ライフサイエンスコーパス: tRNA(Phe)

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

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

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

4 tRNAPhe conformational states that interchange much more

5 1H NMR spectra acquired for Mg(2+)-tRNAPhe suggest that NC 1-71 and NC 12-55 (lacking resid

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

21 om those seen for other tRNAs exemplified by tRNAPhe.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

46 on/peroxidation at position 37 of eukaryotic tRNAPhe.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

89 unit known to interact with the anticodon of tRNAPhe.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

176 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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