Ustyantsev Kirill, Blinov Alexandr, Smyshlyaev Georgy
Institute of Cytology and Genetics, Laboratory of Molecular Genetic Systems, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Mob DNA. 2017 Mar 14;8:4. doi: 10.1186/s13100-017-0087-y. eCollection 2017.
Retrotransposons comprise a ubiquitous and abundant class of eukaryotic transposable elements. All members of this class rely on reverse transcriptase activity to produce a DNA copy of the element from the RNA template. However, other activities of the retrotransposon-encoded polyprotein may differ between diverse retrotransposons. The polyprotein domains corresponding to each of these activities may have their own evolutionary history independent from that of the reverse transcriptase, thus underlying the modular view on the evolution of retrotransposons. Furthermore, some transposable elements can independently evolve similar domain architectures by acquiring functionally similar but phylogenetically distinct modules. This convergent evolution of retrotransposons may ultimately suggest similar regulatory pathways underlying the lifecycle of the elements.
Here, we provide new examples of the convergent evolution of retrotransposons of species from two unrelated taxa: green plants and parasitic protozoan oomycetes. In the present study we first analyzed the available genomic sequences of oomycete species and characterized two groups of Ty3/Gypsy long terminal repeat retrotransposons, namely Chronos and Archon, and a subgroup of L1 non-long terminal repeat retrotransposons. The results demonstrated that the retroelements from these three groups each have independently acquired plant-related ribonuclease H domains. This process closely resembles the evolution of retrotransposons in the genomes of green plants. In addition, we showed that Chronos elements captured a chromodomain, mimicking the process of chromodomain acquisition by Chromoviruses, another group of Ty3/Gypsy retrotransposons of plants, fungi, and vertebrates.
Repeated and strikingly similar acquisitions of ribonuclease H domains and chromodomains by different retrotransposon groups from unrelated taxa indicate similar selection pressure acting on these elements. Thus, there are some major trends in the evolution of the structural composition of retrotransposons, and characterizing these trends may enhance the current understanding of the retrotransposon life cycle.
逆转录转座子是真核生物中普遍存在且数量丰富的一类转座元件。该类元件的所有成员都依赖逆转录酶活性，从RNA模板生成元件的DNA拷贝。然而，逆转录转座子编码的多聚蛋白的其他活性在不同的逆转录转座子之间可能存在差异。与这些活性相对应的多聚蛋白结构域可能有其独立于逆转录酶的进化历史，从而形成了逆转录转座子进化的模块化观点。此外，一些转座元件可以通过获取功能相似但系统发育不同的模块，独立进化出相似的结构域架构。逆转录转座子的这种趋同进化最终可能暗示元件生命周期背后存在相似的调控途径。
在此，我们提供了来自两个不相关分类群的物种逆转录转座子趋同进化的新例子：绿色植物和寄生原生动物卵菌。在本研究中，我们首先分析了卵菌物种的可用基因组序列，并鉴定了两组Ty3/Gypsy长末端重复逆转录转座子，即Chronos和Archon，以及一组L1非长末端重复逆转录转座子亚群。结果表明，这三组逆转录元件各自独立获得了与植物相关的核糖核酸酶H结构域。这一过程与绿色植物基因组中逆转录转座子的进化极为相似。此外，我们还表明，Chronos元件捕获了一个染色质结构域，类似于植物、真菌和脊椎动物的另一组Ty3/Gypsy逆转录转座子——染色质病毒获取染色质结构域的过程。
来自不相关分类群的不同逆转录转座子群体反复且惊人地相似地获得核糖核酸酶H结构域和染色质结构域，表明这些元件受到相似的选择压力。因此，逆转录转座子的结构组成进化存在一些主要趋势，表征这些趋势可能会加深当前对逆转录转座子生命周期的理解。
