The School of Plant Sciences, University of Arizona, Tucson, USA.
Department of Molecular and Cellular Biology, University of Arizona, Tucson, USA.
Genome Biol Evol. 2024 Jun 4;16(6). doi: 10.1093/gbe/evae119.
In flowering plants, euchromatic transposons are transcriptionally silenced by RNA-directed DNA Methylation, a small RNA-guided de novo methylation pathway. RNA-directed DNA Methylation requires the activity of the RNA Polymerases IV and V, which produce small RNA precursors and noncoding targets of small RNAs, respectively. These polymerases are distinguished from Polymerase II by multiple plant-specific paralogous subunits. Most RNA-directed DNA Methylation components are present in all land plants, and some have been found in the charophytic green algae, a paraphyletic group that is sister to land plants. However, the evolutionary origin of key RNA-directed DNA Methylation components, including the two largest subunits of Polymerase IV and Polymerase V, remains unclear. Here, we show that multiple lineages of charophytic green algae encode a single-copy precursor of the largest subunits of Polymerase IV and Polymerase V, resolving the two presumed duplications in this gene family. We further demonstrate the presence of a Polymerase V-like C-terminal domain, suggesting that the earliest form of RNA-directed DNA Methylation utilized a single Polymerase V-like polymerase. Finally, we reveal that charophytic green algae encode a single CLSY/DRD1-type chromatin remodeling protein, further supporting the presence of a single specialized polymerase in charophytic green algae.
在开花植物中， euchromatic 转座子通过 RNA 指导的 DNA 甲基化被转录沉默，这是一种小 RNA 指导的从头甲基化途径。RNA 指导的 DNA 甲基化需要 RNA 聚合酶 IV 和 V 的活性，它们分别产生小 RNA 前体和小 RNA 的非编码靶标。这些聚合酶通过多个植物特异性的 paralogous 亚基与聚合酶 II 区分开来。大多数 RNA 指导的 DNA 甲基化成分存在于所有陆地植物中，有些成分在绿藻 Charophyta 中也有发现，绿藻是与陆地植物亲缘关系较近的一个分支。然而，关键 RNA 指导的 DNA 甲基化成分的进化起源，包括聚合酶 IV 和聚合酶 V 的两个最大亚基，仍然不清楚。在这里，我们表明，绿藻 Charophyta 的多个谱系编码了聚合酶 IV 和聚合酶 V 最大亚基的单个拷贝前体，解决了该基因家族中两个假定的重复问题。我们进一步证明了存在类似于聚合酶 V 的 C 端结构域，表明最早形式的 RNA 指导的 DNA 甲基化使用了单个类似于聚合酶 V 的聚合酶。最后，我们揭示了绿藻 Charophyta 编码了单个 CLSY/DRD1 型染色质重塑蛋白，进一步支持了绿藻 Charophyta 中存在单个专门的聚合酶。
