Different Patterns of Codon Usage and Amino Acid Composition across Primate Lentiviruses.
Different Patterns of Codon Usage and Amino Acid Composition across Primate Lentiviruses.
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DOI：
10.3390/v15071580
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发表时间：
2023-07-20
期刊：
影响因子：
--
通讯作者：
Romerio F
中科院分区：
文献类型：
--
作者：
Pavesi A;Romerio F
哺乳动物慢病毒(逆转录病毒科)的一个共同特征是RNA基因组含有极高的腺嘌呤(31.7-38.2%)，而胞嘧啶(13.9-21.2%)频率极低。这种有偏见的核苷酸组成对密码子的使用有影响，导致慢病毒中同义密码子的频率与其宿主中的密码子频率显著不同。为了测试灵长类慢病毒在密码子和氨基酸组成上是否存在差异，我们组装了一个基因组序列数据集，其中包括感染旧大陆猴子和非洲猿的SIV物种、HIV-2和四组HIV-1。通过主成分分析，我们发现HIV-1在第三个同义密码子位置上的腺嘌呤和胸腺嘧啶以及在第一和第二个非同义密码子位置上的腺嘌呤和鸟嘌呤具有显著的富集性。同样，我们观察到腺嘌呤和鸟嘌呤在非同义第一和第二密码子位置富含，这影响了蛋白质Gag、Pol、Vif、Vpr、Tat、Rev、Env和Nef的氨基酸组成。这一结果表明了自然选择对密码子使用的影响。在假设HIV-1同义词的使用可以反映对特定细胞类型表达的基因的适应性的假设下，我们发现HIV-1的密码子使用与单核细胞之间存在高度显著的相关性，显著高于B淋巴细胞和T淋巴细胞。这一发现与单核细胞在感染患者中代表HIV-1储存库的概念是一致的，它可能有助于理解这个储存库是如何建立和维持的。
A common feature of the mammalian Lentiviruses (family Retroviridae) is an RNA genome that contains an extremely high frequency of adenine (31.7–38.2%) while being extremely poor in cytosine (13.9–21.2%). Such a biased nucleotide composition has implications for codon usage, causing a striking difference between the frequency of synonymous codons in Lentiviruses and that in their hosts. To test whether primate Lentiviruses present differences in codon and amino acid composition, we assembled a dataset of genome sequences that includes SIV species infecting Old-World monkeys and African apes, HIV-2, and the four groups of HIV-1. Using principal component analysis, we found that HIV-1 shows a significant enrichment in adenine plus thymine in the third synonymous codon position and in adenine and guanine in the first and second nonsynonymous codon positions. Similarly, we observed an enrichment in adenine and in guanine in nonsynonymous first and second codon positions, which affects the amino acid composition of the proteins Gag, Pol, Vif, Vpr, Tat, Rev, Env, and Nef. This result suggests an effect of natural selection in shaping codon usage. Under the hypothesis that the use of synonyms in HIV-1 could reflect adaptation to that of genes expressed in specific cell types, we found a highly significant correlation between codon usage in HIV-1 and monocytes, which was remarkably higher than that with B and T lymphocytes. This finding is in line with the notion that monocytes represent an HIV-1 reservoir in infected patients, and it could help understand how this reservoir is established and maintained.
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