phe-tRNA(Phe) determined.

102 tive E. coli, bovine liver, yeast, and wheat tRNA(Phe) do not, nor do a variety of base- or sugar-mod

103 Furthermore, G34A hmt-tRNA(Phe) does not undergo adenosine-to-inosine (A-to-I)

104 ric protein responsible for synthesizing Phe-tRNA(Phe) during protein synthesis.

105 tion of Tyr-tRNAPhe (5%), but not deacylated tRNAPhe during amino acid starvation, limiting Gcn2p kin

106 Three analogs of unmodified yeast tRNAPhe, each possessing a single disulfide cross-link,

107 an Escherichia coli strain defective in Tyr-tRNA(Phe) editing was used.

108 ructurally homologous ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog.

109 perature of the cloverleaf, unmodified yeast tRNAPhe exists in a Mg2+-dependent equilibrium between s

110 Wild-type yeast tRNA(Phe) expressed in mammalian cells was transported t

111 virus that relies on the expression of yeast tRNA(Phe) for infectivity was determined.

112 onding to the anticodon stem-loop of E. coli tRNA(Phe) formed a stem-loop minihelix (minihelix(Phe))

113 ed anticodon stem-loop from Escherichia coli tRNA(Phe) forms a trinucleotide loop in solution, but Mg

114 ed anticodon stem-loop from Escherichia coli tRNA(Phe) forms a trinucleotide loop in solution, but Mg

115 metal-binding sites of the anticodon loop of tRNA(Phe) from E. coli and of a tetraloop containing a G

116 e report the crystal structure of unmodified tRNA(Phe) from Escherichia coli at a resolution of 3 A.

117 the PRF occurred through +1 slippage of the tRNA(phe) from UUU to UUC within a conserved msi172-enco

118 and doubled the apparent K(D) for noncognate tRNA(Phe) (from 7.3 to 14.5 microM).

119 he genes tRNA(Thr)(UGU), tRNA(Leu)(UAA), and tRNA(Phe) (GAA) therefore attributes the seemingly neutr

120 However, a single tRNA(phe) gene with modest TFIIIC enrichment is insuffic

121 e D-loop region, immediately upstream of the tRNAPhe gene.

122 andem repeats between the CSB1 motif and the tRNAPhe gene.

123 S. pneumoniae tRNA(Phe) has an unusual U4:C69 mismatch in its acceptor

124 ntrast, tertiary folding of unmodified yeast tRNAPhe has an absolute requirement for Mg2+.

125 in the catalytic efficiency (kcat/KM) of Tyr-tRNA(Phe) hydrolysis, suggesting a role for the B2 domai

126 ) stabilizes the tertiary structure of yeast tRNA(Phe) in part by accumulating in regions of high neg

127 izing the native tertiary structure of yeast tRNA(Phe) in solution.

128 g of frameshift efficiency could explain why tRNA(Phe) in some eukaryotes is not fully modified but,

129 of editing lowered the amount of deacylated tRNA(Phe) in the cell.

130 ) synthesis, but abolished hydrolysis of Tyr-tRNA(Phe) in vitro.

131 of PKR by a natively folded T7 transcript of tRNA(Phe)in vivo supporting the importance of tRNA modif

132 in complexes carrying an aminoacyl tRNA, Phe-tRNA(Phe), in the A site, indicating that the SD interac

133 ce of a peptidyl tRNA analogue, N-acetyl-Phe-tRNA(Phe), in the A site, which mimicked the post-peptid

134 helix are insufficient to transform E. coli tRNAPhe into an effective valine acceptor.

135 A dual-specific derivative of yeast tRNA(Phe) is described whose features facilitate structu

136 equilibrium folding of the unmodified yeast tRNA(Phe) is studied as a function of Na(+), Mg(2+), and

137 entary RNA duplexes and the unmodified yeast tRNA(Phe) is studied as a function of urea and Mg(2+) co

138 it, it is extremely specific as only one Tyr-tRNA(Phe) is synthesized for every approximately 7,300 P

139 hift frequencies are highest if the slippery tRNAPhe is capable of stable base pairing in the shifted

140 ce of Mg2+, the extent of destabilization of tRNAPhe is greater but appears to be confined to interna

141 em in which yeast (Saccharomyces cerevisiae) tRNAPhe is provided in trans to complement the replicati

142 agnesium ions: the interstem angle for yeast tRNAPhe is reduced by nearly 50 % upon addition of 2 mM

143 , and m7G46 to C48 in the variable loop (for tRNAPhe), is identified in the free tRNA, conforming wit

144 d ASL(Phe)-Gm(34),m(5)C(40) and native yeast tRNA(Phe) (K(d) congruent with 2.3 and 3.8 microM, respe

145 ted that the B2 domain is distant from bound tRNA(Phe), leaving the role of this module in question.

146 ve strain, increased levels of aminoacylated tRNA(Phe) led to continued synthesis of the PheL leader

147 G0731 polypeptide participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.

148 ion enthalpy for tertiary unfolding of yeast tRNAPhe measured previously by temperature-jump relaxati

149 ption was the G34A anticodon mutation of hmt-tRNA(Phe) (mitochondrial DNA mutation G611A), which is a

150 , the tRNA construct comprises an unmodified tRNA(Phe) molecule in which the anticodon and acceptor s

151 unctions of individual, specifically labeled tRNAPhe molecules exhibit nonexponential character as a

152 ity about 17-fold lower than that for intact tRNAPhe, mostly due to a decrease in apparent substrate

153 A tRNA(Phe) mutant (tRNA(Phe)UUA) that did not have the ca

154 tRNA(Phe) mutants that retained the capacity for nucleoc

155 sport and the selection of the primer, yeast tRNA(Phe) mutants were designed such that the native tRN

156 tRNA(Phe) mutants with an extended 5' end had reduced ca

157 restored by extension of the 3' end of these tRNA(Phe) mutants with sequences complementary to the HI

158 tRNA(Phe) mutants with two- or four-nucleotide deletions

159 We tested the impact of hmt-tRNA(Phe) mutations on aminoacylation, structure, and tr

160 taining the peptidyl-tRNA analogues N-Ac-Phe-tRNAPhe, N-Ac-Met-tRNAMet or f-Met-tRNAfMet with puromyc

161 ks were determined in the presence of deacyl-tRNA(Phe) or N-acetyl-Phe-tRNA(Phe) using poly(U) or an

162 ffect their incorporation of IAP RNA, primer tRNAPhe (phenylalanine tRNA), or IAP Gag.

163 he hypermodified wybutosine-37 in the native tRNA(Phe) placed the peptide across the anticodon loop a

164 cleic acids including: calf thymus (CT) DNA, tRNA(Phe), polymeric RNAs and DNAs, and viral RNAs inclu

165 the nonexponential decay indicates that the tRNAPhe-probe adduct fluctuates between two states, one

166 a primer binding site complementary to yeast tRNA(Phe) (psHIV-Phe) was not infectious unless yeast tR

167 er binding site (PBS) complementary to yeast tRNA(Phe) (psHIV-Phe), which relies on exogenous yeast t

168 enosine of the peptidyl-tRNA analogue, AcPhe-tRNA(Phe), remains in close contact with U2506 regardles

169 cleotide changes in the T(Psi)C stem-loop of tRNA(Phe) revealed an unexpected, essential role of this

170 bacterial RNase P holoenzyme in complex with tRNAPhe revealed the structural basis for substrate reco

171 riphosphate (EF-Tu.GDPNP) bound to yeast Phe-tRNA(Phe) reveals that EF-Tu interacts with the tRNA bod

172 te RNA comprising the anticodon stem loop of tRNA(Phe) reveals that enzyme binding induces a dramatic

173 contrast, substitution of the 3'-OH group of tRNA(Phe) severely impaired editing and revealed an esse

174 catalytic hydrolysis of mispaired aminoacyl-tRNA(Phe) species.

175 Wyosine bases are tRNA(Phe)-specific modifications that are distinguished

176 e reaction (k2) have been determined using a tRNA(Phe) substrate containing a 2'-deoxy residue at the

177 binding and catalysis are determined using a tRNAPhe substrate that is significantly cleaved at more

178 1H NMR spectra acquired for Mg(2+)-tRNAPhe suggest that NC 1-71 and NC 12-55 (lacking resid

179 nalysis of mutations in the acceptor stem of tRNA(Phe) suggested that an intact acceptor stem RNA str

180 within the editing site had no effect on Phe-tRNA(Phe) synthesis, but abolished hydrolysis of Tyr-tRN

181 the association of variously modified yeast tRNA(Phe) T-half molecules (nucleosides 40-72) with the

182 The structure of an analogue of the yeast tRNAPhe T Psi C stem-loop has been determined by NMR spe

183 mation and dissociation of the EF-Tu-GTP-Phe-tRNA(Phe) ternary complex.

184 ough deletion analysis of unmodified E. coli tRNA(Phe) that the minimum substrate for s4U modificatio

185 ing the poorest results in this recent work: tRNA(Phe), the adenine and cyclic-di-GMP riboswitches, a

186 al substrates, including synthetic wild-type tRNAPhe, the anticodon stem-loop (ACSLPhe) of tRNAPhe, a

187 ive in polymerization with mitochondrial Phe-tRNA(Phe), this variant has low activity in the formatio

188 re-determined the crystal structure of yeast tRNA(Phe) to 2.0 A resolution using 15 year old crystals

189 virus (MuLV) were created that require yeast tRNA(Phe) to be supplied in trans for infectivity.

190 The capacity of the mutant tRNA(Phe) to complement a defective HIV-1 provirus that

191 onse by switching to the incorporation of mt-tRNA(Phe) to generate translationally competent machiner

192 , we use a variety of known mutations in hmt-tRNA(Phe) to investigate the mechanisms that lead to mal

193 Resampling of Tyr-tRNA(Phe) to PheRS increasing the number of correctly ch

194 nthetic anticodon stem-loop analogs (ASL) of tRNA(Phe) to systematically identify ribose 2'-hydroxyl

195 plex formation by analyzing hybridization of tRNAphe to a complete set of complementary oligonucleoti

196 be impaired in the enzymatic binding of Phe-tRNAPhe to the A site, although the interaction of N-ace

197 placed by 4-thiouridines in transfer RNAPhe (tRNAPhe) transcribed in a T7 RNA polymerase system.

198 An unmodified tRNA(Phe) transcript in which the 3'-terminal ACCA seque

199 With a single exception (tRNA(Phe)-tRNA(Glu) pair), the parallelism is especially

200 bound with ternary complexes containing Phe-tRNA(Phe), Trp-tRNA(Trp), or Leu-tRNA(LeuI).

201 termolecular cross-link, 16S rRNA (C1400) to tRNA(Phe)(U33), was made with either poly(U) or the mRNA

202 o that for the normal substrate (full-length tRNA(Phe) unmodified at A37), although the K(m) for mini

203 Undermodified tRNA(Phe) used as substrate in the DMAPP-tRNA transferas

204 presence of deacyl-tRNA(Phe) or N-acetyl-Phe-tRNA(Phe) using poly(U) or an mRNA analogue containing a

205 A tRNA(Phe) mutant (tRNA(Phe)UUA) that did not have the capacity to be amino

206 eotide in which the loop sequence of E. coli tRNA(Phe) was preserved, but the 5 base pair helix stem

207 (psHIV-Phe) was not infectious unless yeast tRNA(Phe) was supplied in trans.

208 Asp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52

209 RNA(Val) compared with the porcine use of mt-tRNA(Phe) We have explored this observation further.

210 ine derivative m-Tyr after its attachment to tRNA(Phe) We now show in Saccharomyces cerevisiae that P

211 ing to the anticodon arm of Escherichia coli tRNA(Phe), we have investigated the structural and dynam

212 th similar affinities, and aminoacylation of tRNAphe weakened its interaction with GCN2.

213 of editing, cellular levels of aminoacylated tRNA(Phe) were elevated during amino acid stress, wherea

214 intracellular E. coli tRNA3Lys than of yeast tRNAPhe were needed to achieve equal levels of infectiou

215 graphically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage

216 site can readily accommodate a model of Tyr-tRNA(Phe) where deacylation occurs from either the 2'- o

217 helix analogue of the anticodon stem-loop of tRNA(Phe) where the base corresponding to A37 was replac

218 to bind only in the presence of poly(U) and tRNA(Phe), whereas quinolines bind in a similar manner t

219 mentation were lower than that for wild-type tRNA(Phe), which did undergo transport and aminoacylatio

220 te secondary structure constraints for yeast tRNA(Phe), which is accurately predicted in the absence

221 mplexes were assembled with participation of tRNA(Phe), which targeted triplet UUC of the derivative

222 firmed by converting E.coli tRNAAlaand yeast tRNAPhe, whose acceptor stem sequences differ significan

223 DMAPP-tRNA transferase bound tRNA(Phe) with a dissociation constant of 5.2 +/- 1.2 nM

224 nyl-tRNA synthetase, which aminoacylates hmt-tRNA(Phe) with cognate phenylalanine.

225 Mutant tRNA(Phe) with deletions in TPsiC stem-loop, anticodon s

226 Mutant tRNA(Phe) with disrupted TPsiC stem-loop did not rescue

227 For N-acetyl-Phe-tRNA(Phe) with either poly(U) or the mRNA analogue, the

228 proportional effect was true also for deacyl-tRNA(Phe) with poly(U), but the decrease in the C967 x C

229 omyces cerevisiae that PheRS misacylation of tRNA(Phe) with the more abundant Phe oxidation product o

230 Replacing the anticodon stem of tRNAPhe with that of tRNAVal, however, converts the tRNA

231 te, although the interaction of N-acetyl-Phe-tRNAPhe with the P site was largely unperturbed.

232 d the free energy of Mg(2+) binding to yeast tRNA(Phe) without any fitted parameters.

233 In contrast, tRNA(Phe) without the D loop (tRNA(Phe)D(-)) was retaine

234 In contrast, a mutant tRNA(Phe) without the D stem-loop was fully functional f

235 cipates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.