5月27日，學(xué)術(shù)期刊Nucleic Acids Res發(fā)表了中科院上海生命科學(xué)研究院生化與細(xì)胞所裴鋼研究組研究成果：進(jìn)化過程中的單一氨基酸替換增強(qiáng)了哺乳動(dòng)物Dnmt3b甲基化基因組DNA的能力。

旁系同源蛋白是指存在于某一物種中，由相同的祖先基因經(jīng)由基因倍增產(chǎn)生的基因所編碼的蛋白。以往的研究表明，旁系同源蛋白在進(jìn)化中必須產(chǎn)生一定的功能差異才能得以保留，而進(jìn)化過程中蛋白序列的變異不僅是導(dǎo)致同源蛋白功能差異的重要原因，也是一種自然選擇參與其中的適應(yīng)性進(jìn)化。但進(jìn)化過程中的氨基酸替換如何影響蛋白質(zhì)功能，以及自然選擇在其中的作用還很不清楚。

DNA甲基轉(zhuǎn)移酶Dnmt3a和Dnmt3b是負(fù)責(zé)基因組起始性DNA甲基化的旁系同源蛋白，在表觀遺傳調(diào)控中起著重要的作用。雖然它們具有較高的同源性，但是體內(nèi)功能并不相同。在小鼠中，敲除Dnmt3b是胚胎致死的，并且可以觀察到小鼠全基因組及各種重復(fù)序列DNA的低甲基化現(xiàn)象；而Dnmt3a的基因敲除小鼠出生后大約四周死亡，而且沒有明顯的全基因組DNA低甲基化。因此Dnmt3a和Dnmt3b的序列演化和功能改變的關(guān)系，不僅能夠加深對(duì)DNA甲基化這一重要的表觀遺傳調(diào)控機(jī)制的理解，而且有助于回答進(jìn)化過程中氨基酸替換和自然選擇如何影響蛋白質(zhì)功能這個(gè)重要理論問題。

生化與細(xì)胞所細(xì)胞信號(hào)轉(zhuǎn)導(dǎo)研究組的研究成果表明，Dnmt3a和Dnmt3b起源于脊椎動(dòng)物產(chǎn)生時(shí)期附近的一次基因倍增事件，但哺乳動(dòng)物Dnmt3b甲基化染色體DNA的能力顯著高于Dnmt3a以及非哺乳動(dòng)物的Dnmt3b。后續(xù)的序列比對(duì)和氨基酸突變實(shí)驗(yàn)表明，一個(gè)僅在哺乳動(dòng)物Dnmt3b中存在的單一氨基酸替換I662N決定了其較高的甲基化染色體DNA的能力。該研究組進(jìn)一步的研究提示，這個(gè)氨基酸替換顯著增強(qiáng)了Dnmt3b結(jié)合核小體DNA的能力。而且，該氨基酸替換對(duì)于Dnmt3b甲基化哺乳動(dòng)物基因組中的重復(fù)序列具有重要的作用。有趣的是，他們發(fā)現(xiàn)在哺乳動(dòng)物產(chǎn)生的過程中，隨著這些重復(fù)序列占基因組比例的大大提高，Dnmt3b的進(jìn)化速率也顯著高于Dnmt3a。這一研究成果表明哺乳動(dòng)物Dnmt3b中的I662N氨基酸替換提高了它甲基化染色體DNA的能力，使之更好地適應(yīng)了哺乳動(dòng)物中重復(fù)序列增加等自然選擇，從而豐富了哺乳動(dòng)物的表觀遺傳調(diào)控系統(tǒng)，并為進(jìn)化過程中氨基酸替換和自然選擇如何影響蛋白質(zhì)功能這個(gè)重要理論問題提供了一個(gè)很好的范例。

該項(xiàng)工作得到了國家科技部、國家自然科學(xué)基金委及中國科學(xué)院經(jīng)費(fèi)支持。

上海勁馬生物（）推薦原文出處：

Nucleic Acids Research, doi:10.1093/nar/gkq456

A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA
Li Shen1,2, Ge Gao3,*, Ying Zhang1,2, He Zhang3, Zhiqiang Ye3, Shichao Huang1,2, Jinyan Huang4 and Jiuhong Kang1,2,4,*

1Laboratory of Molecular Cell Biology and Center of Cell Signaling, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 2Graduate School of the Chinese Academy of Sciences, Shanghai 200031, 3Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 and 4Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai 200092, P.R. China

Dnmt3a and Dnmt3b are paralogous enzymes responsible for de novo DNA methylation but with distinguished biological functions. In mice, disruption of Dnmt3b but not Dnmt3a causes global DNA hypomethylation, especially in repetitive sequences, which comprise the large majority of methylated DNA in the genome. By measuring DNA methylation activity of Dnmt3a and Dnmt3b homologues from five species, we found that mammalian Dnmt3b possessed significantly higher methylation activity on chromatin DNA than Dnmt3a and non-mammalian Dnmt3b. Sequence comparison and mutagenesis experiments identified a single amino acid substitution （I662N） in mammalian Dnmt3b as being crucial for its high chromatin DNA methylation activity. Further mechanistic studies demonstrated this substitution markedly enhanced the binding of Dnmt3b to nucleosomes and hence increased the chromatin DNA methylation activity. Moreover, this substitution was crucial for Dnmt3b to efficiently methylate repetitive sequences, which increased dramatically in mammalian genomes. Consistent with our observation that Dnmt3b evolved more rapidly than Dnmt3a during the emergence of mammals, these results demonstrated that the I662N substitution in mammalian Dnmt3b conferred enhanced chromatin DNA methylation activity and contributed to functional adaptation in the epigenetic system.