Dahal Ujwal, Bansal Anu
Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India.
Curr Genomics. 2025;26(2):81-94. doi: 10.2174/0113892029325491240919151045. Epub 2024 Oct 1.
Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.
分析原核生物密码子使用趋势已成为一个关键的研究课题，对于理解微生物遗传学、分类、进化以及基因表达控制具有重大影响。本综述研究探讨了原核生物密码子使用模式的多个方面，通过强调密码子重编程在适应性策略中的作用及其融入系统生物学，研究了原核生物广泛类群中的不同参数，如栖息地和生活方式。我们还通过对当前文献的深入研究，探讨了驱动密码子使用偏好的众多变量，包括自然选择、突变、水平基因转移、密码子-反密码子相互作用以及原核生物的基因组组成。此外，还讨论了关于致病原核生物密码子使用以及密码子使用在原核生物系统发育中的作用的专题会议。我们还研究了最近应用于原核生物基因组的各种软件和指标。强调了绘制原核生物密码子使用研究未来方向的前景。通过结合环境、宏基因组学和系统生物学方法，可以更好地理解原核生物群落中的密码子使用差异。
