Independent birth of a novel TRIMCyp in Tupaia belangeri with a divergent function from its paralog TRIM5.
Independent birth of a novel TRIMCyp in Tupaia belangeri with a divergent function from its paralog TRIM5.
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DOI：
10.1093/molbev/msu238
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发表时间：
2014-11
影响因子：
10.7
通讯作者：
D. Mu;Hui Yang;Jia-Wu Zhu;Feng-Liang Liu;Ren-Rong Tian;Hong-yi Zheng;Jian-bao Han;P. Shi;
中科院分区：
文献类型：
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作者：
D. Mu;Hui Yang;Jia-Wu Zhu;Feng-Liang Liu;Ren-Rong Tian;Hong-yi Zheng;Jian-bao Han;P. Shi;
新基因的起源及其进化命运是进化生物学中的一个长期问题。这些问题变得更加复杂的基因保守在不同的血统，如TRIM5，抗逆转录病毒限制因子和逆转录病毒衣壳传感器在免疫信号。TRIM5受到了许多致病性挑战，并经历了动态进化，使其成为研究基因多样性的一个很好的例子。先前在几个物种中的研究表明，TRIM5以谱系特异性方式获得遗传和功能新颖性，通过基因复制或亲环素A逆转录转座到TRIM5基因座中，产生称为TRIM5-亲环素A（TRIMCyp）的基因融合。迄今为止，TRIM5在哺乳动物谱系中的一般模式仍然难以捉摸。在这项研究中，我们调查了36种哺乳动物基因组，以验证一种潜在的新型TRIM 5模式，这种模式似乎在树鼩（Tupaia belangeri）中唯一发生，并发现基因复制和反转录转座共同作用，形成了一个特定的TRIM 5/TRIMCyp簇。在其他哺乳动物中没有发现。进化分析表明，树鼩 TRIMCyp（tsTRIMCyp）独立起源于先前报道的TRIMCyps相比，并进行了强烈的正选择，而没有信号的正选择检测到其他树鼩 TRIM5（tsTRIM5）基因。功能测定结果表明，tsTRIMCyp和其最接近的parasynTRIM5 - 4之间的功能分歧，可能反映不同的进化力量下的不同命运。这些发现提供了一个罕见的例子，新的基因起源的基因复制，反转录转座和外显子改组过程的组合，提供了一个新的范式来研究遗传创新和重复基因的进化命运。
The origin of novel genes and their evolutionary fates are long-standing questions in evolutionary biology. These questions become more complicated for genes conserved across various lineages, such as TRIM5, an antiretroviral restriction factor and a retrovirus capsid sensor in immune signaling. TRIM5 has been subjected to numerous pathogenic challenges and undergone dynamic evolution, making it an excellent example for studying gene diversification. Previous studies among several species showed that TRIM5 gained genetic and functional novelty in a lineage-specific manner, either through gene duplication or a cyclophilin A retrotransposing into the TRIM5 locus, creating the gene fusion known as TRIM5-Cyclophilin A (TRIMCyp). To date, the general pattern of TRIM5 across the mammalian lineage remains elusive. In this study, we surveyed 36 mammalian genomes to verify a potentially novel TRIM5 pattern that uniquely seems to have occurred in tree shrews (Tupaia belangeri), and found that both gene duplication and retrotransposition worked jointly to form a specific TRIM5/TRIMCyp cluster not found among other mammals. Evolutionary analyses showed that tree shrew TRIMCyp (tsTRIMCyp) originated independently in comparison with previously reported TRIMCyps and underwent strong positive selection, whereas no signal of positive selection was detected for other tree shrew TRIM5 (tsTRIM5) genes. Functional assay results suggest a functional divergence between tsTRIMCyp and its closest paralog TRIM5-4, likely reflecting different fates under diverse evolutionary forces. These findings present a rare example of novel gene origination resulting from a combination of gene duplication, retrotransposition, and exon shuffling processes, providing a new paradigm to study genetic innovations and evolutionary fates of duplicated genes.