Identification of rDNA-Specific Non-LTR retrotransposons in Cnidaria
Identification of rDNA-Specific Non-LTR retrotransposons in Cnidaria
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DOI：
10.1093/molbev/msl067
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发表时间：
2006-10-01
影响因子：
10.7
通讯作者：
Fujiwara, Haruhiko
中科院分区：
文献类型：
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作者：
Kojima, Kenji K.;Kuma, Kei-ichi;Fujiwara, Haruhiko
核糖体RNA基因在大多数真核生物中是丰富的重复序列。核糖体DNA（rDNA）含有许多来自移动的元件的插入片段，包括非长末端重复（non-LTR）反转录转座子。R2是28 S rDNA特异性非LTR反转录转座子家族，分布于至少4个两侧门。R2是一个具有相同插入特异性的大家族，根据N-末端结构域和同源性分为4个进化枝（R2-A、-B、-C和-D）。没有观察到R2的水平转移;因此，R2的起源可以追溯到原口动物和后口动物之间的分裂之前。在这里，我们在硅片上确定了1个R2元件的海葵Nematostella vectensis和2个R2类逆转录转座子的水螅magnipripiata。R2从N。vectensis与其他R2一样插入到28 S rDNA中，但来自H. magnipripiata的特异序列插入到18 S rDNA高度保守区。我们将类似Hydra R2的元素命名为R8。R8插入在R7上游37 bp处，R7是另一个18 S rDNA特异性反转录转座子家族。R2和R8的靶标之间没有明显的序列相似性，可能是因为它们识别长DNA序列。结构域结构和同源性分析表明，来自N. vectensis是R2-D进化枝的成员，R8来自H. magnipripiata属于R2-A进化枝，尽管其不同的序列特异性。这些结果表明，R2已经产生之前的分裂刺胞动物和bilaterians和R8是一个逆转录转座子家族，改变了其目标从28 S rDNA的18 S rDNA。
Ribosomal RNA genes are abundant repetitive sequences in most eukaryotes. Ribosomal DNA (rDNA) contains many insertions derived from mobile elements including non-long terminal repeat (non-LTR) retrotransposons. R2 is the well-characterized 28S rDNA-specific non-LTR retrotransposon family that is distributed over at least 4 bilaterian phyla. R2 is a large family sharing the same insertion specificity and classified into 4 clades (R2-A, -B, -C, and -D) based on the N-terminal domain structure and the phylogeny. There is no observation of horizontal transfer of R2; therefore, the origin of R2 dates back to before the split between protostomes and deuterostomes. Here, we in silico identified 1 R2 element from the sea anemone Nematostella vectensis and 2 R2-like retrotransposons from the hydrozoan Hydra magnipapillata. R2 from N. vectensis was inserted into the 28S rDNA like other R2, but the R2-like elements from H. magnipapillata were inserted into the specific sequence in the highly conserved region of the 18S rDNA. We designated the Hydra R2-like elements R8. R8 is inserted at 37 bp upstream from R7, another 18S rDNA-specific retrotransposon family. There is no obvious sequence similarity between targets of R2 and R8, probably because they recognize long DNA sequences. Domain structure and phylogeny indicate that R2 from N. vectensis is the member of the R2-D clade, and R8 from H. magnipapillata belongs to the R2-A clade despite its different sequence specificity. These results suggest that R2 had been generated before the split between cnidarians and bilaterians and that R8 is a retrotransposon family that changed its target from the 28S rDNA to the 18S rDNA.