ライフサイエンスコーパス: codon bias

1 d by peculiar rates of mutation or levels of codon bias.

2 respectively, of human and mouse TNRs showed codon bias.

3 with theoretical predictions of the level of codon bias.

4 on efficiency in vitro through alteration of codon bias.

5 more compatible with the observed levels of codon bias.

6 ein in Chlamydomonas reinhardtii chloroplast codon bias.

7 natural selection as a mechanism leading to codon bias.

8 relative mutational load of genes caused by codon bias.

9 e association between recombination rate and codon bias.

10 atistically significant N1 context-dependent codon bias.

11 DNA divergence is inversely correlated with codon bias.

12 d approximate estimation methods that ignore codon bias.

13 tual correlation between synonymous rate and codon bias.

14 , in that synonymous rates were unrelated to codon bias.

15 at their low diversity is not due to extreme codon bias.

16 g region and the recombination rate modulate codon bias.

17 t, can have a moderately strong influence on codon bias.

18 tween protein abundance, mRNA abundance, and codon bias.

19 s to have allowed a genome-wide reduction in codon bias.

20 with high codon bias than in genes with low codon bias.

21 did not alter the amino acid sequence or the codon bias.

22 a model from a strictly mutational model of codon bias.

23 rgone a reduction in selection intensity for codon bias.

24 timal for a cell generates the phenomenon of codon bias.

25 as is the major driving force for generating codon bias.

26 an evolutionary theory on the origin of this codon bias.

27 inement than other commonly used measures of codon bias.

28 ticipates in the creation and maintenance of codon bias.

29 different frequencies, a phenomenon known as codon bias.

30 ound no changes in nucleotide composition or codon bias.

31 lationships with other known determinants of codon bias.

32 RNA structural elements and use of different codon biases.

33 to translation activities) show less extreme codon biases.

34 selection weak independently of the level of codon bias?

35 iv) What is the exact nature of selection on codon bias?

36 ematically characterize the contributions of codon bias, AA bias and protein structural motifs to the

37 olutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial geno

38 en GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whol

39 and may explain the unexpected constancy of codon bias across species of very different census popul

40 tly linked genes, can change very greatly in codon bias across species.

41 determine many of a gene's features, such as codon bias, amino acid composition, and size.

42 This insensitivity indicates a consistent codon bias amongst highly expressed genes.

43 This phenomenon is known as codon bias and appears to be a universal feature of geno

44 by synthesizing the lsc gene in chloroplast codon bias and by driving expression of the chimeric gen

45 lihood-based method for estimating levels of codon bias and determining major codon preference that r

46 Intragenic variation in codon bias and elongation rate is significant, with a st

47 nificant, with a strong trend for increasing codon bias and elongation rate towards the 3' end of the

48 In some species, patterns of codon bias and empirical findings on the biology of tran

49 and SSD are similarly biased with respect to codon bias and evolutionary rate, although differing sig

50 gly, there is a negative correlation between codon bias and expression levels for group 3 genes, i.e.

51 ions are neutral, which we test by analyzing codon bias and G+C content in a set of 92 gene loci.

52 Codon bias and GC content differs among MyHC genes with

53 Levels of codon bias and gene expression are highest for those gen

54 Long coding regions have both a lower codon bias and higher synonymous substitution rates, sug

55 Here we review currently known types of codon bias and how they may influence translation.

56 also predicts a negative correlation between codon bias and Ks, which is also not found.

57 nes, Adh and Adhr, which differ in degree of codon bias and level of gene expression.

58 This may result in atypical codon bias and particular evolutionary constraints.

59 me with a GC content that relates synonymous codon bias and protein folding.

60 Here we show that codon bias and recombination rate are correlated strongl

61 e controversies over the roles of N-terminal codon bias and suggest a straightforward method for opti

62 discuss how understanding the principles of codon bias and translation can contribute to improved pr

63 ategories: preferred mutations that increase codon bias and unpreferred changes in the opposite direc

64 imulations were performed to maintain/remove codon bias and/or to maintain or alter third-codon posit

65 he translation machinery, known to be highly codon biased and using preferentially fast codons, are h

66 rough small variations in codon frequencies, codon biases and context-dependent codon biases between

67 ression levels are correlated with proteins' codon biases and mRNA expression levels, as measured by

68 est that elongation rate is affected by both codon biases and specific amino acid composition.

69 investigations into the connections between codon biases and translation rates.

70 gher repeat density, larger gene size, lower codon bias, and a higher rate of gene rearrangement comp

71 pecies-specific GC content, GC and AT skews, codon bias, and mutation bias.

72 tionship among the coding region length, the codon bias, and the synonymous divergence and polymorphi

73 ce can considerably reduce adaptation, e.g., codon bias, and, to a lesser extent, levels of polymorph

74 enforce mutation synonynimity, preserve the codon-bias, and leave untranslated regions intact.

75 divergences (dinucleotide bias); extremes of codon bias; and anomalies of amino acid usage.

76 In this lineage, codon bias appears to be maintained under roughly equal

77 ction for preferred codons is weak only when codon bias approaches equilibrium and may be quite stron

78 We find that while context-dependent codon biases are widespread in bacteria, few are conserv

79 rience stronger natural selection for higher codon bias as a result of maladaptive reduction of their

80 f 69 in human, and 18 of 42 in mouse) showed codon bias at p<0.05.

81 ot-specific catalases are their extreme high codon bias at the third position and low degree of seque

82 consistent with translational selection for codon bias being stronger in the larval stage and sugges

83 quencies, codon biases and context-dependent codon biases between the samples.

84 We detected a stronger codon bias but a lower frequency of GC at synonymous sit

85 This was not attributable to codon bias but to the change in prohormone sequence.

86 of genes and even the particular pattern of codon bias can remain phylogenetically invariant for ver

87 ed; quantify the effects of genomic context, codon bias, chromatin accessibility, and number of prote

88 hat X-linked genes have significantly higher codon bias compared to autosomal genes in both Drosophil

89 fus1 gene in the mt+ locus, mid displays low codon bias compared with other nuclear genes.

90 ein synthesis, it is generally accepted that codon bias contributes to translation efficiency by tuni

91 In this formulation, codon bias correlations for Escherichia coli genes are e

92 bout half of all cases the context-dependent codon bias could not be explained by the sequence compos

93 In addition, a few data repositories of codon bias data are available, differing in the metrics

94 e have created a new web resource called the Codon Bias Database (CBDB) which provides information re

95 The Codon Bias Database provides a centralized repository of

96 nge" which was also regarded as a measure of codon bias (defined as preferential use either in TNR or

97 Codon bias deoptimization has been previously used to su

98 and bacterial growth rates also varied, but codon bias did not correlate with gene expression.

99 This study addresses the cause of codon bias differences between the sibling species, Dros

100 Unusual codon bias differences between the two families may resu

101 synthesis in HIV-infected cells by means of codon-bias discrimination.

102 integrate the effect of purifying selection, codon bias, DNA repair and GC content on s/v ratio of pr

103 dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR express

104 uences to determine the pattern of change in codon bias during angiosperm divergence.

105 Codon bias engendered by an A + T rich genome may influe

106 nonymous codons, including one gene with low codon bias, esterase-6.

107 Codon bias even varies by isoform within a species.

108 Here we investigate patterns of codon bias evolution on the X chromosome and autosomes i

109 limit plausible explanations for patterns of codon bias evolution to selection- or drift-based proces

110 A favorable codon bias for the mutated codon with consequently incre

111 cs were applied to compare context-dependent codon biases for codons from different synonymous groups

112 The fus1 gene is remarkable in lacking the codon bias found in all other nuclear genes of C. reinha

113 es are conventional in length, with the same codon bias found in other minicircle genes.

114 s highly deviant in its genome signature and codon bias from the rest of the genome.

115 ual validation, ranged from 5 to 39 kDa, had codon biases from 0.93 to 0.083, and were primarily asso

116 We used sequence-based analysis to examine codon bias, gene duplications, and levels of divergence

117 anisms with nucleotide-biased, and therefore codon-biased, genomes or isochores.

118 re, genes that become X-linked evolve higher codon bias gradually, over tens of millions of years.

119 Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significa

120 There is limited evidence that selection on codon bias has an effect on differentiation (as measured

121 s that codon arrangement, rather than simply codon bias, has a key role in determining translational

122 , and not simply relaxation of constraint on codon bias, has contributed to the higher levels of unpr

123 pendent on local nucleotide context, and not codon bias, has occurred in these species.

124 crystallins produced from mRNAs with changed codon bias have the same amino acid sequence but attain

125 The NNNNT codon set enables low codon bias, high fidelity, and high efficiency for the p

126 d nucleotide/amino acid composition bias and codon bias higher, in more-overlapped than in less-overl

127 ter regimes in which fast initiation or high codon bias in a transgene increases protein yield and in

128 us studies have investigated codon usage and codon bias in an effort to better understand how species

129 ide a resource for researchers investigating codon bias in bacteria, facilitating comparisons between

130 Thus, our results show intragenic codon bias in both mouse and human genes expressed in di

131 te of nonsynonymous substitutions (d(N)) and codon bias in D. melanogaster.

132 sence is positively correlated with a gene's codon bias in D. melanogaster.

133 Evolutionary analysis of codon bias in Drosophila indicates that synonymous mutat

134 The total codon bias in each taxon, when regressed against the tot

135 Therefore, genome-wide codon bias in eubacteria and archaea may be predicted fr

136 s, natural selection leads to high levels of codon bias in genes that are highly expressed.

137 This difference is ascribed to common codon bias in HRAS, which leads to much higher protein e

138 riation over different function classes, for codon bias in relation to possible lateral transfer and

139 ithout introns showing significantly reduced codon bias in the center of coding regions.

140 entrally located introns do not show reduced codon bias in the center of the coding region.

141 onstrated that the experimental reduction of codon bias in the Drosophila alcohol dehydrogenase (Adh)

142 ontradict each other and cloud the origin of codon bias in the taxon.

143 th the nucleotide bias 3' of the stop codon, codon bias in the two codon positions 5' of the terminat

144 undance played a role in creating intragenic codon bias in these genes.

145 hly expressed, tandem-repeated genes display codon bias in Trypanosoma cruzi, Trypanosoma brucei and

146 generating both global and local synonymous codon biases in many unicellular organisms, this explana

147 e two strands, on differences in residue and codon biases in relation to gene function, expression le

148 leotides, evaluations and interpretations of codon biases in several large prokaryotic genomes, and c

149 Independent of gene size, the codon biases in the 5' third of genes deviate by more th

150 Factors with proposed roles in causing codon bias include degree and timing of gene expression,

151 Known causes of codon bias include differences in mutation rates as well

152 pression levels of individual genes, whereas codon bias influences global translation efficiency and

153 Thus codon bias is an indicator of the intensity of one kind

154 In addition, relative codon bias is broadly conserved among syntenic genes fro

155 It is shown that average relative codon bias is correlated with expression level and that,

156 Synonymous codon bias is correlated with tRNA gene copy number and

157 esults suggest that, in general, genome-wide codon bias is determined primarily by mutational process

158 ral lines of evidence that this elevation in codon bias is due exclusively to their chromosomal locat

159 mous sites are under weak selection and that codon bias is maintained by a balance between selection,

160 Another interesting observation is that codon bias is not a predictor of either protein or mRNA

161 However, unlike other organisms, Plasmodium codon bias is not correlated to tRNA gene copy number.

162 f dietary nitrogen on genome composition and codon bias is poorly understood.

163 Whereas the degree of codon bias is positively correlated with level of gene e

164 honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of partic

165 However, codon bias is significantly negatively correlated with f

166 , the role of selective pressures in shaping codon bias is still controversial in vertebrates, partic

167 Codon bias is strongly related to gene expression levels

168 ppears that the major cause for selection on codon bias is that certain preferred codons are translat

169 Codon bias is very low, as seen for other genes in regio

170 However, codon bias, itself, does not indicate that selection is

171 uestions are addressed: (1) How variable are codon bias levels across the phylogeny? (2) How variable

172 ibrium and may be quite strong on genes with codon bias levels that are much lower and/or above equil

173 Here we report that differences in codon bias limit TLR7 expression relative to TLR9.

174 As judged by calculation of codon bias, low-abundance proteins were identified from

175 m again have similar values, and genome-wide codon bias may also be predicted from intergenic sequenc

176 ces cerevisiae, and Drosophila melanogaster, codon bias may be maintained by a balance among mutation

177 techniques nor predictable by mRNA levels or codon bias measurements.

178 for each strain in addition to the strain's codon bias measurements.

179 odon bias, the relationship between d(N) and codon bias might be a by-product of gene expression.

180 conversion (BGC) models and selection-driven codon bias models.

181 mechanism involving selective translation of codon-biased mRNA for crucial proteins.

182 gain insights into the relationship between codon bias, mRNA secondary structure, third-codon positi

183 The potential use of this kind of codon bias mutant as a master donor strain to generate o

184 The viral proteins generated from the codon bias mutants are identical to the wild-type viral

185 (iii) How do shifts in codon bias occur?

186 rs effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms.

187 plays a significant role in determining the codon bias of chloroplast genes but that it acts with di

188 ion among the algae genomes in the degree of codon bias of homologous genes.

189 er, our data indicate that the inherent rare codon bias of KRAS plays an integral role in tumorigenes

190 A new measure for assessing codon bias of one group of genes with respect to a secon

191 The codon bias of the actual gene is then compared to a dist

192 Here, to determine the effect of the rare codon bias of the KRAS gene on de novo tumorigenesis, we

193 a zero order Markov chain determined by the codon bias of the same set of sequences.

194 based on the two lines of evidence, that the codon bias of this gene currently is not being maintaine

195 Among the function classes, codon biases of ribosomal proteins are the most deviant

196 It is shown that the codon biases of the ancestral genes are much stronger th

197 nd (3) Are there phylogenetic constraints on codon bias or preference?

198 als related, for instance, to reading frame, codon bias, pairwise codon bias, splice sites and transc

199 as without changing N3 content indicate that codon bias per se has only a weak effect on the formatio

200 ective translation of mRNAs from families of codon-biased persistence genes.

201 These findings demonstrate that codon bias plays a critical role in KRAS-driven resistan

202 Moreover, codon bias plays an important role in controlling a mult

203 known correlations with mRNA abundances and codon bias, providing absolute protein concentrations ac

204 verage gene exceeds a high threshold and the codon bias relative to ribosomal proteins is also approp

205 n (possibly horizontally transferred) if its codon bias relative to the average gene exceeds a high t

206 biases and natural selection in maintaining codon bias remain a contentious issue.

207 The mechanisms that induce codon biases remain an open question; studies have attri

208 lation between mRNA half-lives and ORF size, codon bias, ribosome density, or abundance.

209 he C. reinhardtii chloroplast was due to the codon bias seen in the C. reinhardtii chloroplast genome

210 he efficiency of selection, and thus average codon bias, should decline with gene density.

211 Analysis of genome-wide codon bias shows that only two parameters effectively di

212 Rather, the atypical codon bias simply may be a remnant of an ancestral codon

213 ance, to reading frame, codon bias, pairwise codon bias, splice sites and transcription regulation, n

214 is explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC cont

215 w that differences in transcript leaders and codon bias substantially contribute to divergent transla

216 to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this

217 d the impact of CDS recoding using different codon bias tables.

218 selection on codon usage in genes with high codon bias than in genes with low codon bias.

219 he codons that overlap have lower synonymous codon bias than those which do not.

220 bias simply may be a remnant of an ancestral codon bias that now is being degraded by the mutation bi

221 t gene expression is a strong determinant of codon bias, the relationship between d(N) and codon bias

222 The evolution of codon bias, the unequal usage of synonymous codons, is t

223 permutation of an ultralong DH with a severe codon bias toward mutation to cysteine.

224 tem of tRNA modifications and translation of codon-biased transcripts that enhance expression of stre

225 ned by a mechanism of tRNA reprogramming and codon-biased translation.

226 There is high variation in the level of codon bias values among the 88 taxa, but few readily app

227 horetic separation, proteins from genes with codon bias values of <0.1 (lower abundance proteins) wer

228 Proteins from genes with codon bias values of <0.1 were found, however, if protei

229 Other codon bias variants include biased codon pairs and codon

230 A synthetic gene containing an E. coli codon bias was cloned into a modified pET32 plasmid, and

231 ide survey, similar gene pairs with opposing codon bias were identified that not only manifest dichot

232 le to detect position dependent selection on codon bias which correlates with gene expression levels

233 We propose that suboptimal codon bias, which correlates with low guanine-cytosine (

234 ribosome density, tRNA adaptation index and codon bias while achieving a feature reduction from 37 t

235 e found regularities in N1 context-dependent codon bias with respect to the codon nucleotide composit

236 DB) which provides information regarding the codon bias within the set of highly expressed genes for

237 On the other hand, simulations that reduce codon bias without changing N3 content indicate that cod