Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China.
J Basic Microbiol. 2018 May;58(5):425-439. doi: 10.1002/jobm.201700490. Epub 2018 Mar 14.
The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.
分析了影响 18 种支原体核苷酸、同义密码子和氨基酸使用的遗传特征的进化因素。决定蛋白质氨基酸组成的第 1 位和第 2 位密码子位置的核苷酸使用与这些支原体物种基因群体的总核苷酸组成具有显著相关性，然而，影响同义密码子使用模式的第 3 位密码子位置的核苷酸使用与总核苷酸组成或第 1 位和第 2 位密码子位置的核苷酸使用都只有轻微相关性。除了基于核苷酸使用约束引起的突变压力之外，其他进化因素也参与了支原体的进化过程，这种约束是基于有效密码子数/密码子适应指数与第 3 位密码子位置的核苷酸使用之间的关系。尽管支原体基因群体的核苷酸使用在形成整体密码子使用趋势中占主导地位，但密码子的相对丰度与核苷酸上下文和氨基酸使用模式表明，涉及翻译准确性和效率的翻译选择在同义密码子使用模式中发挥着重要作用。此外，基因群体的同义密码子使用模式比氨基酸使用模式更能代表不同物种之间的遗传多样性。这些结果表明，尽管支原体在进化过程中减少了基因组大小，并形成了与宿主相反的 AT 使用形式，但这种生物体仍然依赖于第 1 位和第 2 位密码子位置的核苷酸使用来控制所需蛋白质的合成，以在宿主中生存，以及第 3 位密码子位置的核苷酸使用来发展不同支原体物种的遗传多样性。对 18 种支原体的系统分析可能为进一步研究相关物种的体内遗传提供有用线索。
