Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes
Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes
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DOI：
10.1111/j.1469-185x.2012.00242.x
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发表时间：
2013-02-01
影响因子：
10
通讯作者：
Severson, David W.
中科院分区：
文献类型：
--
作者：
Behura, Susanta K.;Severson, David W.
密码子使用偏性是指在基因翻译过程中，特定密码子的使用频率高于其他同义密码子的现象，其程度在物种内和物种间存在差异。分子进化研究表明，密码子偏好性表现为这些基因的突变和翻译选择之间的平衡，这种现象在物种中广泛存在，并可能以显着的方式促进基因组进化。随着原核生物和真核生物的全基因组测序的出现，密码子偏好的全基因组模式在不同的生物体中出现。各种因素，如表达水平，GC含量，重组率，RNA稳定性，密码子位置，基因长度和其他（包括环境压力和种群大小）可以影响物种内和物种间的密码子使用偏好。此外，人们一直在不断探索开发新的概念和工具来衡量基因的密码子使用偏好的程度。在这篇综述中，我们概述了遗传密码进化的基本概念，讨论了可能影响同义密码子使用偏差的各种因素，然后概述了不同的原则和测量密码子使用偏差的方法。最后，我们讨论了使用不同昆虫物种的全基因组序列进行的选定研究，以显示密码子偏好模式在基因组内和基因组之间的变化。最后，我们概括性地评论了密码子偏好性研究的具体新兴方面，并强调了最近在节肢动物基因组测序方面的努力（如12种果蝇，蚂蚁，蜜蜂，纳索尼亚和按蚊，以及最近启动的涉及5000种昆虫和其他节肢动物的基因组测序项目）这可能有助于我们更好地了解密码子偏好的进化及其生物学意义。
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 between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.