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the customary manner in which a language (or a form of a language) is spoken or written; "English usage"; "a usage borrowed from French"
major food fish of Arctic and cold-temperate waters (同)codfish
lean white flesh of important North Atlantic food fish; usually baked or poached (同)codfish
a specific sequence of three adjacent nucleotides on a strand of DNA or RNA that specifies the genetic code information for synthesizing a particular amino acid

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2014/10/23 08:22:09」(JST)

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Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons).

There are 64 different codons (61 codons encoding for amino acids plus 3 stop codons) but only 20 different translated amino acids. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. Because of such redundancy it is said that the genetic code is degenerate. Different organisms often show particular preferences for one of the several codons that encode the same amino acid- that is, a greater frequency of one will be found than expected by chance. How such preferences arise is a much debated area of molecular evolution.

It is generally acknowledged that codon preferences reflect a balance between mutational biases and natural selection for translational optimization. Optimal codons in fast-growing microorganisms, like Escherichia coli or Saccharomyces cerevisiae (baker's yeast), reflect the composition of their respective genomic tRNA pool. It is thought that optimal codons help to achieve faster translation rates and high accuracy. As a result of these factors, translational selection is expected to be stronger in highly expressed genes, as is indeed the case for the above-mentioned organisms. In other organisms that do not show high growing rates or that present small genomes, codon usage optimization is normally absent, and codon preferences are determined by the characteristic mutational biases seen in that particular genome. Examples of this are Homo sapiens (human) and Helicobacter pylori. Organisms that show an intermediate level of codon usage optimization include Drosophila melanogaster (fruit fly), Caenorhabditis elegans (nematode worm), Strongylocentrotus purpuratus (sea urchin) or Arabidopsis thaliana (thale cress).

The nature of the codon usage-tRNA optimization has been fiercely debated. It is not clear whether codon usage drives tRNA evolution or vice versa. At least one mathematical model has been developed where both codon-usage and tRNA-expression co-evolve in feedback fashion (i.e., codons already present in high frequencies drive up the expression of their corresponding tRNAs, and tRNAs normally expressed at high levels drive up the frequency of their corresponding codons), however this model does not seem to yet have experimental confirmation. Another problem is that the evolution of tRNA genes has been a very inactive area of research.

Factors contributing to codon usage bias

Different factors have been proposed to be related to codon usage bias, including gene expression level (reflecting selection for optimizing translation process by tRNA abundance), %G+C composition (reflecting horizontal gene transfer or mutational bias), GC skew (reflecting strand-specific mutational bias), amino acid conservation, protein hydropathy, transcriptional selection, RNA stability, optimal growth temperature and hypersaline adaptation.^[1]^[2]^[3]^[4]

Methods of analyzing codon usage bias

In the field of bioinformatics and computational biology, many statistical methods have been proposed and used to analyze codon usage bias.^[5] Methods such as the 'frequency of optimal codons' (Fop),^[6] the Relative Codon Adaptation (RCA) ^[7] or the 'Codon Adaptation Index' (CAI) ^[8] are used to predict gene expression levels, while methods such as the 'effective number of codons' (Nc) and Shannon entropy from information theory are used to measure codon usage evenness.^[9] Multivariate statistical methods, such as correspondence analysis and principal component analysis, are widely used to analyze variations in codon usage among genes.^[10] There are many computer programs to implement the statistical analyses enumerated above, including CodonW, GCUA, INCA, etc. Codon optimization has applications in designing synthetic genes and DNA vaccines. Several software packages are available online for this purpose (refer to external links). Optimizing the occurrence of desired/undesired motifs and sequence composition in all possible reverse translated gene sequences increases the search space exponentially with respect to gene length. For those reasons, the problem could be addressed using optimization algorithms like genetic algorithms (Sandhu et al., In Silico Biol. 2008;8(2):187-92).

References

^ Ermolaeva MD (October 2001). "Synonymous codon usage in bacteria". Curr Issues Mol Biol 3 (4): 91–7. PMID 11719972.
^ Lynn DJ, Singer GA, Hickey DA (October 2002). "Synonymous codon usage is subject to selection in thermophilic bacteria". Nucleic Acids Res. 30 (19): 4272–7. doi:10.1093/nar/gkf546. PMC 140546. PMID 12364606.
^ Paul S, Bag SK, Das S, Harvill ET, Dutta C (2008). "Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes". Genome Biol. 9 (4): R70. doi:10.1186/gb-2008-9-4-r70. PMC 2643941. PMID 18397532.
^ Kober, K. M.; Pogson, G. H. (2013). "Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus". G3: Genes|Genomes|Genetics 3 (7): 1069. doi:10.1534/g3.113.005769. edit
^ Comeron JM, Aguadé M (September 1998). "An evaluation of measures of synonymous codon usage bias". J. Mol. Evol. 47 (3): 268–74. doi:10.1007/PL00006384. PMID 9732453.
^ Ikemura T (September 1981). "Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system.". J. Mol. Biol. 151 (3): 389–409. doi:10.1016/0022-2836(81)90003-6. PMID 6175758.
^ Fox JM, Erill I (June 2010). "Relative codon adaptation: a generic codon bias index for prediction of gene expression". DNA Res. 17 (3): 185–96. doi:10.1093/dnares/dsq012. PMC 2885275. PMID 20453079.
^ Sharp PM, Li WH (February 1987). "The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications". Nucleic Acids Res. 15 (3): 1281–95. doi:10.1093/nar/15.3.1281. PMC 340524. PMID 3547335.
^ Peden J (2005-04-15). "Codon usage indices". Correspondence Analysis of Codon Usage. SourceForge. Retrieved 2010-10-20.
^ Suzuki H, Brown CJ, Forney LJ, Top EM (December 2008). "Comparison of correspondence analysis methods for synonymous codon usage in bacteria". DNA Res. 15 (6): 357–65. doi:10.1093/dnares/dsn028. PMC 2608848. PMID 18940873.

External links

Composition Analysis Toolkit: estimating codon usage bias and its statistical significance
Codon Usage Database
CodonW
GCUA - General Codon Usage Analysis
Graphical Codon Usage Analyser
JCat - Java Codon Usage Adaptation Tool
INCA - Interactive Codon Analysis software
ACUA - Automated Codon Usage Analysis Tool
OPTIMIZER - Codon usage optimization
HEG-DB - Highly Expressed Genes Database
E-CAI - Expected value of Codon Adaptation Index
CAIcal -Set of tools to assess codon usage adaptation
scRCA - Automatic determination of translational codon usage bias
Online Synonymous Codon Usage Analyses with the ade4 and seqinR packages
Genetic Algorithm Simulation for Codon Optimization

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English Journal

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes.

Behura SK, Severson DW.SourceDepartment of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
Biological reviews of the Cambridge Philosophical Society.Biol Rev Camb Philos Soc.2013 Feb;88(1):49-61. doi: 10.1111/j.1469-185X.2012.00242.x. Epub 2012 Aug 14.
Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance betwee
PMID 22889422

A more accurate relationship between 'effective number of codons' and GC3s under assumptions of no selection.

Liu X.SourceSchool of Computer and Information, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address: hoesy@163.com.
Computational biology and chemistry.Comput Biol Chem.2013 Feb;42:35-9. doi: 10.1016/j.compbiolchem.2012.11.003. Epub 2012 Nov 24.
The 'effective number of codons' (Nc) introduced by Frank Wright in 1990 is one of the best measures to show the state of codon usage biases in genes and genomes. Although estimate methods of Nc have been improved by several investigators since then, no one noticed that the relationship between Nc a
PMID 23257412

Reply to "codon usage frequency of RNA virus genomes from high-temperature acidic-environment metagenomes".

Young M, Bolduc B, Shaughnessy DP, Roberto FF, Wolf YI, Koonin EV.SourceThermal Biology Institute.
Journal of virology.J Virol.2013 Feb;87(3):1920-1. doi: 10.1128/JVI.02883-12.
PMID 23308028

Japanese Journal

Porphyromonas gingivalis 40-kDa外膜タンパク遺伝子のコドン使用頻度と遺伝子産物の構造

山口康介,平塚浩一,安孫子宜光
医学と生物学 156(4), 200-204, 2012-04
NAID 40019296931

Prophylactic effect of Lactobacillus oral vaccine expressing a Japanese cedar pollen allergen(MEDICAL BIOTECHNOLOGY)

Ohkouchi Kayo,Kawamoto Seiji,Tatsugawa Kenji,Yoshikawa Noboru,Takaoka Yuki,Miyauchi Sayumi,Aki Tsunehiro,Yamashita Mitsuo,Murooka Yoshikatsu,Ono Kazuhisa
Journal of bioscience and bioengineering 113(4), 536-541, 2012-04
… To facilitate heterologous expression, the codon usage in the Cry j 1 gene was optimized for the host LAB strain Lactobacillus plantarum by the recursive PCR-based exhaustive site-directed mutagenesis. … Use of the codon-optimized Cry j 1 cDNA and a lactate dehydrogenase gene fusion system led to a successful production of recombinant Cry j 1 in L. …
NAID 110009444564

Establishment of a Bacterial Expression System and Immunoassay Platform for the Major Capsid Protein of HcRNAV, a Dinoflagellate-Infecting RNA Virus

Wada Kei,Kimura Kei,Hasegawa Akifumi,Fukuyama Keiichi,Nagasaki Keizo
Microbes and Environments 27(4), 483-489, 2012
… Its major capsid protein (MCP) gene sequence is not expressed by various strains of Escherichia coli, possibly because of a codon usage problem. … coli strain C41 (DE3), in which codon usage was universally optimized to efficiently express the polypeptide having the viral MCP amino acid sequence. …
NAID 130001877566