Institute of Botany, Dresden University of Technology, Dresden D-01062, Germany.
Mob DNA. 2013 Mar 1;4(1):8. doi: 10.1186/1759-8753-4-8.
Chromoviruses are one of the three genera of Ty3-gypsy long terminal repeat (LTR) retrotransposons, and are present in high copy numbers in plant genomes. They are widely distributed within the plant kingdom, with representatives even in lower plants such as green and red algae. Their hallmark is the presence of a chromodomain at the C-terminus of the integrase. The chromodomain exhibits structural characteristics similar to proteins of the heterochromatin protein 1 (HP1) family, which mediate the binding of each chromovirus type to specific histone variants. A specific integration via the chromodomain has been shown for only a few chromoviruses. However, a detailed study of different chromoviral clades populating a single plant genome has not yet been carried out.
We conducted a comprehensive survey of chromoviruses within the Beta vulgaris (sugar beet) genome, and found a highly diverse chromovirus population, with significant differences in element size, primarily caused by their flanking LTRs. In total, we identified and annotated full-length members of 16 families belonging to the four plant chromoviral clades: CRM, Tekay, Reina, and Galadriel. The families within each clade are structurally highly conserved; in particular, the position of the chromodomain coding region relative to the polypurine tract is clade-specific. Two distinct groups of chromodomains were identified. The group II chromodomain was present in three chromoviral clades, whereas families of the CRM clade contained a more divergent motif. Physical mapping using representatives of all four clades identified a clade-specific integration pattern. For some chromoviral families, we detected the presence of expressed sequence tags, indicating transcriptional activity.
We present a detailed study of chromoviruses, belonging to the four major clades, which populate a single plant genome. Our results illustrate the diversity and family structure of B. vulgaris chromoviruses, and emphasize the role of chromodomains in the targeted integration of these viruses. We suggest that the diverse sets of plant chromoviruses with their different localization patterns might help to facilitate plant-genome organization in a structural and functional manner.
Chromoviruses 是 Ty3-gypsy 长末端重复 (LTR) 反转录转座子的三个属之一，在植物基因组中以高拷贝数存在。它们广泛分布于植物界，甚至在藻类等低等植物中也有代表。它们的标志是整合酶 C 末端存在 chromodomain。chromodomain 表现出与异染色质蛋白 1 (HP1) 家族蛋白相似的结构特征，后者介导每种 chromovirus 类型与特定组蛋白变体的结合。仅少数 chromoviruses 显示出特定的通过 chromodomain 的整合。然而，对单个植物基因组中不同 chromoviral 分支的详细研究尚未进行。
我们对 Beta vulgaris（糖甜菜）基因组中的 chromoviruses 进行了全面调查，发现了一个高度多样化的 chromovirus 群体，其元件大小差异显著，主要是由其侧翼 LTR 引起的。总共，我们鉴定并注释了属于四个植物 chromoviral 分支的 16 个家族的全长成员：CRM、Tekay、Reina 和 Galadriel。每个分支内的家族在结构上高度保守；特别是，chromodomain 编码区相对于多嘧啶 tract 的位置是分支特异性的。鉴定出两个不同的 chromodomain 组。组 II chromodomain 存在于三个 chromoviral 分支中，而 CRM 分支的家族含有更分化的基序。使用所有四个分支的代表进行物理作图确定了分支特异性的整合模式。对于一些 chromoviral 家族，我们检测到表达序列标签的存在，表明转录活性。
我们对属于四个主要分支的 populate 单个植物基因组的 chromoviruses 进行了详细研究。我们的结果说明了 B. vulgaris chromoviruses 的多样性和家族结构，并强调了 chromodomains 在这些病毒靶向整合中的作用。我们认为，具有不同定位模式的多样化植物 chromoviruses 可能有助于以结构和功能方式促进植物基因组的组织。
