Evolution of the R2 retrotransposon ribozyme and its self-cleavage site.
Evolution of the R2 retrotransposon ribozyme and its self-cleavage site.
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DOI：
10.1371/journal.pone.0066441
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Eickbush TH
中科院分区：
文献类型：
--
作者：
Eickbush DG;Burke WD;Eickbush TH
R2是一种非长末端重复反转录转座子，在许多动物的串联28S rRNA基因中特异插入位点。先前，来自不同种类果蝇的R2 RNA被编码在其5'端的D型肝炎病毒（HDV）样核酶从28S rRNA/R2共转录物中自我切割。RNA切割发生在元件与28S基因的精确5'交界处。在这里，我们报道了包含R2元件5'端的rna在其整个物种范围内折叠成hdv样核酶。在许多R2谱系中进行的RNA自裂体外实验证实了其活性。对于许多R2s， RNA自裂不是在元件的5'端，而是在连接上游36个核苷酸的28S rRNA序列上。切割的位置与不同物种内源R2 5’连接的类型密切相关。大多数R2s的R2 5'连接是均匀的，其中RNA切割位于rRNA序列的上游。假设在反转录过程中合成的第一条DNA链上剩余的28S序列退火到目标位点并均匀地启动第二链DNA合成。在R2 5‘端发生RNA切割的物种中，5’连接是可变的。这种连接变异被认为是由于靶位点和第一DNA链之间偶然的微同源性引发了第二链DNA合成。最后，讨论了R2核酶的进化特征，特别是在同一活性位点序列上的裂解位点和收敛位点的变化。
R2 is a non-long terminal repeat retrotransposon that inserts site-specifically in the tandem 28S rRNA genes of many animals. Previously, R2 RNA from various species of Drosophila was shown to self-cleave from the 28S rRNA/R2 co-transcript by a hepatitis D virus (HDV)-like ribozyme encoded at its 5' end. RNA cleavage was at the precise 5' junction of the element with the 28S gene. Here we report that RNAs encompassing the 5' ends of R2 elements from throughout its species range fold into HDV-like ribozymes. In vitro assays of RNA self-cleavage conducted in many R2 lineages confirmed activity. For many R2s, RNA self-cleavage was not at the 5' end of the element but at 28S rRNA sequences up to 36 nucleotides upstream of the junction. The location of cleavage correlated well with the types of endogenous R2 5' junctions from different species. R2 5' junctions were uniform for most R2s in which RNA cleavage was upstream in the rRNA sequences. The 28S sequences remaining on the first DNA strand synthesized during retrotransposition are postulated to anneal to the target site and uniformly prime second strand DNA synthesis. In species where RNA cleavage occurred at the R2 5' end, the 5' junctions were variable. This junction variation is postulated to result from the priming of second strand DNA synthesis by chance microhomologies between the target site and the first DNA strand. Finally, features of R2 ribozyme evolution, especially changes in cleavage site and convergence on the same active site sequences, are discussed.
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影响因子：
14.9
作者：
BURKE, WD;MULLER, F;EICKBUSH, TH
通讯作者：
EICKBUSH, TH
影响因子：
3.5
作者：
Gladyshev, Eugene A.;Arkhipova, Irina R.
通讯作者：
Arkhipova, Irina R.
影响因子：
5.6
作者：
Chadalavada, DM;Knudsen, SM;Bevilacqua, PC
通讯作者：
Bevilacqua, PC
影响因子：
4.8
作者：
Bibillo, A;Eickbush, TH
通讯作者：
Eickbush, TH
影响因子：
4.8
作者：
Bibillo, A;Eickbush, TH
通讯作者：
Eickbush, TH