ライフサイエンスコーパス: proofreading

1 er-end to the exonuclease site as a "cost of proofreading".

2 corporated nucleotides from the nascent DNA (proofreading).

3 imilar to that adopted by the subunit during proofreading.

4 s the central step in co-transcriptional RNA proofreading.

5 ated event sequence during translocation and proofreading.

6 -Tu can contribute to efficient and accurate proofreading.

7 l-chemical properties of the ribosome enable proofreading.

8 epresent distinct steps in target search and proofreading.

9 length protein by interfering with ribosomal proofreading.

10 ns that impair DNA polymerase epsilon (POLE) proofreading.

11 oration by both substrate discrimination and proofreading.

12 family relies on a built-in exonuclease for proofreading.

13 creased mismatch extension at the expense of proofreading.

14 key to understanding the kinetics of epitope proofreading.

15 y of Dnmt5 via mechanisms related to kinetic proofreading.

16 correcting biosynthetic errors that escaped proofreading.

17 ions, and deaths without the need for manual proofreading.

18 it is involved in transcription fidelity and proofreading.

19 ed for high-fidelity replication, likely via proofreading.

20 erroneously incorporated nucleotides during proofreading.

21 e mutant, invoking a mechanism for substrate proofreading.

22 ribosome subunit joining and pre-40S subunit proofreading.

23 synthesis fidelities, even in the absence of proofreading.

24 many possible ways to inactivate Polepsilon proofreading.

25 physically coordinated to achieve efficient proofreading.

26 nt in solution, which is expected to enhance proofreading.

27 gainst the non-cognate amino acid by kinetic proofreading.

28 action acceleration and strongly reinforcing proofreading.

29 sidues and were strongly predicted to affect proofreading.

30 xoN) activity that probably functions in RNA proofreading.

31 incorporation, RNA transcript extension, and proofreading.

32 elongation and are processed via exonuclease proofreading.

33 oupled to a leak of the driving ion, akin to proofreading.

34 or lagging strand (Poldelta) DNA polymerase proofreading.

35 also achieved this in the absence of kinetic proofreading.

36 (pol) and a 3'-5' exonuclease site (exo) for proofreading.

37 le roles in ribosome assembly and metabolite proofreading.

38 error-correcting mechanism known as kinetic proofreading.

39 High-fidelity DNA replication depends on a proofreading 3'-5' exonuclease that is associated with t

40 rently error prone, owing to their lack of a proofreading (3'- 5' exonuclease) domain.

41 heckpoint protein, consisting of testing the proofreading ability of the 30S subunit.

42 '- to 5'-exonuclease activity, which confers proofreading ability.

43 tases prevent mistranslation by relying upon proofreading activities at multiple stages of the aminoa

44 al domain of Pol3, containing polymerase and proofreading activities, could be effectively replaced b

45 integration of RNA polymerase, capping, and proofreading activities.

46 deficient for mitochondrial polymerase-gamma proofreading activity (polG(-/-)/ApoE(-/-)).

47 s characteristic low fidelity and absence of proofreading activity allow FMDV to rapidly mutate and a

48 DNA polymerases with proofreading activity are important for accurate amplifi

49 Viral proofreading activity does not markedly impact sensitivi

50 These results are consistent with a proofreading activity for WRN during single-nucleotide a

51 izes with T1 subunits that provide essential proofreading activity in trans.

52 mutagenesis resulting from loss of Poldelta proofreading activity may in part be explained by enhanc

53 In addition, altering the processivity or proofreading activity of DNA polymerase delta shortened

54 early all mismatch correction depends on the proofreading activity of DNA polymerase-delta, although

55 ds normally excluded from translation by the proofreading activity of phenylalanyl-tRNA synthetase (P

56 This created a notion that loss of the proofreading activity of Polepsilon is an initiating cau

57 NA viral polymerases; and that for CoVs, the proofreading activity of the nsp14-ExoN is epistatic to

58 This has been attributed to the proofreading activity of the viral 3'-5' exoribonuclease

59 Mistranslation is prevented by a robust proofreading activity of ThrRS towards Ala-tRNAThr.

60 Mutations preventing DNA polymerase proofreading activity or MMR function cause mutator phen

61 NHC inhibited MHV lacking ExoN proofreading activity similarly to wild-type (WT) MHV, s

62 xpressed (T1) and another (T2) with impaired proofreading activity that also generates mischarged Ser

63 r, in vitro and ex vivo analyses reveal that proofreading activity to hydrolyze Tyr-tRNA(Phe) is incr

64 mutation that is defective in signal peptide proofreading activity were employed to distinguish betwe

65 moves the 3'-slipped hairpin using its 3'-5' proofreading activity when the hairpin contains no immed

66 on of DNA polymerase nucleotide selectivity, proofreading activity, and DNA mismatch repair (MMR).

67 Despite its fidelity and proofreading activity, B35DNAP was able to successfully

68 found that this RNAP has very high intrinsic proofreading activity, resulting in nearly as low a leve

69 ations, was effectively masked by nsp14-ExoN proofreading activity.

70 sion is improved to about [1/10(7)] by their proofreading activity.

71 isplay a certain level of resistance to this proofreading activity.

72 g play important roles in controlling Pol II proofreading activity.

73 ain, a finding consistent with PolA1 lacking proofreading activity.

74 NA(Ala) by escaping from the intrinsic AlaRS proofreading activity.

75 binding by the co-chaperone Sgt2 and kinetic proofreading after ATP hydrolysis by the targeting facto

76 nitial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis).

77 rate was 99.85% (20,273 spots), and after a proofreading algorithm was added, 100% of 20,304 spots a

78 nal constraints due to the energetic cost of proofreading also play a role in the error correcting pr

79 onlinearities that arise from, e.g., kinetic proofreading and cluster formation.

80 ts were gradually expanded as new synthetic, proofreading and coding mechanisms became biologically a

81 hemselves from accidental genome change with proofreading and DNA damage repair systems; localized po

82 Exonucleolytic proofreading and DNA mismatch repair (MMR) act in series

83 The Polg-D257A protein is defective in proofreading and increases mtDNA mutations.

84 The cellular consequences of proofreading and membrane slippage are discussed as well

85 Here, we draw an analogy between proofreading and microtubule growth which share some of

86 s are repaired by two components: polymerase proofreading and mismatch repair.

87 sequence instability conferred by defects in proofreading and MMR have important biological implicati

88 on gene suggests that factors in addition to proofreading and MMR influence leading-strand DNA replic

89 Pole-P301R errors are corrected by Poldelta proofreading and MMR.

90 ffect the backtracking of RNAP necessary for proofreading and potentially the reactivity of the backt

91 ing DNA maintenance methylation, providing a proofreading and protective mechanism against a possible

92 r work broadens the applicability of kinetic proofreading and sets the stage for studying spatial gra

93 ch as coronaviruses (CoVs), RNA viruses lack proofreading and thus are dependent on RdRps to control

94 nition or those that also participate in the proofreading and translocation functions of SecA.

95 f hundreds of genes involved in replication, proofreading, and damage repair.

96 er and phosphorelay networks, T-cell kinetic proofreading, and ERK signalling.

97 bortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoi

98 on machinery can switch between replication, proofreading, and translesion synthesis.

99 e details of substrate selection, catalysis, proofreading, and translocation, focusing on rate-limiti

100 Nucleotide selectivity and proofreading are affected by the balance and concentrati

101 s, such as oxidative stress, demands on aaRS proofreading are altered by changes in the availability

102 replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR).

103 Rare errors that elude proofreading are extended into duplex DNA and excised by

104 The energetic costs of this proofreading are met by the hydrolytic turnover of a pho

105 eering of XNA RTs with active exonucleolytic proofreading as well as the directed evolution of RNA RT

106 rved across all life forms, performs "chiral proofreading," as it removes d-amino acids erroneously a

107 ed for pre-spliceosome assembly and splicing proofreading at the branch-point region.

108 introns that may otherwise be discarded via proofreading ATPases.

109 Moreover, viomycin shuts down proofreading-based error correction.

110 ctural modifications of the familiar kinetic proofreading biochemical network diagram.

111 most half of inserted ribonucleotides escape proofreading by 3' --> 5' exonuclease-proficient Pol eps

112 herichia coli DNA polymerase II and inhibits proofreading by E. coli DNA polymerase III, while permit

113 terminal transferase, blocks exonucleolytic proofreading by Escherichia coli DNA polymerase II and i

114 lication rate after misincorporation, and 3) proofreading by excision of misincorporated bases.

115 synthesis by Pol zeta as well as diminished proofreading by Pol delta during replication.

116 Proofreading by replicative DNA polymerases is a fundame

117 ia coli, GreB is an SC protein that promotes proofreading by transcript cleavage in elongation comple

118 nition and removal of mispaired nucleotides (proofreading) by the exonuclease activity of DNA polymer

119 We also show that proofreading can remain effective when the intended sign

120 We show that a generic proofreading cascade supplemented by a single negative f

121 he first and rate-limiting step in a kinetic proofreading chain of events that eventually leads to TC

122 re, we review the molecular basis of the CoV proofreading complex and evaluate its potential as a dru

123 ts proposed role in a multiprotein replicase-proofreading complex.

124 lectivity defect is combined with a Poldelta proofreading defect, demonstrating extrinsic proofreadin

125 es of hydrogen peroxide-induced mutations in proofreading-defective yeast mutants supported the concl

126 Proofreading defects in the replicative polymerases sele

127 Proofreading defects in this enzyme drive a number of hu

128 ldelta nucleotide selectivity and Polepsilon proofreading defects produces no synergy, indicating tha

129 AN1 locus, and is synthetic lethal with both proofreading deficiency and mismatch repair deficiency.

130 Furthermore, proofreading deficiency enhances the capability of Polde

131 gnificantly more pathogenic than Pol epsilon proofreading deficiency per se.

132 or phenotype of pol2-4 (encoding Pol epsilon proofreading deficiency) and is synthetically lethal wit

133 A mismatch repair and DNA polymerase epsilon proofreading deficiency, along with concordant mutation

134 nvolves yet unknown mechanisms beyond simple proofreading deficiency.

135 In Drosophila, knock-in of a proofreading deficient mtDNA polymerase (POLG) generates

136 ma) mutant mice, we found that mice with the proofreading deficient mtDNA polymerase have a significa

137 During nuclear DNA replication, proofreading-deficient DNA polymerase alpha (Pol alpha)

138 based on the limited mutagenesis of mtDNA by proofreading-deficient DNA-polymerase gamma followed by

139 Purified proofreading-deficient human Poldelta holoenzyme perform

140 ns in the skeletal muscle of patients with a proofreading-deficient mtDNA polymerase gamma due to POL

141 he mtDNA mutator mouse, a mouse model with a proofreading-deficient mtDNA polymerase gamma, was shown

142 y strong mutator phenotype exceeding that of proofreading-deficient mutants by two orders of magnitud

143 GGGG and GGGGHGG can cause PCR failure using proofreading DNA polymerases but not Taq DNA polymerase.

144 Here we showed that proofreading DNA polymerases can be inhibited by certain

145 merous efforts have been made to improve the proofreading DNA polymerases, they are more susceptible

146 ore susceptible to be failed in PCR than non-proofreading DNA polymerases.

147 bacterial ProRSs possess an alanine-specific proofreading domain (INS) but lack the capability to edi

148 We examined the association of POLE proofreading domain mutation with clinicopathological va

149 POLE proofreading domain mutations identify a subset of immun

150 We also identified POLE proofreading domain mutations in three endometrioid ovar

151 uctural protein 14 (nsp14-ExoN) mediates RNA proofreading during genome replication.

152 Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by th

153 This kinetic proofreading effect would additionally serve as a stocha

154 elerate the tedious and time-consuming human proofreading effort.

155 ubstrate discrimination and rigorous product proofreading ensure tRNAs are paired with the correct am

156 ei, confirming that this conserved metabolic proofreading enzyme is essential in Plasmodium In summar

157 mplex that in turn associates with the nsp14 proofreading enzyme sheds light on how coronaviruses ass

158 2) How can additional functionality, such as proofreading/error-correction, be built into machine fun

159 e the second phosphorylation site allows for proofreading, especially when phosphorylation is distrib

160 idelity polymerase with polymerase (pol) and proofreading exonuclease (exo) activities.

161 ) are the only known RNA viruses to encode a proofreading exonuclease (nsp14-ExoN), as well as other

162 The proofreading exonuclease activity of replicative DNA pol

163 Deleting the 3'-5' proofreading exonuclease activity reduced fidelity twofo

164 se reverse transcriptase (RT) lacks 3' to 5' proofreading exonuclease and can extend mismatches.

165 Tumors with somatic mutations in the proofreading exonuclease domain of DNA polymerase epsilo

166 it relies on the DNA sliding clamp beta, the proofreading exonuclease epsilon and the C-terminal doma

167 CoVs encode a proofreading exonuclease in nonstructural protein 14 (ns

168 Inactivation of the 3' --> 5' proofreading exonuclease of DNA polymerase II did not en

169 ut also contains a second Zn(2)(+)-dependent proofreading exonuclease, at least in some bacteria.

170 The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases var

171 Both Pols possess intrinsic proofreading exonucleases that edit errors during polyme

172 ronaviruses encode the first known viral RNA proofreading exoribonuclease, a function that likely all

173 cells, and 5-7% of all ECs in cells lacking proofreading factors are, in fact, misincorporated compl

174 ed complexes may be the main function of the proofreading factors Gre and TFIIS.

175 This proofreading favors binding of U2AF2 at stronger Py-trac

176 bonuclease activity (ExoN), which performs a proofreading function and is required for high-fidelity

177 recombinants showed evidence that Pol delta proofreading function is active during MMEJ-mediated DSB

178 CRC risk variants that adversely affect the proofreading function of DNA polymerases encoded by POLE

179 Human DUE-B also retains the aminoacyl-tRNA proofreading function of its shorter orthologs in lower

180 trates less efficiently in vitro, allows the proofreading function of polymerase III to reverse their

181 mtDNA mutations via a targeted defect in the proofreading function of the mtDNA polymerase, PolgA, an

182 ls that receptor clustering serves a kinetic proofreading function, enabling ligands with longer boun

183 of Sec proteins, and lose the signal-peptide proofreading function, resembling the effects of PrlA mu

184 the bifurcate pathways of translocation and proofreading have been unwittingly captured by hundreds

185 Importantly, a proofreading hierarchy was uncovered, where a QcrA mutan

186 Phosphoryl transfer and proofreading hydrolysis are controlled in part by a dyna

187 ttle effect on either phosphoryl transfer or proofreading hydrolysis by Escherichia coli RNAP.

188 Our findings identify the molecular basis of proofreading in bacteria, highlight the pivotal role of

189 The results rationalize the existence of proofreading in code reading and have implications for t

190 his hypothesis, we have inactivated Poldelta proofreading in pold3 cells.

191 es increase responsiveness and allow kinetic proofreading in receptor signaling.

192 eters and provide direct evidence of kinetic proofreading in T cell signaling.

193 er, phylogenetic analysis of DNA replication proofreading in the bacterial kingdom suggests that E. c

194 This argues for the presence of this proofreading in the common ancestor of both IleRS types

195 (~50 seconds) establish a basis for kinetic proofreading in the receptor-mediated activation of Ras.

196 his analogy, we find a new kinetic regime of proofreading in which an exponential speed-up of the pro

197 To determine if the lack of proofreading is a historical coincidence or a functional

198 The creation of RTX confirms that proofreading is compatible with reverse transcription.

199 intracellular H(2)O(2), we found that PheRS proofreading is increased by 11%, thereby providing pote

200 We demonstrate that Prp5p's splicing proofreading is modulated by Spt8p and Spt3p.

201 We further demonstrate that this kinetic proofreading is modulated by the LAT (linker for activat

202 that in response to oxidative stress, PheRS proofreading is positively regulated without negative ef

203 genetic outlier and that PHP domain-mediated proofreading is widely conserved and indeed may be the a

204 The kinetic proofreading (KPR) model postulates that strand passage

205 The kinetic proofreading (KPR) model proposes that T cells discrimin

206 The model highlights how kinetic proofreading leads to heterogeneous cell responses and r

207 Coronaviruses encode proofreading machinery, unique in the RNA virus world, t

208 Our results highlight a proofreading mechanism beyond initial protospacer adjace

209 verall assembly rates, primarily serves as a proofreading mechanism for quality control of endocytosi

210 We suggest that the proofreading mechanism has evolved to attenuate error ho

211 Our findings support a kinetic proofreading mechanism in which the active site residues

212 The number of bases removed by this proofreading mechanism is much larger than the number of

213 ity in our model is analogous to the classic proofreading mechanism originally proposed for tRNA synt

214 the proteasome, which thus employs a kinetic proofreading mechanism to ensure degradation fidelity an

215 ll receptor avidity for self-pMHC provides a proofreading mechanism to maintain some of the fittest T

216 requency, and we propose that it serves as a proofreading mechanism to protect primer-ends from mutag

217 tively, our work unveils a unique structural proofreading mechanism where toggling between two confor

218 rect nucleotides after misincorporation as a proofreading mechanism.

219 e accuracy by utilizing a multi-step kinetic proofreading mechanism.

220 etic intermediates, through a conformational proofreading mechanism.

221 be an obligatory step in the DNA polymerase proofreading mechanism.

222 individually or in combination to target the proofreading mechanism.

223 nities, in an apparent extracellular "ligand proofreading" mechanism that modulates biological activi

224 Kinetic proofreading mechanisms can provide the required specifi

225 Proofreading mechanisms increase specificity in biochemi

226 in part by aminoacyl-tRNA synthetases (aaRS) proofreading mechanisms that ensure correct attachment o

227 roducing charged tRNAs and are equipped with proofreading mechanisms to ensure correct pairing of tRN

228 complexes in the space of chemical states in proofreading mechanisms.

229 In proofreading, mis-incorporated nucleotides are excised t

230 e DNA polymerase (nucleotide selectivity and proofreading), mismatch repair, a balanced supply of nuc

231 The kinetic proofreading model can explain T cell antigen receptor (

232 Such a kinetic proofreading model has been difficult to test directly,

233 nduced rebinding to the same pMHC in kinetic proofreading models enhances the sensitivity of TCR reco

234 and is sharply defined in the limit of large proofreading networks.

235 ent affinities for EF-Tu to demonstrate that proofreading of aa-tRNAs occurs in two consecutive steps

236 We show that kinetic proofreading of activator-DNA recognition-insertion of a

237 e the species that promote resection of DNA, proofreading of homologous pairing, and migration of Hol

238 Specific regulatory pathways promote kinetic proofreading of membrane surfaces by Rab GTPases, and pe

239 proofreading defect, demonstrating extrinsic proofreading of Polepsilon errors by Poldelta.

240 loop and protective proteins control kinetic proofreading of potential NMD substrates, presenting a n

241 imize cell-fate errors, analogous to kinetic proofreading of stem-cell differentiation.

242 r accurate annealing involving DdrB-mediated proofreading of strand complementarity.

243 ipation of the Tat translocase in structural proofreading of substrate proteins and reveals epitopes

244 etic information and is ensured, in part, by proofreading of the newly synthesized aminoacyl-tRNAs.

245 pwise release of bound assembly factors, and proofreading of their functional centers.

246 ic activity of Gre, while ensuring efficient proofreading of transcription and resolution of backtrac

247 Similarly, two metal ions are required for proofreading; one helps to lower the pKa of the attackin

248 appears to be largely divided, but Poldelta proofreading operates on both strands.

249 ons in a 3' to 5' direction to achieve 3'-ss proofreading or exon release, respectively.

250 tution is lethal in strains lacking Poldelta proofreading or mismatch repair (MMR).

251 o specimens had somatic mutations in the DNA proofreading or mismatch repair genes POLE, MLH1, and MS

252 tation was combined with defects in Poldelta proofreading or mismatch repair, indicating that pathway

253 Strains that lack Pol proofreading or MMR exhibit a 10- to 100-fold increase i

254 table, suggesting that defects in either DNA proofreading or MMR provide alternative mechanisms to ac

255 using electron microscopy demands laborious proofreading or reconciliation of multiple independent r

256 x formation can occur on the ribosome during proofreading, particularly when peptide bond formation i

257 ory syndrome (SARS)-CoV an RNA synthesis and proofreading pathway through association of nsp14 with t

258 widespread evolutionary conservation of aaRS proofreading pathways, requirements for translation qual

259 length scales of molecular gradients dictate proofreading performance, and quantify the limitations i

260 4PE is detoxified by metabolite-proofreading phosphatases such as yeast Pho13.

261 onship exists between defects in Pol epsilon proofreading (pol2-4) and MMR.

262 enotype), and inactivation of both Pol delta proofreading (pol3-01) and MMR is lethal due to replicat

263 defects in DNA polymerase delta (Pol delta) proofreading (pol3-01) and nucleotide selectivity (pol3-

264 ompounded by somatic loss of function in DNA proofreading polymerases, resulting in 'ultra-hypermutat

265 with lower fidelity than bulk replication by proofreading-proficient Pol delta or Pol epsilon.

266 beneficial under some conditions, increased proofreading provides a mechanism for the cell to approp

267 This aaRS proofreading provides quality control checkpoints that e

268 ctural mechanism of how EF-Tu is involved in proofreading remains to be fully resolved.

269 This 'tag-team proofreading' represents a more general mechanism to ens

270 clease epsilon that provide processivity and proofreading, respectively.

271 We show that kinetic proofreading results from the stochastic removal and ref

272 These functions include proofreading, scavenging of nutrients, removal of antime

273 ss this question in the context of a kinetic proofreading scheme used in a simple model of early-time

274 of speed-error tradeoff might be present in proofreading schemes studied earlier in the charging of

275 The applicability of traditional proofreading schemes, however, is limited because they t

276 decoded by the topology and rates of kinetic proofreading signaling steps inside T cells.

277 intermediates, with the 0-layer serving as a proofreading site for correct SNARE assembly.

278 omes in initial selection states(5,6) and in proofreading states, which together govern the efficient

279 tor Tu (EF-Tu) and GTP and then, again, in a proofreading step after GTP hydrolysis on EF-Tu.

280 NLISA is surface-free and includes a kinetic-proofreading step for purification, enabling both enhanc

281 o understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catal

282 A processing steps contributing to a kinetic proofreading step that allows properly processed mRNA to

283 Thus, PHLPP1 provides a proofreading step that maintains the fidelity of PKC aut

284 t the slow phosphorylation of Y132 acts as a proofreading step to facilitate T cell ligand discrimina

285 e of EF-Tu during aa-tRNA accommodation (the proofreading step) through the use of energy landscape p

286 lular pool of L-aminoacyl-tRNAs escapes this proofreading step.

287 A polymerases (Pol-D) comprise a small (DP1) proofreading subunit and a large (DP2) polymerase subuni

288 Pol III alpha, ablating interaction with the proofreading subunit and distorting the polymerase activ

289 trolled by a dynamic interaction between the proofreading subunit of the replicative polymerase and t

290 independent of its exonuclease activity, the proofreading subunit of the replisome acts as a gatekeep

291 In Escherichia coli, the proofreading subunit of the replisome, the varepsilon ex

292 ome instability by disrupting exonucleolytic proofreading, the P286R variant was later found to be si

293 rom thermodynamic equilibrium, as in kinetic proofreading, this barrier can be breached and greater s

294 um error correction mechanism called kinetic proofreading to enhance their specificity.

295 ch repair system providing a second level of proofreading, to ensure that ectopic sequences are not r

296 ograde tRNA nuclear import might function in proofreading tRNAs to ensure that only proper tRNAs resi

297 ction through Gly-cisPro motif during chiral proofreading underlies the inability of D-aminoacyl-tRNA

298 owed us to investigate the mechanisms of the proofreading using the method of first-passage processes

299 he kinetic interplay between replication and proofreading, we used high-resolution optical tweezers t

300 of cellular signaling incorporating kinetic proofreading with limited signaling coupled to an incohe