College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
Guangdong Open Laboratory of Veterinary Public Health, Guangdong Laboratory for Animal Diseases, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
Int J Mol Sci. 2016 Feb 24;17(3):277. doi: 10.3390/ijms17030277.
Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts.
无乳链球菌是一种重要的人类和动物病原体。为了更好地了解无乳链球菌的遗传特征和进化，本研究分析了影响无乳链球菌同义密码子使用模式的多种因素。通过整体密码子使用分析，发现 A 和 U 结尾丰富的密码子被用于无乳链球菌功能基因，这表明腺嘌呤（A）/胸腺嘧啶（T）组成约束可能对同义密码子使用模式起重要作用。GC3%与有效密码子数（ENC）值的比值表明，翻译选择是微生物中密码子偏好的重要因素。主成分分析（PCA）表明，（i）突变压力是影响无乳链球菌基因组中所有开放阅读框（ORFs）密码子使用的最重要因素；（ii）链特异性突变偏倚不能影响前导链和滞后链的密码子使用偏好；（iii）基因长度不是该生物体中同义密码子使用模式的重要因素。此外，tRNA 适应指数（tAI）值与密码子适应指数（CAI）值、最佳密码子频率（Fop）值之间的高度相关性，强化了自然选择在无乳链球菌中对高效翻译的作用。无乳链球菌与易感宿主（人类和罗非鱼）之间同义密码子使用模式的比较表明，无乳链球菌的同义密码子使用与易感宿主的同义密码子使用无关。无乳链球菌密码子使用的研究可为该细菌的分子进化提供证据，并加深对无乳链球菌与其宿主之间进化关系的理解。
