ライフサイエンスコーパス: codon usage

1 es, nascent-protein behavior, and synonymous codon usage.

2 on protein abundance than mRNA structure or codon usage.

3 ers, KRAS employs an intriguing differential codon usage.

4 ion, and optimizing translation kinetics via codon usage.

5 s) are dependent on the nature of the skewed codon usage.

6 flipped simply by changing the nature of the codon usage.

7 RF57 dependent by distinctive changes to its codon usage.

8 at identifying general roles for synonymous codon usage.

9 s involved in multicellularity obey distinct codon usage.

10 ce GC content, secondary structure, and rare codon usage.

11 ual rules associated with tRNA abundance and codon usage.

12 cs have been developed to identify biases in codon usage.

13 te, which varies as a function of synonymous codon usage.

14 els supporting SANE as a major force shaping codon usage.

15 election interfering with weak selection for codon usage.

16 noted to have a highly aberrant, suboptimal codon usage.

17 is associated with optimized changes in tRNA codon usage.

18 egulate the activity of vRdRp, which selects codon usage.

19 ssibly to accommodate concomitant changes in codon usage.

20 G codon, protein coding sequence length, and codon usage.

21 of mRNA secondary structure independent from codon usage.

22 h signaling, independently of mRNA levels or codon usage.

23 timization of the tRNA pool to the demand in codon usage.

24 th translation rate modulation by synonymous codon usage.

25 imilar AT nucleotide bias, AT-, GC-skews and codon usage.

26 creased CpG/UpA frequencies independently of codon usage.

27 s could arise through similar alterations in codon usage.

28 Optimization of frq codon usage abolishes both overt and molecular circadian

29 as determined on a pathway-by-pathway basis; codon usage, abundance, and sequence similarity contribu

30 synonymous nucleotide differences affecting codon usage account for differences between HRas and KRa

31 enes in Neurospora, frq exhibits non-optimal codon usage across its entire open reading frame.

32 ncepts of translational optimization through codon usage adaptation, we demonstrated that community-w

33 ns as an inducer of gene expression, we used codon-usage adaption and structure-based design to devel

34 Finally, we show that codon usage affects protein structure and function in vi

35 Synonymous codon usage affects the efficiency/stringency of mRNA de

36 protein folding based on the assumption that codon usage affects translation dynamics.

37 Codon usage also controls ribosome traffic on mRNA.

38 ms of these methods based on single-sequence codon usage analysis.

39 We discovered a relationship between codon usage and a general property of circadian rhythms

40 se sequence-directed nucleosomes and affects codon usage and amino acid composition in genes.

41 In the end, we suggest codon usage and amino acid profiles as powerful tools th

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

43 set of eGFP mRNAs with independently altered codon usage and CDS structure, we find that the structur

44 As such, numerous studies have investigated codon usage and codon bias in an effort to better unders

45 ce for selection associated with both biased codon usage and conservation of regulatory sequences inv

46 acid sequence, given a background model for codon usage and dinucleotide biases.

47 ttle is known about the relationship between codon usage and frameshifting errors, an important form

48 s construct based on their similarity to the codon usage and GC content of the tobacco plastome.

49 ding of translational dynamics indicate that codon usage and mRNA secondary structure influence trans

50 ccounted for by two important mRNA features: codon usage and mRNA secondary structure.

51 lyses revealed that dipterans follow similar codon usage and nucleotide biases that could be due to m

52 Furthermore, the correlations between codon usage and protein disorder tendency are conserved

53 The relationship between codon usage and protein structures and the in vivo role

54 he independent contributions of factors like codon usage and secondary structure to regulating protei

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

56 ve importance of different features (such as codon usage and the 5' ramp effect) in determining the a

57 Genomic traits such as codon usage and the lengths of noncoding sequences may b

58 The correspondence of mRNA codon usage and the relative abundance of their cognate

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

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

61 in gene content, nucleotide composition, and codon usage, and have retained a large gene syntenty.

62 heir inability to maintain plasmids, unusual codon usage, and inefficient homologous recombination ar

63 mple covariation between sequence evolution, codon usage, and mRNA level in E. coli, yeast, worm, fly

64 posed by biases in mRNA secondary structure, codon usage, and Ssb action.

65 ngle the relationship between GC content and codon usage, and suggest simple strategies to overcome t

66 ted from Ensembl, and analyzed via RCC using codon usage appropriate for each species.

67 Mutations altering synonymous codon usage are linked to human diseases.

68 GC content and codon usage are the two key sequence features known to i

69 genes, and their nucleotide composition and codon usage are very similar to those of the chromosomes

70 arginine codons using three strategies; rare codon usage, arginine starvation, and inactivation of ar

71 nt relationship between expression noise and codon usage as compared to other genes.

72 In particular, focusing on codon usage as one of the sequence features associated w

73 tradictory selective forces appear to affect codon usage as well.

74 homology searching, hydropathy plotting, and codon usage assessment) strongly suggested that Wzy is a

75 ostly AU-rich mRNAs, which have a particular codon usage associated with a low protein yield; AU-rich

76 accounts for metabolism, gene expression and codon usage at both transcription and translation levels

77 ribosome usage is a central force in shaping codon usage at the genomic scale.

78 ere may be a selective conflict over optimal codon usage between different developmental stages.

79 ies, such as the ability to view and compare codon usage between individual organisms and across taxo

80 Most previous studies of the evolution of codon usage bias (CUB) and intronic GC content (iGC) in

81 nonadaptive forces driving the evolution of codon usage bias (CUB) has been an area of intense focus

82 Codon usage bias (CUB) has been documented across a wide

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

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

85 e of non-synonymous substitutions (d(N)) and codon usage bias (F(op)), showing that fast-evolving gen

86 Differences in codon usage bias across genes reveal that weak selection

87 ebserver service as a user-friendly tool for codon usage bias analyses across and within genomes in r

88 A codon usage bias pipeline is demanding for codon usage bias analyses within and across genomes.

89 Finally, analyses of codon usage bias and RNA-editing processes of the conoto

90 y to common belief, amino acid (AA) bias and codon usage bias are insufficient to create base-3 perio

91 highly expressed proteins (with adherence to codon usage bias as a proxy for expressivity) to utilize

92 recombination, saturation, and variation in codon usage bias as factors contributing to this high le

93 are an interesting system in which to study codon usage bias because of their length, expression, an

94 ute the position-specific scoring matrix and codon usage bias for all such RNA sequences.

95 Accurately quantifying codon usage bias for different organisms is useful not o

96 Quantification of codon usage bias helps understand evolution of living or

97 Reduced codon usage bias in D. miranda may thus result from the

98 Codon usage bias in Drosophila melanogaster genes has be

99 thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutationa

100 hts into protein maturation and homeostasis, codon usage bias in organisms, the origins of translatio

101 Further, we find highly significant codon usage bias in regions downstream of the PTC in 38

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

103 Here, we show that there is a strong codon usage bias in the filamentous fungus Neurospora.

104 we calibrated each genome in turn using the codon usage bias indices of highly expressed ribosomal p

105 Synonymous codon usage bias is a broadly observed phenomenon in bac

106 Codon usage bias is a universal feature of all genomes,

107 Codon usage bias is a universal feature of eukaryotic an

108 Codon usage bias is a universal feature of eukaryotic an

109 The pattern of its codon usage bias is also consistent with that of HAV.

110 host cell for protein translation, but their codon usage bias is often different from that of the hos

111 Codon usage bias is the nonrandom use of synonymous codo

112 centralized repository of look-up tables and codon usage bias measures for a wide variety of genera,

113 Given the impact of codon usage bias on recombinant gene technologies, this

114 A codon usage bias pipeline is demanding for codon usage b

115 e conclusion that the formation of G. biloba codon usage bias was dominated by natural selection.

116 Furthermore, codon usage bias was relaxed for these genes in post-WGD

117 e pattern of non-uniform codon use (known as codon usage bias) varies between organisms and represent

118 howing that fast-evolving genes have a lower codon usage bias, consistent with strong positive select

119 We here introduce an explicit model of codon usage bias, inspired by statistical physics.

120 A variety of factors, including gene length, codon usage bias, protein abundance, protein function, a

121 d constraint appears to be a major driver of codon usage bias.

122 in different organisms, a phenomenon termed codon usage bias.

123 ated to but clearly distinct from individual codon usage bias.

124 was put forward to explain the existence of codon usage bias.

125 to use G/C-ending codons together with more codon usage bias.

126 Codon-usage bias has been observed in almost all genomes

127 e usually encoded by optimal codons, yet the codon-usage bias of the kaiBC genes is not optimized for

128 Many genes exhibit little codon-usage bias, which is thought to reflect a lack of

129 Synonymous codon usage biases are associated with various biologica

130 Differences between codon usage biases are attributed, in part, to changes i

131 Codon usage biases are found in all eukaryotic and proka

132 ce of organisms with varying GC composition, codon usage biases etc., and consequently gene identific

133 virus attenuation strategy makes use of the codon usage biases of human and avian influenza viruses

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

135 ransfer from species not only with different codon usage but possibly that did not have introns, perh

136 e been devised to infer ongoing selection on codon usage by comparing the derived state frequency spe

137 tterns of synonymous polymorphisms affecting codon usage can be quite erratic after such a change; st

138 we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifesty

139 studies now foster the idea that patterns of codon usage can control ribosome speed, fine-tuning tran

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

141 d genomes suggest that different patterns of codon usage changes in genes of different functional cat

142 recent studies have shown strong effects of codon usage changes on protein expression levels and cel

143 ntal question and suggest the existence of a codon usage code for protein folding.

144 niversal mechanism in eukaryotes that uses a codon usage "code" within genetic codons to regulate cot

145 Importantly, codon usage (Codon Adaptation Index) correlates with pre

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

147 of synthetic hEGF containing preferred rice codon usage comprises up to 7.8% of TSP in hypoxic trans

148 Here, we ask whether different codon usage controls gene expression programmes in self-

149 Silencing of eRF1 expression resulted in codon usage-dependent changes in protein expression. Tog

150 biting the expression of viral proteins in a codon-usage-dependent manner.

151 ing three model bacteria with different stop codon usage (Escherichia coli, Mycobacterium smegmatis,

152 ing the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation

153 Most population genetic models of codon usage evolution assume that the population is at m

154 es the likelihood of misannealing, optimizes codon usage for expression in a selected host, allows fo

155 ear at the present time whether the aberrant codon usage for gH and gL of RRV is an intentional regul

156 Comparisons of codon usage for the respective variants indicated that g

157 Additionally, codon usage frequencies in nonoverlapping regions are mo

158 echnique relies on the accurate knowledge of codon usage frequencies.

159 This is especially the case if the codon usage frequency of the organism of origin and the

160 lation rates in a manner that is superior to codon usage frequency, which occur during the elongation

161 ric that correlates only weakly with genomic codon-usage frequency, but strongly with global physiolo

162 study provides an example of how non-optimal codon usage functions to regulate protein expression and

163 The results indicate that the codon usage greatly affects the expression of CFTR.

164 These results indicate that codon usage has an effect on mRNA levels and protein exp

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

166 Codon usage has been proposed to play a role in regulati

167 strains provides a comprehensive look at how codon usage has been shaped over evolutionary time and c

168 Furthermore, codon usage has been shown to affect protein structure a

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

170 ion (77- to 111-fold) when compared with the codon usage hierarchy of the psbA genes.

171 This study reports that inefficient codon usage in a herpesviral gene is strikingly correlat

172 To investigate the in vivo role of codon usage in animals, we took advantage of the sensiti

173 95% and 98% AT, resulting in the most biased codon usage in any genome described to date.

174 We present a comprehensive analysis of stop codon usage in bacteria by analyzing over eight million

175 available mitochondrial genomes and analyze codon usage in Chiroptera.

176 n vivo example that demonstrates the role of codon usage in determining protein structure and functio

177 ance on transcript length, the importance of codon usage in determining protein synthesis rates, and

178 echanisms based on tRNA modifications change codon usage in embryonic stem cells.

179 nd is the most frequent pattern (GTG) of the codon usage in Escherichia coli.

180 d protein structures and the in vivo role of codon usage in eukaryotic protein folding is not clear.

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

182 Biased codon usage in many species results from a balance among

183 Therefore, patterns of codon usage in MyHC genes are consistent with models sup

184 ion against nonsense errors (SANE) acting on codon usage in MyHC genes.

185 suggesting an important role for synonymous codon usage in organism physiology.

186 DNA composition in general, and codon usage in particular, is crucial for understanding

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

188 ng that evolution may have shaped synonymous codon usage in the genomes of organisms in part to incre

189 Codon usage in the transcriptome of each tissue is deriv

190 Here we show that codon usage in the v-FLIP gene is strikingly suboptimal.

191 explanation for the evolution of inefficient codon usage in this gene and point to a strong connectio

192 wing for the first time ongoing selection on codon usage in this species.

193 The roles of codon usage in translation, however, are not clear and h

194 , which combines sequencing error models and codon usages in a hidden Markov model to improve the pre

195 ors that are implicated in the selection for codon usage include facilitation of fast and accurate tr

196 cent literature on the functional effects of codon usage, including bioinformatics approaches aimed a

197 on, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that

198 used this measure to test if the pattern of codon usage indicates optimization against frameshifting

199 Codon usage is also implicated in the control of transcr

200 In many organisms, synonymous codon usage is biased by a history of natural selection.

201 In many organisms, codon usage is biased toward particular codons.

202 While codon usage is classically considered a major determinan

203 lification of noise strength associated with codon usage is comparable to that of the TATA box, sugge

204 Among species of Drosophila, codon usage is constant with the exception of the Drosop

205 nribosomal genes we found that sequence high codon usage is correlated with increased noise relative

206 sent, which could contain ND3 if a different codon usage is employed.

207 osition-dependent relationship of synonymous codon usage is evidence for a novel form of codon positi

208 he circadian oscillator, we showed that dper codon usage is important for circadian clock function.

209 ing translation speed, we find that relative codon usage is less informative than tRNA concentration.

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

211 Codon usage is one of the factors influencing recombinan

212 e evidence in support of the hypothesis that codon usage is optimized to minimize missense errors.

213 GC content and/or codon usage, we show that codon usage is the key factor determining translational

214 The codon usage is therefore constrained by the obligation o

215 A major role of codon usage is thought to regulate protein expression le

216 Codon usage limitation, rather than promoter type and th

217 Alternatively, however, non-optimal codon usage may be of biological importance.

218 o a changing environment: pathway structure, codon usage, metabolism.

219 We were interested in the codon usage of an antibody Fab fragment gene exhibiting

220 These results indicate that non-optimal codon usage of frq is essential for its circadian clock

221 By comparing the codon usage of genes shared among strains (primarily ver

222 modification, which included optimising the codon usage of the coding sequence to better suit sugar

223 ORF57 is related in some way to the aberrant codon usage of the gH and gL RNAs.

224 polysome-associated tRNA levels reflect the codon usage of viral genes, suggesting the existence of

225 'cell differentiation-induced' genes, while codon-usage of H3F3A resembles that of 'cell proliferati

226 er, these results show the direct effects of codon usage on a complex phenotype and organismal fitnes

227 rimental testing of the impact of synonymous codon usage on the production of functional proteins.

228 er, these results suggest that the effect of codon usage on translation elongation speed is a conserv

229 To investigate the impact of synonymous codons usage on protein expression and function, we desi

230 m modern biology that demonstrate this bias (codon usage optimality and gene expression, gene duplica

231 Here we generated codon-usage optimized and hyperfunctional factor IX (FIX

232 ng differences in elongation rates driven by codon usage or other factors.

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

234 andS facilitates a comprehensive analysis of codon usage over many organisms.

235 can accurately estimate both demographic and codon usage parameters.

236 As one of the most ancient tree species, the codon usage pattern analysis of Ginkgo biloba is a usefu

237 The codon usage pattern and the distribution of a particular

238 ulated proteins with similar composition and codon usage pattern of specific amino acids behave simil

239 The codon usage pattern tended towards more frequently use o

240 eins and investigate the correlation between codon usage patterns and protein regulation levels in tw

241 ncerted evolution have radically altered the codon usage patterns in D. melanogaster, D. pseudoobscur

242 erent hosts have been found to have distinct codon usage patterns, which may reflect host adaptation.

243 Codon usage plays a crucial role when recombinant protei

244 In both Neurospora and Drosophila cells, codon usage plays an important role in regulating mRNA t

245 (ii) On the other hand, changes in codon usage preferences in these extremophilic/non-extre

246 Additionally, H3F3B codon-usage preferences resemble those of broadly expres

247 iction of cellular functions solely based on codon usage profile data.

248 a correlation between cellular function and codon usage profiles of the genes in the studied pairs.

249 on of DS-Cav1 pre-F stabilization, optimized codon usage, reduced CpG content, and vector packaging s

250 these results establish a mechanism for how codon usage regulates mRNA translation efficiency.

251 Finally, we demonstrate that codon usage regulates protein function by affecting co-t

252 In addition, codon usage regulates ribosome movement and stalling on

253 osome profiling results, here we showed that codon usage regulates translation elongation rate and th

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

255 The significance of unequal codon usage remains unclear.

256 Synonymous codon usage (SCU) varies widely among human genes.

257 Synonymous codon usage significantly impacts translational and tran

258 relationships, may be explored through their codon usage similarities.

259 uman cells but not in eggs by converting its codon usage so that it is similar to that observed from

260 ino-acid contents, but they display distinct codon usages so that Nrd1 and Nab3-binding sites can ari

261 d significantly better than the conventional codon-usage statistic method (CSM).

262 of unusual tRNAs, and a distinct pattern of codon usage suggest the "out-of-frame pairing" model of

263 h-performance Integrated Virtual Environment-Codon Usage Tables (HIVE-CUTs), to present and analyse c

264 e Tables (HIVE-CUTs), to present and analyse codon usage tables for every organism with publicly avai

265 Despite the obvious need for accurate codon usage tables, currently available resources are ei

266 aGene clusters mapped to metabolic pathways, codon usage tables, NemFam protein families which repres

267 Building on our recent HIVE-Codon Usage Tables, we constructed a new database to inc

268 Thus, strategies such as changes in codon usage that aim solely at altering the expression l

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

270 derived from transcripts that use an unusual codon usage that is quite different from that of the hos

271 nt families of persisting viruses use a poor codon usage that is skewed in a distinctive way to tempo

272 Codon usage thus evolved as a means to optimise translat

273 RNA polymerase, thus placing constraints on codon usage to balance viral RNA synthesis.

274 tent with the general lack of sensitivity of codon usage to effective population size.

275 e molecular mechanisms connecting synonymous codon usage to efficient protein biogenesis and proper c

276 ermining the contributions of GC content and codon usage to gene expression efficiency.

277 ations (DS-Cav1), and we also modified RSV F codon usage to have a lower CpG content and a higher lev

278 tional control mechanism is known that links codon usage to protein expression levels.

279 ations highlight the relevance of synonymous codon usage to protein function and implicate homeostati

280 on and folding, but the mechanism connecting codon usage to protein homeostasis is not known.

281 By adapting their codon usage to that of the Mycobacterium tuberculosis ge

282 synthesized the flp(m) gene by adapting the codon usage to that preferred by M. tuberculosis.

283 the relative contributions of GC content and codon usage to the efficiency of nuclear gene expression

284 in an open question; studies have attributed codon usage to translational selection, mutational bias

285 stabilization and strategic manipulation of codon usage, together with efficient pre-F packaging int

286 ty might explain the observed differences in codon usage trends in genes of different functions.

287 r different assumptions regarding synonymous codon usage, tRNA level modifications, or ribosome pause

288 We also performed association analysis for codon usage-tRNA expression for the cell lines.

289 approach to synthesize pools of thousands of codon-usage variants of lacZalpha and 74 challenging Dro

290 account for only a fraction of the observed codon usage variation.

291 Synonymous codon usage was once thought to be functionally neutral,

292 acterium Synechococcus elongate, non-optimal codon usage was selected as a post-transcriptional mecha

293 the evolution of mutation biased synonymous codon usage, we examined nucleotide co-occurrence patter

294 quence but differ in their GC content and/or codon usage, we show that codon usage is the key factor

295 ent functional categories display a distinct codon usage, which was interpreted as evidence that SCU

296 m a cross-species comparison of selection on codon usage, while accounting for changes in mutational

297 Furthermore, correlations between codon usage within host genomes and their viral pathogen

298 e replacement has led to modified synonymous codon usage within the class Deinococci that affects whi

299 Through our analysis of the variation in codon usage within the strains presently available, we f

300 High variation in terms of codon-usage within the gene cluster, together with the d