Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.
Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
Nature. 2021 Jan;589(7841):306-309. doi: 10.1038/s41586-020-2921-5. Epub 2020 Nov 18.
CrAss-like phages are a recently described expansive group of viruses that includes the most abundant virus in the human gut. The genomes of all crAss-like phages encode a large virion-packaged protein that contains a DFDxD sequence motif, which forms the catalytic site in cellular multisubunit RNA polymerases (RNAPs). Here, using Cellulophaga baltica crAss-like phage phi14:2 as a model system, we show that this protein is a DNA-dependent RNAP that is translocated into the host cell along with the phage DNA and transcribes early phage genes. We determined the crystal structure of this 2,180-residue enzyme in a self-inhibited state, which probably occurs before virion packaging. This conformation is attained with the help of a cleft-blocking domain that interacts with the active site and occupies the cavity in which the RNA-DNA hybrid binds. Structurally, phi14:2 RNAP is most similar to eukaryotic RNAPs that are involved in RNA interference, although most of the phi14:2 RNAP structure (nearly 1,600 residues) maps to a new region of the protein fold space. Considering this structural similarity, we propose that eukaryal RNA interference polymerases have their origins in phage, which parallels the emergence of the mitochondrial transcription apparatus.
类 CrAss 噬菌体是最近描述的一个庞大的病毒群，其中包括人类肠道中最丰富的病毒。所有类 CrAss 噬菌体的基因组都编码一种大型病毒衣壳蛋白，该蛋白包含一个 DFDxD 序列基序，该基序构成了细胞多亚基 RNA 聚合酶（RNAP）的催化位点。在这里，我们使用巴氏噬纤维菌 CrAss 样噬菌体 phi14:2 作为模型系统，表明该蛋白是一种依赖于 DNA 的 RNAP，它与噬菌体 DNA 一起被转运到宿主细胞中，并转录早期噬菌体基因。我们确定了该 2180 个残基酶在自我抑制状态下的晶体结构，该状态可能发生在衣壳包装之前。这种构象的形成得益于一个与活性位点相互作用并占据 RNA-DNA 杂交结合腔的裂缝阻断结构域。从结构上看，phi14:2 RNAP 与参与 RNA 干扰的真核 RNAP 最为相似，尽管 phi14:2 RNAP 的大部分结构（近 1600 个残基）映射到蛋白质折叠空间的一个新区域。考虑到这种结构相似性，我们提出真核 RNA 干扰聚合酶起源于噬菌体，这与线粒体转录装置的出现相平行。
