State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
Nucleic Acids Res. 2024 Oct 14;52(18):11336-11348. doi: 10.1093/nar/gkae750.
Recently, a novel two-gene bacterial defense system against phages, encoding a SIR2 NADase and a HerA ATPase/helicase, has been identified. However, the molecular mechanism of the bacterial SIR2-HerA immune system remains unclear. Here, we determine the cryo-EM structures of SIR2, HerA and their complex from Paenibacillus sp. 453MF in different functional states. The SIR2 proteins oligomerize into a dodecameric ring-shaped structure consisting of two layers of interlocked hexamers, in which each subunit exhibits an auto-inhibited conformation. Distinct from the canonical AAA+ proteins, HerA hexamer alone in this antiphage system adopts a split spiral arrangement, which is stabilized by a unique C-terminal extension. SIR2 and HerA proteins assemble into a ∼1.1 MDa torch-shaped complex to fight against phage infection. Importantly, disruption of the interactions between SIR2 and HerA largely abolishes the antiphage activity. Interestingly, binding alters the oligomer state of SIR2, switching from a dodecamer to a tetradecamer state. The formation of the SIR2-HerA binary complex activates NADase and nuclease activities in SIR2 and ATPase and helicase activities in HerA. Together, our study not only provides a structural basis for the functional communications between SIR2 and HerA proteins, but also unravels a novel concerted antiviral mechanism through NAD+ degradation, ATP hydrolysis, and DNA cleavage.
最近，人们发现了一种新型的针对噬菌体的双基因细菌防御系统，该系统编码一种 SIR2 NAD 酶和一种 HerA ATP 酶/解旋酶。然而，细菌 SIR2-HerA 免疫系统的分子机制尚不清楚。在这里，我们确定了来自 Paenibacillus sp. 453MF 的 SIR2、HerA 及其复合物在不同功能状态下的冷冻电镜结构。SIR2 蛋白寡聚形成一个由两层互锁六聚体组成的十二聚体环形结构，其中每个亚基呈现自动抑制构象。与典型的 AAA+ 蛋白不同，该抗噬菌体系统中的 HerA 六聚体单独采用分裂螺旋排列，由独特的 C 端延伸稳定。SIR2 和 HerA 蛋白组装成一个约 1.1 MDa 的火炬形复合物，以抵抗噬菌体感染。重要的是，破坏 SIR2 和 HerA 之间的相互作用会大大降低抗噬菌体活性。有趣的是，结合改变了 SIR2 的寡聚状态，从十二聚体转变为十四聚体状态。SIR2-HerA 二元复合物的形成激活了 SIR2 的 NAD 酶和核酸酶活性以及 HerA 的 ATP 酶和解旋酶活性。总之，我们的研究不仅为 SIR2 和 HerA 蛋白之间的功能通讯提供了结构基础，还揭示了一种通过 NAD+ 降解、ATP 水解和 DNA 切割的新型协同抗病毒机制。
