Department of Life Sciences, Ben-Gurion University of the Negevgrid.7489.2, Beer-Sheva, Israel.
Macromolecular Crystallography and Cryo-EM Research Center, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negevgrid.7489.2, Beer-Sheva, Israel.
mBio. 2021 Aug 31;12(4):e0124221. doi: 10.1128/mBio.01242-21. Epub 2021 Aug 3.
-Adenosylmethionine lyase (SAMase) of bacteriophage T3 degrades the intracellular SAM pools of the host Escherichia coli cells, thereby inactivating a crucial metabolite involved in a plethora of cellular functions, including DNA methylation. SAMase is the first viral protein expressed upon infection, and its activity prevents methylation of the T3 genome. Maintenance of the phage genome in a fully unmethylated state has a profound effect on the infection strategy. It allows T3 to shift from a lytic infection under normal growth conditions to a transient lysogenic infection under glucose starvation. Using single-particle cryoelectron microscopy (cryo-EM) and biochemical assays, we demonstrate that SAMase performs its function by not only degrading SAM but also by interacting with and efficiently inhibiting the host's methionine -adenosyltransferase (MAT), the enzyme that produces SAM. Specifically, SAMase triggers open-ended head-to-tail assembly of E. coli MAT into an unusual linear filamentous structure in which adjacent MAT tetramers are joined by two SAMase dimers. Molecular dynamics simulations together with normal mode analyses suggest that the entrapment of MAT tetramers within filaments leads to an allosteric inhibition of MAT activity due to a shift to low-frequency, high-amplitude active-site-deforming modes. The amplification of uncorrelated motions between active-site residues weakens MAT's substrate binding affinity, providing a possible explanation for the observed loss of function. We propose that the dual function of SAMase as an enzyme that degrades SAM and as an inhibitor of MAT activity has emerged to achieve an efficient depletion of the intracellular SAM pools. Self-assembly of enzymes into filamentous structures in response to specific metabolic cues has recently emerged as a widespread strategy of metabolic regulation. In many instances, filamentation of metabolic enzymes occurs in response to starvation and leads to functional inactivation. Here, we report that bacteriophage T3 modulates the metabolism of the host E. coli cells by recruiting a similar strategy: silencing a central metabolic enzyme by subjecting it to phage-mediated polymerization. This observation points to an intriguing possibility that virus-induced polymerization of the host metabolic enzymes is a common mechanism implemented by viruses to metabolically reprogram and subdue infected cells.
噬菌体 T3 的腺苷甲硫氨酸裂解酶 (SAMase) 降解宿主大肠杆菌细胞内的 SAM 池，从而使参与多种细胞功能的关键代谢物失活，包括 DNA 甲基化。SAMase 是感染后表达的第一种病毒蛋白，其活性可防止 T3 基因组的甲基化。保持噬菌体基因组处于完全未甲基化状态对感染策略有深远影响。它使 T3 能够从正常生长条件下的裂解感染转变为葡萄糖饥饿下的短暂溶原性感染。使用单颗粒冷冻电镜 (cryo-EM) 和生化测定，我们证明 SAMase 不仅通过降解 SAM 发挥其功能，还通过与宿主的蛋氨酸腺苷转移酶 (MAT) 相互作用并有效地抑制 MAT 发挥其功能，MAT 是产生 SAM 的酶。具体来说，SAMase 触发大肠杆菌 MAT 的无终止头对头尾组装成一种不寻常的线性丝状结构，其中相邻的 MAT 四聚体由两个 SAMase 二聚体连接。分子动力学模拟和正常模式分析表明，MAT 四聚体被捕获在细丝中会导致 MAT 活性的变构抑制，这是由于向低频、高振幅活性位点变形模式的转变。活性位点残基之间无关联运动的放大降低了 MAT 的底物结合亲和力，为观察到的功能丧失提供了可能的解释。我们提出，SAMase 作为降解 SAM 的酶和作为 MAT 活性抑制剂的双重功能是为了有效地耗尽细胞内的 SAM 池而出现的。酶的自组装成纤维状结构以响应特定代谢信号已成为代谢调节的广泛策略。在许多情况下，代谢酶的丝状化是对饥饿的反应，导致功能失活。在这里，我们报告噬菌体 T3 通过采用类似的策略来调节宿主大肠杆菌细胞的代谢：通过噬菌体介导的聚合使中央代谢酶沉默。这一观察结果指出了一个有趣的可能性，即病毒诱导的宿主代谢酶聚合是病毒用来代谢重编程和抑制感染细胞的常见机制。
