ライフサイエンスコーパス: codon usage

1 s involved in multicellularity obey distinct codon usage.

2 th translation rate modulation by synonymous codon usage.

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

4 ual rules associated with tRNA abundance and codon usage.

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

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

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

8 election interfering with weak selection for codon usage.

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

10 ssibly to accommodate concomitant changes in codon usage.

11 luorescent protein (GFP) using C. neoformans codon usage.

12 on proteins on the basis of their synonymous codon usage.

13 o be largely unaltered by the restriction in codon usage.

14 re decreasing and one is increasing in major codon usage.

15 synonymous substitutions, and differences in codon usage.

16 coding triplets, is the main determinant of codon usage.

17 creased CpG/UpA frequencies independently of codon usage.

18 ition as the primary predictor of synonymous codon usage.

19 s could arise through similar alterations in codon usage.

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

21 on protein abundance than mRNA structure or 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 ion, and optimizing translation kinetics via codon usage.

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

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

27 RF57 dependent by distinctive changes to its codon usage.

28 at identifying general roles for synonymous codon usage.

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

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

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

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

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

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

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

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

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

38 Codon usage also controls ribosome traffic on mRNA.

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

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

41 by the features at elongation stages, i.e., codon usage and amino acid composition (5.3-15.7% and 5.

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

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

44 y, and start codon context; (ii) elongation, codon usage and amino acid usage; and (iii) termination,

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

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

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

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

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

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

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

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

53 rstanding the extent and causes of biases in codon usage and nucleotide composition is essential to t

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

55 In this study, we compare patterns of codon usage and protein evolution in 22 genes (>11,000 c

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

57 e coding region of the human genome, data on codon usage and pseudogene-derived mutation rates for di

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

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

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

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

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

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

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

65 we can expect to draw inferences from biased codon usage, and we estimate the time scales required to

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

67 rus replicative fitness by deoptimization of codon usage are discussed.

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

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

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

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

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

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

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

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

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 ted from mosquito bodies and heads indicated codon usage at this position corresponded with that of t

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

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

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

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

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

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

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

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

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

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

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

90 This revealed that patterns of codon usage bias are strongly correlated with overall ge

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 sts itself even in the absence of synonymous codon usage bias at the 4-fold degenerate sites.

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

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

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

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

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

99 Codon usage bias in Drosophila melanogaster genes has be

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

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

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

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 ubiquitous phenomenon, which may b

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

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 It was demonstrated that codon usage bias is correlated positively with gene tran

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 , more tRNA genes and more strongly selected codon usage bias.

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

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

125 ncreases in S288c occur in genes with strong codon usage bias; (iii) genes under stronger negative se

126 ation pattern or in tDNA copy number changed codon-usage bias and increased the K(S) distance between

127 orthologues in non-WGD species, we show that codon-usage bias and protein-sequence conservation are t

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

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

130 is effective only in the presence of strong codon-usage bias or protein-sequence conservation.

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

132 Synonymous codon usage biases are associated with various biologica

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

134 Codon usage biases are found in all eukaryotic and proka

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

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

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

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

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

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

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

142 We find that synonymous codon usage can reliably distinguish between negative se

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

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

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

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

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

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

149 Although synonymous codon usage contributes to this pattern, it is intrinsic

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 onal evolution and exploiting GC content and codon usage frequency to identify genes with composition

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

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

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

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

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

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

170 ding information for comparative analysis of codon usage in 12 plant species, including 6 eudicots, 5

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

174 available mitochondrial genomes and analyze codon usage in Chiroptera.

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

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

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

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

179 g a more direct role of natural selection on codon usage in humans.

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

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

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

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

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

185 The patterns of codon usage in plants are not well understood.

186 Because viruses are expected to evolve codon usage in the context of their host's molecular mac

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

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

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

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

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

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

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

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

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

196 The results suggest that plant codon usage is affected by translational selection, and

197 Codon usage is also implicated in the control of transcr

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

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

200 While codon usage is classically considered a major determinan

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

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

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

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

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

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

207 However, in many organisms, codon usage is influenced by natural selection, particul

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

209 Codon usage is one of the factors influencing recombinan

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

211 e is predicted highly expressed (PHX) if its codon usage is rather similar to the average codon usage

212 ere I show that selection to maintain biased codon usage is reduced in Drosophila miranda relative to

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

214 Codon usage limitation, rather than promoter type and th

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

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

217 the H.influenzae clinical isolates displayed codon usages most similar to Haemophilus sp.

218 The G + C content and codon usage observed in the functional groups suggested

219 Factor analysis was performed on codon usage of 16,654 genes annotated in Build 34 of the

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

221 codon usage is rather similar to the average codon usage of at least one of the RP, transcription/tra

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

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

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

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

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

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

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

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

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

234 can accurately estimate both demographic and codon usage parameters.

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

236 The codon usage pattern and the distribution of a particular

237 included YEF3, RNR1, and RNR3, with a unique codon usage pattern linked to Trm9.

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 Among bacteria, many species have synonymous codon usage patterns that have been influenced by natura

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

244 rces for large-scale comparative analysis of codon usage patterns.

245 Codon usage plays a crucial role when recombinant protei

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

247 s are strongest for genes with highly biased codon usage, probably reflecting the ability of such loc

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

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

250 sequences either by deoptimizing synonymous codon usage (PV-AB) or by maximizing synonymous codon po

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

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

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

254 The significance of unequal codon usage remains unclear.

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

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

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

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

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

260 Genes displaying codon usage statistics >1 SD above this range were eithe

261 folding, posttranslational modification, and codon usage still limit the number of improved antibodie

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

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

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

270 ewide departures from equilibrium synonymous codon usage; three are decreasing and one is increasing

271 Codon usage thus evolved as a means to optimise translat

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

288 A similarity statistic for codon usage was developed and used to compare novel gene

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

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

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

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

293 e composition, gene number, gene boundaries, codon usage) were highly similar among all species and t

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

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

296 es, the search for unusual GC composition or codon usage within a genome, and identification of simil

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