ライフサイエンスコーパス: codon

1 a cryptic exon with a premature termination codon.

2 es a frame shift leading to a premature stop codon.

3 rived from ribosomes stalled at the take-off codon.

4 of continuation of translation beyond a stop codon.

5 then scans along the mRNA to locate a start codon.

6 are each encoded by more than one synonymous codon.

7 ind upstream of the ompA translational start codon.

8 g longer mRNAs that extend beyond the A-site codon.

9 e ribosome in the context of a slippery mRNA codon.

10 d fidelity of aa-tRNA selection at each mRNA codon.

11 th their expected stalling at the tryptophan codon.

12 rough translation across premature Ter5 stop codon.

13 no acids are encoded by either 4, 3, 2, or 1 codon.

14 e resulting in formation of a premature stop-codon.

15 s, beginning with a 5'-AUG or GUG initiation codon.

16 d and that initiation likely occurs at a CUG codon.

17 occurs when the ribosome miscodes at a stop codon.

18 es of tRNAs that did not match commonly used codons.

19 evolutionary conservation of start and stop codons.

20 itors to reveal ribosome pausing at specific codons.

21 g in frameshifts that lead to premature stop codons.

22 ns' sequences lack conserved C-terminal rare codons.

23 and therefore the relative decoding time of codons.

24 d, leading to frameshifts and premature stop codons.

25 d rare, non-conserved rare and commonly used codons.

26 g on 10-20% of synonymous sites in preferred codons.

27 nd serine (Ser)-are encoded by six different codons.

28 sion of a GFP(rare) reporter encoded by rare codons.

29 increased availability of tRNAs for its rare codons.

30 enhanced initiation at near-cognate non-AUG codons.

31 altered protein sequences and premature stop codons.

32 re blocked by non-recycled ribosomes at stop codons.

33 ocessing, thus preventing translation of Glu codons.

34 ersed 32-38 pair on cognate and near-cognate codons.

35 ctopic transcripts naturally coded with rare codons.

36 to the reduced performance of some unnatural codons.

37 no acids (ncAAs) into proteins at amber stop codons.

38 tion, regulating ribosome occupancy of these codons.

39 +1 frameshifting on polynucleotide, slippery codons.

40 metabolic genes enriched in cognate tyrosine codons.

41 oduced frameshifts or encoded premature stop codons.

42 ients (aged >=18 years) with KRAS wild-type (codons 12, 13, and 61) resectable or suboptimally resect

43 1-2 type-mixed cases (valine homozygosity at codon 129 of the prion protein, PrP, gene harboring dise

44 JDMM1-2 (methionine homozygosity at PrP gene codon 129) establishes the type-mixed sCJD variants as a

45 eron antagonist NS2 gene and (2) deletion of codon 1313 of the RSV polymerase gene and the stabilizin

46 exploit the oncogenic GOF mechanisms of p53 codon 158 (Arg(158)) mutation, a DBD mutant found to be

47 Ethambutol RAVs at embB codons 306, 405 and 497 were responsible for resistance

48 cysteine-to-alanine substitution at Krt14's codon 373 (C373A) exhibit alterations in disulfide-bonde

49 Moxifloxacin RAVs (gyrA codon 90) were a dilution or two higher than the ECV(99)

50 e additional information on the influence of codon 96 polymorphisms and the ability of PMCA to detect

51 report only included animals homozygous for codon 96G, the most common polymorphic version of the pr

52 ctly different from the other primordial Ser codon, AGY.

53 ations of ribosomes downstream of tryptophan codons, along with their expected stalling at the trypto

54 formation of a stem-loop 5' of the take-off codon and allowing greater peptidyl-tRNA drop off.

55 Distances between tissue-specific codon and codon-pair frequencies were used to generate a

56 a dendrogram based on the unique patterns of codon and codon-pair usage in each tissue that are clear

57 rs the Shine-Dalgarno (SD) sequence or start codon and prevents formation of the translation initiati

58 a, Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing rib

59 g was inhibited, disomes accumulated at stop codons and could move into the 3' UTR to reinitiate tran

60 gradually decreased in the vicinity of start codons and increased near stop codons, revealing complex

61 es, deprioritize the wobble position in each codon, and group codon synonyms found in the codon table

62 identity, the nucleotide following the stop codon, and the surrounding mRNA sequence context all inf

63 s on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-m

64 nd translation, attenuation, incorrect start codons, and a failed gate.

65 frameshift mutations causing premature stop codons, and led to specific differences in grain morphol

66 All but two amino acids have multiple codons, and the frequency that such synonymous codons oc

67 g small open reading frames of less than 100 codons, and the translational regulation of many genes.

68 that variants that create new upstream start codons, and variants disrupting stop sites of existing u

69 The structures reveal that certain codon-anticodon contexts and the lack of m(1)G37 destabi

70 that structurally and functionally mimics a codon-anticodon helix.

71 al changes that are dependent on whether the codon-anticodon interaction is cognate or near cognate.

72 nt through the channel and/or disrupt A-site codon-anticodon interaction.

73 bosomal decoding centre dynamically monitors codon-anticodon interactions before and after GTP hydrol

74 estabilized in the context of a near-cognate codon-anticodon pair.

75 To determine the codon-anticodon pairs that are efficiently accepted by t

76 tein folding and that positions of some rare codons are evolutionarily conserved.

77 While near-cognate codons are frequently used for translation initiation in

78 same pathways, genes, and-in some instances-codons are implicated in H(2)S adaptation in lineages th

79 anscription in the factory regions when stop codons are introduced near the N terminus of the ATI or

80 utions, in contrast to Leu and Arg, of which codons are mutually exchangeable by a single-base substi

81 nsfer RNA supply within the cell, synonymous codons are not used with equal frequency, a phenomenon t

82 Transcripts enriched in rare codons are typically associated with poor translation, b

83 Codon usage bias (CUB), where certain codons are used more frequently than expected by chance,

84 ion of the mRNA stem-loop 5' of the take-off codon, as well as the importance of ribosome loading den

85 ve disparities in the usage of these two Ser codons, as some genes use only AGY for Ser in their gene

86 titutions reduced recognition of a UUG start codon at HIS4 in Sui- cells (Ssu- phenotype); and in vit

87 (Ter5H) mice having a premature termination codon at position +5 in leader exon of Igh (Ter5H) allel

88 in the 5' untranslated region (UTR) and rare codons at the beginning of their coding sequence.

89 The 2stop component is two tandem stop codons at the G gene terminus, preceding the gene end tr

90 n-specific differences in codon frequencies, codon aversion, identical codon pairing, co-tRNA codon p

91 veal the existence of an underlying adaptive codon-based regulatory response inherent to the genetic

92 the hybrid deep neural network is a stacked codon-based scheme.

93 Therefore, we propose this codon bias as a regulatory layer to control cell context

94 observed featuring a clustering of tRNA anti-codon binding domains on one MSC face.

95 e performance of a wide variety of unnatural codons, both in vitro and in the in vivo environment of

96 G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in

97 rly, Ser is separated into two disparate Ser codon boxes, differing by at least two-base substitution

98 induces ribosome stalling at all four glycyl codons but does not evoke a stringent response.

99 ate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing deco

100 Recognition of a start codon by the initiator aminoacyl-tRNA determines the rea

101 release factors, Api promotes pervasive stop codon bypass, leading to the expression of proteins with

102 dons in protein sequences revealed that rare codons can impact co-translational protein folding and t

103 sine base pair at the wobble position of the codon cannot be maintained simultaneously with the canon

104 We find that in 84% of proteins, the three codon categories occupy significantly different structur

105 ps between structural positions of the three codon categories.

106 We examine protein groups showing different codon centrality trends, i.e. different relationships be

107 Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichi

108 , we engineered yeast with all 44,604 single codon changes encoding 14,160 amino acid variants in Hsp

109 codons, which suggests that the evolution of codon choice has been influenced by DNA mechanics around

110 This robustness generalizes to codon choices from multiple taxa across all domains of l

111 ar evidence that natural selection optimizes codon content in the human genome.

112 ever, whether natural selection shapes human codon content to optimize translation efficiency is uncl

113 Thus, start codon context is a signal that quantitatively programs b

114 acid change from the individual SNV within a codon could be different from the amino acid change base

115 ning libraries rely on the use of degenerate codons (DCs), mixtures of DNA bases incorporated at spec

116 ein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequen

117 O virus was attenuated by the inclusion of a codon deletion mutation (Delta1313) and a missense mutat

118 lymorphisms in more than one codon or entire codon deletions have also evolved.

119 complex results in misinitiation at non-AUG codons, demonstrating its importance for fidelity.

120 ors of this pathway and confirmed to be both codon-dependent and occur with ectopic transcripts natur

121 e case of IFN-gamma-induced persistence, Trp codon-dependent changes in transcription.

122 ngs can be robustly expressed, suggestive of codon-dependent regulation.

123 s of Elongator-dependent tRNA modifications, codon-dependent translational reprogramming, and inducti

124 or total DC library optimization, degenerate codon design (DeCoDe), based on integer linear programmi

125 rt site (distance: 542 bp) than to the start codon (distance: 704 bp), which corresponds to open chro

126 reading frame, and produces a premature stop codon downstream.

127 reading frame, and creates a premature stop codon downstream.

128 ested that BMAA is misincorporated at serine codons during protein synthesis, but direct evidence of

129 Finally, we uncovered that the longest codon dwell times could be explained by aminoacylation l

130 ary across diurnal time and feeding regimen, codon dwell times were highly stable and conserved in hu

131 rare 6-bp natural deletion of lysine-glycine codons, endemic to wheat landraces of Shaanxi Province,

132 so simulated evolution of slowly translating codons, finding that slower translation speeds at certai

133 viously predicted misincorporation at serine codons, following a screen for amino acid activation in

134 perfamily are encoded by genes that lack the codon for pyrrolysine characteristic of trimethylamine m

135 y in the dimerization domains, we modify the codons for mouse gene targeting and viral production.

136 , suggesting that targeting of critical stop codons for readthrough may be achievable without general

137 ly depict population-specific differences in codon frequencies, codon aversion, identical codon pairi

138 strategy: the acquisition of upstream start codons from host-derived sequences and subsequent transl

139 f Ser codons, UCX, were derived from alanine codons, GCX, distinctly different from the other primord

140 We targeted P2ACre to the Slc26a9 stop codon, generating Slc26a9(P2ACre) mice, and observed CRE

141 ences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-co

142 nslated small ORFs (containing less than 100 codons) have been identified in untranslated mRNA region

143 Stop codon identity, the nucleotide following the stop codon,

144 y-eight variant positions, and a triplet ATT codon (Ile) insertion within ATP synthase subunit 8, wer

145 de polymorphism introducing a premature stop codon in the lysosomal trafficking regulator gene (LYST)

146 In comparison to NTCs, downstream stop codons in 3'UTRs are recognized less efficiently by ribo

147 st time in Drosophila, footprints mapping to codons in a phased pattern, the hallmark of productive t

148 accumulated deletions of integral number of codons in an essential gene and much longer deletions in

149 hat identified evolutionarily conserved rare codons in Escherichia coli genes and associated such cod

150 d new light on how ribosomes can ignore stop codons in messenger RNA.

151 mbined, had 37 nonsynonymous mutations in 36 codons in pbp2x Although to a lesser magnitude than the

152 As a consequence, lysine codons in proinsulin are misread and proinsulin processi

153 lone, might further explain the role of rare codons in protein folding.

154 Analyses of positions of such rare codons in protein sequences revealed that rare codons ca

155 s suggested that ribosomes bypass tryptophan codons in the absence of tryptophan.

156 those in yeast, as well as pairs of adjacent codons in the P and A site that markedly slow down or sp

157 PIC while decreasing TC dissociation at UUG codons in vitro, indicating destabilization of the open

158 We propose that these two different Ser codons independently emerged during evolution.

159 TC) from reconstituted PICs with a UUG start codon, indicating destabilization of the closed complex.

160 es with ribosomes spending more time at stop codons, indicating that the ejection process might delay

161 ted Ebp1-60S binding is highest during start codon initiation and N-terminal peptide elongation, regu

162 are required for stability of the anticodon/codon interaction in the ribosomal A-site.

163 Premature stop codons introduced by mis-splicing of PgABCA2 pre-mRNA we

164 tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG

165 hypomorphic Delta3A mutant, in which a stop codon is inserted downstream from the first ATG and the

166 paradigm is that the proportion of preferred codons is set by weak selection.

167 plication introduces a premature termination codon leading to nonsense-mediated mRNA decay.

168 hrough increased mistranslation of threonine codons leading to cell death.

169 selection pressure at both the gene and the codon level for five of these six hair bundle link prote

170 each pilA1 and pilA2 is maintained and show codon-level diversification, demonstrating their importa

171 e reverse transcriptase inhibitor (NNRTI) at codons Lys103Asn, Tyr181Cys, Gly190Ala, and to lamivudin

172 A G64 codon mutation (G64(Fix)) was used to inhibit emergence

173 ly, these rqh1 mutations, except for a start codon mutation, are all in the helicase domain, indicati

174 quamous cell carcinoma) for the frequency of codon mutations of 10 Rho-GAP and experimentally tested

175 stimulate readthrough of normal termination codons (NTCs) genome-wide.

176 lly monitoring RNA translation; ranging from codon occupancy profiling, identification of actively tr

177 dons, and the frequency that such synonymous codons occur in genomes ranges from rare to common.

178 rom the U5 to upstream of the gag gene start codon of diverse HIV-1 strains by using next-generation

179 tinct pattern of enrichment around the start codon of ribosomal protein genes in all stages but male

180 ferentially positioned within the first five codons of a set of mRNAs that are enriched for translati

181 nt erroneously read through UAG and UGA stop codons of mRNAs.

182 two evolutionarily conserved, in-frame stop codons of MTCH2 using luminescence- and fluorescence-bas

183 are well known for their role in reading the codons on messenger RNAs and translating them into prote

184 (ICG) constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C(32

185 Notably, we illustrate that reductions in codon optimality in BRCA1 can attenuate its function.

186 data establish an essential role of FMRP in codon optimality-dependent mRNA stability as an importan

187 y of the mRNA degradation machinery to sense codon optimality.

188 dated A-site transfer RNA, indicative of low codon optimality.

189 ombinant human BCO2a was further improved by codon optimization and its fusion with maltose-binding p

190 in these two microbial hosts was enhanced by codon optimization and truncation of the putatively auto

191 The in silico cloning and codon optimization supported the proficient expression o

192 In transplastomic tobRsLS lines expressing a codon optimized Rs-rbcLS operon, the messenger RNA (mRNA

193 a chemically modified sgRNA and an mRNA of a codon-optimized base editor that displayed higher base-e

194 Furthermore, human A549 cells expressing codon-optimized C16L/B22R and C12L genes support higher

195 Arabidopsis thaliana by overexpression of a codon-optimized helix-loop-helix transcription factor (V

196 of an adeno-associated viral vector encoding codon-optimized human RPGR (AAV8-coRPGR), meeting the pr

197 Here, we characterized the use of a codon-optimized SARS-COV-2 Spike glycoprotein for the ge

198 ous SNPs, but polymorphisms in more than one codon or entire codon deletions have also evolved.

199 an A4G gene end signal preceded by one stop codon, or the 2stop+A4G virulence-associated combination

200 vaccine development is to generate, through codon pair deoptimization, an attenuated virus.

201 l times from ribosome profiling, considering codon pair interactions between ribosome sites.

202 nome of respiratory syncytial virus (RSV) to codon pair optimization (CPO) by increasing the content

203 me of respiratory syncytial virus (RSV) were codon pair optimized (CPO) by increasing the content of

204 S-CoV-2 genomic sequence (e.g., codon usage, codon pair usage, dinucleotide/junction dinucleotide usa

205 Distances between tissue-specific codon and codon-pair frequencies were used to generate a dendrogra

206 am based on the unique patterns of codon and codon-pair usage in each tissue that are clearly distinc

207 codon frequencies, codon aversion, identical codon pairing, co-tRNA codon pairing, ramp sequences, an

208 n aversion, identical codon pairing, co-tRNA codon pairing, ramp sequences, and nucleotide compositio

209 Inhibitory codon pairs and poly(A) tracts within the translated mRN

210 lation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially re

211 optimized (CPO) by increasing the content of codon pairs that are overrepresented in the human genome

212 imization (CPO) by increasing the content of codon pairs that are overrepresented in the human genome

213 slation efficiency is the origin of variable codon performance.

214 In addition to premature termination codons, plant microRNAs can also direct the degradation

215 ither a wild-type A2 strain G gene (one stop codon preceding a wild-type gene end signal), an A4G gen

216 Addition of a second stop codon preceding the A4G point mutation (2stop+A4G) resto

217 The genotype consists of two tandem stop codons preceding an A-to-G point mutation in the 4th pos

218 show that A-rich sequences upstream of start codons promote initiation.

219 pted prime editors for use in plants through codon, promoter, and editing-condition optimization.

220 cally desirable when a premature termination codon (PTC) is found in a critical gene.

221 shifted protein with a premature termination codon (PTC) predicted to elicit degradation via nonsense

222 in mutations contain a premature termination codon (PTC), thus progranulin haploinsufficiency has bee

223 harboring premature translation termination codons (PTCs) serves to protect cells from accumulating

224 not all mRNAs bearing premature termination codons (PTCs).

225 by the introduction of premature termination codons (PTCs).

226 We find that selection in favor of preferred codons ranges from weak (|N(e)s| ~ 1) to strong (|N(e)s|

227 Stop codon read-through (SCR) is a process of continuation of

228 verrepresentation of m(1)G9-containing tRNAs codons read by tRNA(Gln(TTG)), tRNA(Arg(CCG)), and tRNA(

229 Stop codon readthrough (SCR) occurs when the ribosome miscode

230 C(32) modification is known to negate wobble codon recognition of the rare CGA codon by an unknown me

231 8% sensitivity for animals harboring one 96S codon, regardless of their stage within the pre-clinical

232 ristic ribosome occupancy patterns at single codon resolution.

233 nal control and show that there is extensive codon restriction within the PEST-encoding region of the

234 nity of start codons and increased near stop codons, revealing complex age-related changes in the tra

235 controls translational activation of proline codon rich profibrotic genes in cardiac fibroblasts and

236 ent substitution models, including models of codon selection.

237 ency of substitution was identified at three codon sites in the L gene-which encodes the viral RNA-de

238 ino acids are encoded by multiple synonymous codons, some of which are used more rarely than others.

239 In mouse liver, the model revealed site- and codon-specific dwell times that differed from those in y

240 NA has high ribosome occupancy at exon 1 and codon-specific pauses at positions 171 (CCG) and 172 (CG

241 We modeled codon-specific ribosome dwell times from ribosome profil

242 deficiency in the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, s

243 CUBAP facilitates in-depth gene-specific and codon-specific visualization that will aid in analyzing

244 gene editing, which produced premature stop codons specifically within the mutant BEST1 alleles.

245 he spacer between the SD sequence and P-site codon strongly affects the rate of ribosome translocatio

246 However, synonymous codon substitutions can affect many distinct cellular pr

247 results support a model in which synonymous codon substitutions can impair cell fitness by significa

248 Here we show that synonymous codon substitutions encoding a single essential enzyme l

249 s wobble decoding of its synonymous A-ending codon, suggesting that this function of s(2)C at positio

250 FMRP preferentially binds mRNAs with optimal codons, suggesting that it stabilizes such transcripts t

251 3E substitution enhanced initiation at a UUG codon (Sui- phenotype) and poor-context AUGs, while redu

252 the wobble position in each codon, and group codon synonyms found in the codon table.

253 codon, and group codon synonyms found in the codon table.

254 in ribosomal stalling on two of the six Ser codons, TCC and TCT, and allowed the selective translati

255 otein substructures preceding conserved rare codons tend to have lower contact orders, in line with o

256 er Onc112 treatment suggests that the act of codon testing of noncognate ternary complexes (TCs) at t

257 ading frame of Ma1 leads to a premature stop codon that truncates the protein by 84 amino acids at it

258 ive N-linked glycosylation sites, as well as codons that evolve under positive selection on the viral

259 e proteins' sequences contain conserved rare codons that may slow down synthesis at this optimal wind

260 programs were biased towards selecting start codons that were upstream of the actual start.

261 o, we show that the original elements of the codon theory continue to make important predictions for

262 to form a direct interaction with the A-site codon to possibly interfere with mRNA movement through t

263 RNA(Pro) bound to either cognate or slippery codons to determine how the m(1)G37 modification prevent

264 ribosome stalling at UUG triplets, the only codon translated by an m(5) C34-modified tRNA.

265 ansfer RNAs (tRNAs), which serve to optimize codon translation rates.

266 Later in evolution, another class of Ser codons, UCX, were derived from alanine codons, GCX, dist

267 he spacer between the SD sequence and P-site codon undergoes structural rearrangements, which slow do

268 eliminates all potential in-frame initiation codons upstream of the DNA binding domain.

269 in the human genome without changing overall codon usage and amino acid sequences.

270 Measured tRNA levels correlated with codon usage and several tRNAs showed reduced aminoacylat

271 ptome of each tissue is derived from genomic codon usage and the relative expression level of each ge

272 seful in unraveling the relationship between codon usage and tRNA abundance, which could be critical

273 Codon usage bias (CUB), where certain codons are used mo

274 ed with equal frequency, a phenomenon termed codon usage bias (CUB).

275 tRNA genes, total number of rRNA genes, and codon usage bias in ribosomal protein sequences were all

276 However, population-specific differences in codon usage biases remain largely unexplored.

277 to deconvolve the extent to which synonymous codon usage can promote or frustrate proper protein fold

278 Synonymous codon usage has been identified as a determinant of tran

279 While experimental changes in codon usage have at times shown large phenotypic effects

280 ngation rates, (aminoacyl-) tRNA levels, and codon usage in mammals.

281 re found to adopt significantly less optimal codon usage in subterranean species than in fossorial an

282 Codon usage in the transcriptome of each tissue is deriv

283 Our work shows that codon usage is linked to the final protein structure and

284 We also found no significant changes in codon usage or the ribosome content during the cell cycl

285 e explained by aminoacylation levels or high codon usage relative to tRNA abundance.

286 Synonymous codon usage significantly impacts translational and tran

287 gene in tumor samples employs a differential codon usage that is characteristic of genes involved in

288 atures of SARS-CoV-2 genomic sequence (e.g., codon usage, codon pair usage, dinucleotide/junction din

289 ers, KRAS employs an intriguing differential codon usage.

290 in the lines incorporating a rbcS gene whose codon use and 5' untranslated-region matched rbcL Additi

291 pments include strategies to read quadruplet codons, use non-natural DNA base pairs, synthesize compl

292 mply that patients carrying a premature stop codon versus missense mutations will likely display diff

293 184Val, and when at least one drug-resistant codon was detected in a participant's pre-ART specimen,

294 nucleotides upstream of the atpI initiation codon, was also found in some Chlorophyceae and Ulvale a

295 amulin to trap initiation complexes at start codons, we find that the mutant ribosomes select start s

296 along the transcript and identify individual codons where ribosomal collisions are likely.

297 scan the mRNA until they encounter the start codon, where conformational changes produce a translatio

298 ears after random substitution of synonymous codons, which suggests that the evolution of codon choic

299 n Escherichia coli genes and associated such codons with cotranslational folding intermediates.

300 We hypothesized that start codons within cap-snatched host transcripts could genera