Synonymous Codon Usage In Saccharomyces Cerevisiae

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Gene Conversion and Codon Usage Bias in the Evolution of

Codon usage bias Nonrandom usage of synonymous codons CAI(Codon adaptation index) (Sharp and Li 1987): A measure of the strength of codon usage bias. Value between 0 and 1: The larger the CAI value, the stronger the bias

University of Nebraska - Lincoln [email protected] of

Codon Usage Bias in Different Genomes Table 1 shows the synonymous codon usage of five fourfold degenerate amino acids for four organisms: E. coli, S. cere-visiae, Drosophila melanogaster, and Homo sapiens. Clearly, these synonymous codons are not used equally. Pattern and bias in synonymous codon usage varies greatly among dif-

Widespread positive selection for mRNA secondary structure at

synonymous sites in the population of Saccharomyces cerevisiae, combined with the on synonymous sites is not due to synonymous codon usage bias or tRNA abundance.

Codon usage bias a tool for - Longdom Publishing SL

14. Moriyama EN, Powell JR (1998) Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucl Acids Res 26: 3188-3193. 15. Powell JR, Moriyama EN (1997) Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci U S A 94: 7784-7790. 16.

Elevated evolutionary rates in the laboratory strain of

nonsynonymous or synonymous sites or the ratio of the two are negatively related with gene codon usage bias (21 25). To estimate the mean and variance of the evolutionary rate change between S288c and YJM789 within each ENC category, the same analysis described above for categories of gene function was performed. We report the results based

Intragenic spatial patterns of codon usage bias in

effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated super-sequences at each codon position

Identifi cation of Confl icting Selective Effects on Highly

genome duplication in Saccharmyces cerevisiae. A codon-based model is used that includes asymmetric effects due to selec-tion on highly expressed genes. The largest effect is translational ef fi ciency, which is found to strongly in fl uence synonymous, but not non-synonymous rates. Minimization of the cost of amino acid synthesis is implicated.

Measuring and Detecting Molecular Adaptation in Codon Usage

Saccharomyces cerevisiae S288c genome. Our results provide clear evidence of adaptation to reduce the cost of nonsense errors and increasing adaptation with codon position and expression. The magnitude and nature of this adaptation are also largely consistent with simulation results in which nonsense errors are the

METHODOLOGY ARTICLE Open Access A condition-specific codon

synonymous codons (i.e. different codons all encoding for the same amino acid) within any genome is not uni-form, resulting in both rare and abundant codons. The distribution of preferred codons varies across all organ-isms [1,9,10] giving rise to a host-specific codon usage bias (CUB) [11]. Codon usage, especially the high prevalence

Conserved codon composition of ribosomal protein coding genes

E.coli,4187forM.tuberculosisand 6312 forS.cerevisiae (see above). Based on the dataset of 61-dimensional sense codon vectors, the codon composition of each gene was calculated as the frequency of each codon of the gene. Codon bias (of thekth gene), measured by its relative synonymous codon usage (RSCU; 9), was calculated thus:

Experimental determination of codon usage-dependent selective

Since synonymous mutations can have substantial effects on expressed protein levels, selection for high gene expression levels will favour codon usage patterns compatible with such high levels, but will avoid patterns that restrict attainable expression levels. However, the exact relationship between codon usage, protein expression, other

Nonoptimal codon usage influences protein structure in

Synonymous codons are not used with equal frequen-cies in most genomes. Codon usage has been pro- Saccharomyces cerevisiae genomes.

Translational Selection and Yeast Proteome Evolution

usage in the budding yeast, Saccharomyces cerevisiae. were analyzed from D. melanogaster and C. elegans, respectively. Strong associations between synonymous codon usage E. coli and B. subtilis data are described in Akashi and Gojo-and oligonucleotide DNA array estimates of mRNA lev- bori (2002).

Synonymous but not the same: the causes and consequences of

variation in codon usage among the genes in a genome, usually attributed to selection. in organisms, including Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Arabidopsis thaliana, Drosophila melanogaster and possibly also mammals (see below), there is a sig-nificant positive correlation between a gene s expression

Solving the riddle of codon usage preferences: a test for

Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better under-stood under the proposed model. INTRODUCTION ThecontroversialideasofKimura(1)andofKingandJukes(2)on neutral evolution led some early detractors to postulate that usage of synonymous codons in protein coding genes is not

Tissue-specific codon usage and the expression of human genes

is now clear that codon usage is not random: Among synon-ymous codons, some codons are used preferentially. More-over, taxa differ in their codon usage. For example, various species of Drosophila each have their own particular codon biases, and their usage differs significantly fromEscherichia coli or Saccharomyces cerevisiae(4 6). The

SHORT REPORT Open Access Analysis of codon usage and

Codon usage analysis has been applied to prokaryote and eukaryote, such asEscherichia coli, Bacillus subtilis, Saccharomyces cerevisiae,Caenorhabdi-tis elegans and human beings [6-8]. These observed pat-terns in synonymous codon usage varied among genes within a genome, and among genomes. The codon usage is attributable to the equilibrium

Molecular Biology and Physiology crossm

codon usage in controlling CPC-1 expression and function and establish another genetic example of the importance of codon usage in protein folding. RESULTS Abnormal codon usage profile of cpc-1. Examination of the N. crassa cpc-1 gene revealed that it has an unusual codon usage profile. The Neurospora genome has a

Integratedanalysisofindividual codon

distributed in the Saccharomyces cerevisiae genes, suggesting their determinant role as a speed regulator in protein elongation. Key words: codon usage bias, microbial biotechnology, position-dependent codon usage, rational gene design, yeast genomics 1. Introduction Codon usage bias (CUB) has been a wide-ranging field of research in

RESEARCH ARTICLE Open Access Local synteny and codon usage

codon usage on the sequence evolution of gene duplicates in the S. cerevisiae genome. We further distinguish the gene duplicates into those that originated from a whole-genome duplication (WGD) event (ohnologs) versus small-scale duplications (SSD) to determine if there exist any differences in their patterns of sequence evolution.

Data-driven codon optimization in Saccharomyces cerevisiae

Expected amount of Protein (EP) in S.cerevisiae, de!ned as mRNA levels x Ribosome density [4], from multiple sequence features. We then invert this predictor to see which codon substitutions increase the prediction Alexey A. Gritsenko1,3,4, Frank Koopman2,3,4, Marcel J.T. Reinders1,3,4,5, Jean-Marc Daran2,3,4 and Dick de Ridder1,3,4,5

Homo sapiens, Saccharomyces cerevisiae; Escherichia coil

Codon usage patterns across genes can be investigated by the Nc-plot: a plot of I~I¢ vs. G + C content at synonymous sites. Nc-plots are produced for Homo sapiens, Saccharomyces cerevisiae, Escheriehia coil, Bacillus subtilis,


Saccharomyces cerevisiae, there is a clear positive correlation between degree of codon bias and level of gene expression (3,4). Examination of large data sets from these species reveals that within species differences are largely in the degree rather than the direction of codon usage bias (5,6). For many reasons it is desirable to quantify the

Codon-usage bias versus gene conversion in the evolution of

an extremely strong codon-usage bias (Fig. 4, which is published as supporting information on the PNAS web site). Codon-usage bias is known to increase with gene-expression level (5, 6) and can slow down synonymous divergence between duplicate genes (7). Therefore, we investigated whether gene conversion or

Saccharomyces GenomeDatabase(SGD)provides

The Saccharomyces Genome Database (SGD) collects, organizes, and presents information about the molecular biology and genetics of the budding yeast Saccharomyces cerevisiae. SGD contains diverse types of biological data and provides tools for their search and analysis. Information in SGD is generally organized around a gene; each gene in the

Classification of Genes Based on Synonymous Codon Usage

(Saccharomyces cerevisiae), which is a unicellular eukaryote that has been studied extensively as a model organism. Sharp et. Al demonstrated that yeast genes can be seggregated into two main clusters with different expression levels based on synonymous codon usage (2). Najafabadi et. Al showed that co-

Presyncodon, a Web Server for Gene Design with the

expression host. The synonymous codon-usage pattern of a peptide was studied from three genomic datasets (Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae). Machine-learning models were constructed to predict a selection of synonymous codons (low- or high-frequency-usage codon) in a gene.

Codon Usage and tRNA Content in Unicellular and Multicellular

Saccharomyces cerevisiae are attributed to differences in the actual populations of isoaccepting tRNAs. There exists a strong positive correlation between codon usage and tRNA content in both organisms, and the extent of this correlation relates to the protein production levels of individual genes.

Protein Abundance Prediction Through Machine Learning Methods

Sep 17, 2020 by using codon usage metrics as features. In this study, we explore the evolutionary constraints that shape the codon usage bias of the Saccharomyces cerevisiae genome in the context of protein abundance by comparing highly abundant proteins (HAP) and lowly abundant proteins (LAP). We then apply supervised learning algorithms to a

Explaining complex codon usage patterns with selection for

efficient ribosome usage can explain the genome-wide codon usage patterns in Saccharomyces cerevisiae. Although ours is not the first attempt at using mechanistic models to explain CUB in a population genetics context (5, 6), it is unique in its ability to estimate codon-specific parameters and quantitatively predict

Evolution of Synonymous Codon Usage in the Mitogenomes of

Synonymous codon usage (SCU) is species specific.1 In certain genomes, a subset of codons is used most frequently Saccharomyces cerevisiae, and Dictyostelium

Relationship of codon bias to mRNA concentration and protein

the synonymous codon usage of S. cerevisiae, estimated by relative synonymous codon usages (RSCUs). The RSCU of a codon is the observed frequency of the codon divided by the frequency expected if all the synonyms for that amino acid were used equally (Sharp et al., 1986). Correspondence analysis on RSCUs was implemen-

Comparative analysis of codon usage patterns in chloroplast

codon usage from the random selection that depicted the degree of imbalanced use of synonymous codons in genes or genomes of the specific species. The range of ENc value is 20-61. The smaller the ENc value, the stronger the codon usage bias and vice versa (Wu et al., 2018). When ENc value is 35, the codon usage of genes or genomes has very

SYNTHETIC GENOMICS Design, synthesis, and testing toward

design, synthesis, and progress toward assembly of a 3.97-megabase, 57-codon Escherichia coli genome in which all 62,214 instances of sev en codons were replaced with synonymous alternatives across all protein-coding genes. We have validated 63% of recoded genes by individually testing 55 segments of 50 kilobases each. We observed that 91% of

Explaining complex codon usage patterns with selection for

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift Premal Shaha,b,1 and Michael A. Gilchrista,b aDepartment of Ecology and Evolutionary Biology, University of Tennessee, Knoxville TN 37996; and bNational Institute for Mathematical and Biological

Codon usage bias is correlated with gene expression levels in

this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana and Caenorhabditis elegans, but was

Selection for minimization of translational frameshifting

codon usage bias and gene length in E. coli but negative correlations in S. cerevisiae and D. melanogaster genes. The finding for S. cerevisae has in turn been contradicted by Coghlan and Wolfe (25), who found a positive corre-lation between codon usage and gene length in this organism. These conflicting results serve as an illustration


compared with S. cerevisiae gene dispensability, gene dosage dependence, inter-species evolutionary rate, and gene expression predicted through codon usage bias. The results of these analysis revealed limited explanatory power of this measure, but did indicate a weak relationship with gene evolutionary rate and gene expression.