LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types.
LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types.
复制标题
DOI：
10.3390/v9040078
复制
发表时间：
2017-04-11
期刊：
影响因子：
--
通讯作者：
Arkhipova IR
中科院分区：
文献类型：
--
作者：
Rodriguez F;Kenefick AW;Arkhipova IR
蛭纲轮虫是一种微小的淡水无脊椎动物，拥有高度多样化的转座子家族，然而，在已测序的代表性 Adineta vaga 中，转座子家族仅占基因组 DNA 的不到 4%。我们对 A. vaga 逆转录元件进行了全面分析，发现蛭形长末端重复 (LTR) 逆转录转座子，除了对应于 gag 和 pol 基因的保守开放阅读框 (ORF) 1 和 ORF2 之外，还编码异常丰富的 ORF3 序列。 A. vaga 中的逆转录病毒样 LTR 家族属于四个主要谱系，其中三个是轮虫特异性的并编码 dUTPase 结构域。然而，只有一个谱系含有从副粘病毒（非分段负链 RNA 病毒）获得的典型 env 样融合糖蛋白，尽管具有跨膜结构域的较小 ORF 可能发挥类似的作用。不同的 ORF3 类型编码 GDSL 酯酶/脂肪酶，该酶先前在非 LTR 反转录转座子的几个进化枝中被鉴定为 ORF1，并且与膜靶向有关。另一种 ORF3 类型出现在不相关的 LTR 逆转录转座子谱系中，与参与 RNA 和单链 DNA 3' 端加工的 DEDDy 型核酸外切酶表现出很强的同源性。出乎意料的是，每个酶 ORF3 还与 Penelope 样 Athena 逆转录元件家族的不同子集相关。相同ORF类型与不同类别的逆转录因子的不寻常关联反映了它们具有高度灵活性的模块化结构，并表明不同组逆转录因子之间的基因共享。
Rotifers of the class Bdelloidea, microscopic freshwater invertebrates, possess a highly-diversified repertoire of transposon families, which, however, occupy less than 4% of genomic DNA in the sequenced representative Adineta vaga. We performed a comprehensive analysis of A. vaga retroelements, and found that bdelloid long terminal repeat (LTR)-retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding to gag and pol genes, code for an unusually high variety of ORF3 sequences. Retrovirus-like LTR families in A. vaga belong to four major lineages, three of which are rotifer-specific and encode a dUTPase domain. However only one lineage contains a canonical env-like fusion glycoprotein acquired from paramyxoviruses (non-segmented negative-strand RNA viruses), although smaller ORFs with transmembrane domains may perform similar roles. A different ORF3 type encodes a GDSL esterase/lipase, which was previously identified as ORF1 in several clades of non-LTR retrotransposons, and implicated in membrane targeting. Yet another ORF3 type appears in unrelated LTR-retrotransposon lineages, and displays strong homology to DEDDy-type exonucleases involved in 3′-end processing of RNA and single-stranded DNA. Unexpectedly, each of the enzymatic ORF3s is also associated with different subsets of Penelope-like Athena retroelement families. The unusual association of the same ORF types with retroelements from different classes reflects their modular structure with a high degree of flexibility, and points to gene sharing between different groups of retroelements.