Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.
Mob DNA. 2011 Oct 19;2(1):12. doi: 10.1186/1759-8753-2-12.
"Domestication" of transposable elements (TEs) led to evolutionary breakthroughs such as the origin of telomerase and the vertebrate adaptive immune system. These breakthroughs were accomplished by the adaptation of molecular functions essential for TEs, such as reverse transcription, DNA cutting and ligation or DNA binding. Cryptons represent a unique class of DNA transposons using tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules. Cryptons were originally identified in fungi and later in the sea anemone, sea urchin and insects.
Herein we report new Cryptons from animals, fungi, oomycetes and diatom, as well as widely conserved genes derived from ancient Crypton domestication events. Phylogenetic analysis based on the YR sequences supports four deep divisions of Crypton elements. We found that the domain of unknown function 3504 (DUF3504) in eukaryotes is derived from Crypton YR. DUF3504 is similar to YR but lacks most of the residues of the catalytic tetrad (R-H-R-Y). Genes containing the DUF3504 domain are potassium channel tetramerization domain containing 1 (KCTD1), KIAA1958, zinc finger MYM type 2 (ZMYM2), ZMYM3, ZMYM4, glutamine-rich protein 1 (QRICH1) and "without children" (WOC). The DUF3504 genes are highly conserved and are found in almost all jawed vertebrates. The sequence, domain structure, intron positions and synteny blocks support the view that ZMYM2, ZMYM3, ZMYM4, and possibly QRICH1, were derived from WOC through two rounds of genome duplication in early vertebrate evolution. WOC is observed widely among bilaterians. There could be four independent events of Crypton domestication, and one of them, generating WOC/ZMYM, predated the birth of bilaterian animals. This is the third-oldest domestication event known to date, following the domestication generating telomerase reverse transcriptase (TERT) and Prp8. Many Crypton-derived genes are transcriptional regulators with additional DNA-binding domains, and the acquisition of the DUF3504 domain could have added new regulatory pathways via protein-DNA or protein-protein interactions.
Cryptons have contributed to animal evolution through domestication of their YR sequences. The DUF3504 domains are domesticated YRs of animal Crypton elements.
转座元件 (TEs) 的“驯化”导致了一些进化突破，例如端粒酶和脊椎动物适应性免疫系统的起源。这些突破是通过适应 TE 所必需的分子功能来实现的，例如反转录、DNA 切割和连接或 DNA 结合。Cryptons 代表一类独特的 DNA 转座子，使用酪氨酸重组酶 (YR) 切割和重新连接重组 DNA 分子。Cryptons 最初在真菌中发现，后来在海葵、海胆和昆虫中发现。
本文报告了来自动物、真菌、卵菌和硅藻的新 Cryptons，以及广泛保守的源自古老 Crypton 驯化事件的基因。基于 YR 序列的系统发育分析支持 Crypton 元件的四个深部分支。我们发现，真核生物中的未知功能域 3504 (DUF3504) 来自 Crypton YR。DUF3504 类似于 YR，但缺乏催化四联体 (R-H-R-Y) 的大部分残基。含有 DUF3504 结构域的基因包括钾通道四聚化结构域包含 1 (KCTD1)、KIAA1958、锌指 MYM 型 2 (ZMYM2)、ZMYM3、ZMYM4、富含谷氨酰胺蛋白 1 (QRICH1) 和“无子女” (WOC)。DUF3504 基因高度保守，几乎存在于所有有颌脊椎动物中。序列、结构域结构、内含子位置和基因座块支持 ZMYM2、ZMYM3、ZMYM4 和可能的 QRICH1 是通过早期脊椎动物进化中的两轮基因组复制从 WOC 衍生而来的观点。WOC 在两侧对称动物中广泛存在。可能有四次独立的 Crypton 驯化事件，其中一次产生 WOC/ZMYM 的事件发生在双边动物诞生之前。这是迄今为止已知的第三古老的驯化事件，紧随其后的是产生端粒酶逆转录酶 (TERT) 和 Prp8 的驯化事件。许多 Crypton 衍生基因是具有额外 DNA 结合结构域的转录调节因子，而 DUF3504 结构域的获得可能通过蛋白质-DNA 或蛋白质-蛋白质相互作用增加了新的调节途径。
Cryptons 通过驯化其 YR 序列为动物进化做出了贡献。DUF3504 结构域是动物 Crypton 元件的驯化 YR。
