An Ancient Clade of Penelope-Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes.
An Ancient Clade of Penelope-Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes.
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DOI：
10.1093/molbev/msab225
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发表时间：
2021-10-27
影响因子：
10.7
通讯作者：
Arkhipova IR
中科院分区：
文献类型：
--
作者：
Craig RJ;Yushenova IA;Rodriguez F;Arkhipova IR
Penelope-like elements（PLEs）是反转录转座子的一个神秘分支，其逆转录酶（RTs）与端粒酶RTs共享最近的共同祖先。典型核酸内切酶（EN）+ PLEs的单个ORF编码RT和C-末端GIY-YIG EN，使染色体内整合成为可能，而EN-PLEs缺乏EN，通常仅限于染色体末端。EN+ PLEs仅在动物中发现，除了一个水平转移到针叶树的案例，而EN− PLEs在几个界中发生。在这里，我们报告了一个新的，深分支PLE进化枝与排列的结构域顺序，其中一个N-末端GIY-YIG EN连接到一个C-末端RT由一个短结构域与特征CxC基序。这些N-末端EN+ PLEs共享一个结构组织，包括伪LTRs和复杂的串联/反向插入，与来自Penelope/Poseidon，Neptune和Nematis分支的典型EN+ PLEs，并显示微卫星的插入偏好，但缺乏典型的锤头状核酶基序。然而，它们的系统发育分布要广得多。在许多无脊椎动物门中发现的Naiads，每个基因组可以达到数万个拷贝。在蜘蛛和蛤中，Naiads独立进化为编码含有多个硒代半胱氨酸的硒蛋白。缺乏PLE ENs通用的CCHH基序的Chlamys存在于绿色藻类、穗状苔藓（靶向核糖体DNA）和黏菌中。与典型的PLE不同，N-末端EN+ PLE的RT包含插入指结构域（IFD），加强了PLE和端粒酶之间的联系。此外，我们描述了水螅，一种新的后生动物C-末端EN+分支。总的来说，我们得出结论，PLE多样性，分类分布和丰度与非LTR和LTR反转录转座子。
Penelope-like elements (PLEs) are an enigmatic clade of retrotransposons whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical endonuclease (EN)+ PLEs encodes RT and a C-terminal GIY–YIG EN that enables intrachromosomal integration, whereas EN− PLEs lack EN and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, whereas EN− PLEs occur in several kingdoms. Here, we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY–YIG EN is linked to a C-terminal RT by a short domain with a characteristic CxC motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune, and Nematis clades, and show insertion bias for microsatellites, but lack canonical hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiads, found in numerous invertebrate phyla, can reach tens of thousands of copies per genome. In spiders and clams, Naiads independently evolved to encode selenoproteins containing multiple selenocysteines. Chlamys, which lack the CCHH motif universal to PLE ENs, occur in green algae, spike mosses (targeting ribosomal DNA), and slime molds. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain (IFD), strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, taxonomic distribution, and abundance are comparable with non-LTR and LTR-retrotransposons.
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影响因子：
14.9
作者：
Schostak N;Pyatkov K;Zelentsova E;Arkhipova I;Shagin D;Shagina I;Mudrik E;Blintsov A;Clark I;Finnegan DJ;Evgen'ev M
通讯作者：
Evgen'ev M
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
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作者：
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通讯作者：
Guigó, R
影响因子：
10.7
作者：
Boehne, Astrid;Zhou, Qingchun;Volff, Jean-Nicolas
通讯作者：
Volff, Jean-Nicolas
影响因子：
5.6
作者：
Baclaocos, Janinah;Santesmasses, Didac;Atkins, John F.
通讯作者：
Atkins, John F.