Matveev Vitaliy, Nishihara Hidenori, Okada Norihiro
Faculty of Bioscience and Biotechnology, Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan.
Mol Biol Evol. 2007 Aug;24(8):1656-66. doi: 10.1093/molbev/msm083. Epub 2007 Apr 29.
Short interspersed elements (SINEs) constitute a group of retroposons propagating in the genome via a mechanism of reverse transcription, in which they depend on the enzymatic machinery of long retroposons (LINEs). Over 70 SINE families have been described to date from the genomes of various eukaryotes. Here, we characterize two novel SINEs from salmons (Actinopterygii: Salmonoidei). The first family, termed SlmI, was shown to be widespread among all genera of the suborder. These SINEs have a tRNA(Leu)-related promoter region at their 5'-end, a unique central conserved domain with a subfamily-specific region, and an end with RSg-1-LINE-derived 3'-terminus preceding the A/T-rich tail. The same LINE-related segment is also shared by two other salmonid SINEs: HpaI and OS-SINE1. The structural peculiarities and overall sequence identity of the SlmI 3'-terminus suggest that it has been acquired from HpaI SINEs but not directly from the partner LINE. This region plays a crucial role in the process of retrotransposition of short interspersed elements, and the case of its SINE-to-SINE transmission is the first recorded to date. Possible scenarios and potential evolutionary implications of the observed interaction between short retroposons are discussed. Apart from the above, we found a copy of the SlmI SINE in the GenBank entry for the blood fluke, Schistosoma japonicum (Trematoda: Strigeiformes) -- a trematode causing one of the most important human helminth infections, with its genome known to host other groups of salmonoid retroposons. In the present article, we suggest our views with regard to possible ways in which such an intensive horizontal transfer of salmonoid retroposons to the schistosomal genome occurs. The second novel SINE family, termed SlmII, originates from one of the SlmI subfamilies, with which it shares the same tRNA-related region, central domain, and a part of RSg-1-derived segment, but has a different 3'-tail of unidentified origin. Its distribution among salmonids validates Parahucho (Japanese huchen) as a distinct monotypic genus.
短散在元件（SINEs）是一类反转座子，通过逆转录机制在基因组中传播，在此过程中它们依赖于长反转座子（LINEs）的酶促机制。迄今为止，已从各种真核生物的基因组中描述了70多个SINE家族。在此，我们对鲑鱼（辐鳍鱼纲：鲑形目）中的两个新型SINE进行了表征。第一个家族称为SlmI，已证明在该亚目的所有属中广泛存在。这些SINE在其5'端具有一个与tRNA（Leu）相关的启动子区域，一个具有亚家族特异性区域的独特中央保守结构域，以及在富含A/T的尾巴之前带有源自RSg-1-LINE的3'末端的末端。另外两个鲑科SINE：HpaI和OS-SINE1也共享相同的与LINE相关的片段。SlmI 3'末端的结构特点和整体序列同一性表明它是从HpaI SINEs获得的，而不是直接从伙伴LINE获得的。该区域在短散在元件的逆转录转座过程中起关键作用，其从一个SINE到另一个SINE的传递情况是迄今为止首次记录到的。讨论了观察到的短反转座子之间相互作用的可能情况和潜在进化意义。除此之外，我们在日本血吸虫（吸虫纲：分体科）——一种导致人类最重要的蠕虫感染之一的吸虫——的基因库条目中发现了SlmI SINE的一个拷贝，其基因组已知含有其他鲑科反转座子群体。在本文中，我们就鲑科反转座子如此大量水平转移到血吸虫基因组的可能方式提出了我们的观点。第二个新型SINE家族称为SlmII，起源于SlmI亚家族之一，与之共享相同的与tRNA相关区域、中央结构域和一部分源自RSg-1的片段，但具有一个来源不明的不同3'尾巴。它在鲑科鱼类中的分布证实了石川哲罗鱼（日本哲罗鲑）是一个独特的单型属。
