Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA.
Sci Rep. 2022 Mar 16;12(1):4522. doi: 10.1038/s41598-022-08570-w.
Genomes of different sizes and complexity can be compared using common features. Most genomes contain open reading frames, and most genomes use the same genetic code. Redundancy in the genetic code means that different biases in the third nucleotide position of a codon exist in different genomes. However, the nucleotide composition of viruses can be quite different from host nucleotide composition making it difficult to assess the relevance of these biases. Here we show that grouping codons of a codon-pair according to the GC content of the first two nucleotide positions of each codon reveals patterns in nucleotide usage at the third position of the 1st codon. Differences between the observed and expected biases occur predominantly when the first two nucleotides of the 2nd codon are both S (strong, G or C) or both W (weak, A or T), not a mixture of strong and weak. The data indicates that some codon pairs are preferred because of the strength of the interactions between the codon and anticodon, the adjacent tRNAs and the ribosome. Using base-pairing strength and third position bias facilitates the comparison of genomes of different size and nucleotide composition and reveals patterns not previously described.
可以使用共同特征比较不同大小和复杂度的基因组。大多数基因组包含开放阅读框，并且大多数基因组使用相同的遗传密码。遗传密码的冗余意味着在不同的基因组中存在密码子第三核苷酸位置的不同偏向性。然而，病毒的核苷酸组成可能与宿主核苷酸组成有很大不同，这使得难以评估这些偏向性的相关性。在这里，我们表明，根据每个密码子的前两个核苷酸位置的 GC 含量对密码子对中的密码子进行分组，可以揭示第一密码子第三位的核苷酸使用模式。当第二个密码子的前两个核苷酸都是 S（强，G 或 C）或都是 W（弱，A 或 T）时，观察到的和预期的偏向性之间的差异主要发生，而不是强和弱的混合物。该数据表明，一些密码子对由于密码子和反密码子、相邻 tRNA 和核糖体之间的相互作用强度而被优先选择。使用碱基配对强度和第三位置偏向性可以促进比较大小和核苷酸组成不同的基因组，并揭示以前未描述的模式。
