Compositional biases in RNA viruses: Causes, consequences and applications.
Compositional biases in RNA viruses: Causes, consequences and applications.
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DOI：
10.1002/wrna.1679
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发表时间：
2022-03
期刊：
影响因子：
--
通讯作者：
Digard P
中科院分区：
文献类型：
--
作者：
Gaunt ER;Digard P
如果这四种核苷酸在病毒和它们感染的宿主的基因组中的代表性相等，那么每个碱基的出现频率将为25%。然而，这在自然界中是观察不到的。类似地，核苷酸的顺序不是随机的（例如，在人类基因组中，鸟嘌呤跟随胞嘧啶的频率约为0.0125，或随机表示预测次数的四分之一）。密码子使用和密码子顺序也是非随机的。此外，核苷酸和密码子偏好在物种之间变化。这种偏好有各种驱动因素，包括识别核酸中特定模式的细胞蛋白，一旦触发，诱导突变或引发内在或先天免疫反应。在这篇综述中，我们研究了在病毒基因组中发现的成分偏见的类型和目前对这些趋势的进化机制的理解。最后，我们考虑了大规模同义重编码策略的潜力，以工程RNA病毒疫苗，包括那些具有大流行潜力的疫苗，如甲型流感病毒和严重急性呼吸道综合征冠状病毒2。RNA在疾病和发展> RNA在疾病RNA进化和基因组学>计算分析的RNA RNA与蛋白质和其他分子的相互作用>蛋白质-RNA识别这篇文章分类下：病毒基因组中的核苷酸序列和它们感染的宿主是高度模式化的;这篇评论讨论了这些基因组组成的偏见的原因，后果和应用。
If each of the four nucleotides were represented equally in the genomes of viruses and the hosts they infect, each base would occur at a frequency of 25%. However, this is not observed in nature. Similarly, the order of nucleotides is not random (e.g., in the human genome, guanine follows cytosine at a frequency of ~0.0125, or a quarter the number of times predicted by random representation). Codon usage and codon order are also nonrandom. Furthermore, nucleotide and codon biases vary between species. Such biases have various drivers, including cellular proteins that recognize specific patterns in nucleic acids, that once triggered, induce mutations or invoke intrinsic or innate immune responses. In this review we examine the types of compositional biases identified in viral genomes and current understanding of the evolutionary mechanisms underpinning these trends. Finally, we consider the potential for large scale synonymous recoding strategies to engineer RNA virus vaccines, including those with pandemic potential, such as influenza A virus and Severe Acute Respiratory Syndrome Coronavirus Virus 2. RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein‐RNA Recognition This article is categorized under: Nucleotide sequences in the genomes of viruses and the hosts they infect are highly patterned; this review discusses the causes, consequences and applications of these genomic compositional biases.
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