R-type pyocins are contractile molecular syringes that puncture the cell membrane of target cells and induce cell death. A recent study(1) described the first near-atomic structures of the complete R-2 pyocin in both precontraction and postcontraction states, laying a foundation for a mechanistic understanding of its action as a molecular syringe and for exploitation of these types of bactericidal nanomachines as precision antimicrobials. R-type pyocins are macromolecular bacteriocins produced by bacterial species, such as Pseudomonas aeruginosa. R-type pyocins are known to undergo major contraction upon the attachment to the target cell, resembling the action of a syringe. They belong to an evolutionarily related family of contractile injection systems (CISs), which includes R-type pyocins, contractile bacteriophages, the bacterial type VI secretion system, and the virulence cassette of Photorhabdus. Although the CISs are composed of conserved core components, including a needle, a contractile sheath, and a baseplate, they are among the most diverse and versatile nanomachines that deliver proteins and/or DNA into a bacterial or eukaryotic cell. Given their prevalence and profound impact on bacterial evolution and pathogenesis, CISs have been extensively analyzed to decipher their assemblies and functions.(2−5) However, two essential questions remained: (1) What is the molecular mechanism underlying contraction? (2) How is the contraction activated or initiated at a molecular level? To address these questions, Ge and colleagues combined X-ray crystallography, cryo-electron microscopy (cryo-EM), and the most advanced single-particle analysis to determine near-atomic structures of the complete R-2 pyocin in both precontraction and postcontraction states. In total, they resolved ∼384 subunits of 10 different gene products that are directly involved in the assembly of four distinct components of the contractile machine: the collar, contractile sheath, inner tube or needle, and baseplate with six tail fibers (Figure 1A). Importantly, comparison of the atomic structures of the R-2 pyocin in two distinct states was critical for uncovering molecular mechanisms underlying the contraction and its activation. Figure 1. Precontraction and postcontraction states of R-2 pyocin and T4 phage. (A) Model of R2 pyocin in precontraction and postcontraction states. (B) Model of T4 phage in both precontraction and postcontraction states. After contraction, the needle is ejected into the target cell envelope, including the outer membrane (OM) and peptidoglycan (PG). The baseplates in R-2 pyocin and T4 phage are colored yellow and orange. They form an iris-like ring by lateral dimerization as shown in panel C. The interaction between tail fibers and the host receptor transmits a signal that induces breakage of the iris ring and a conformational change in the baseplate as shown in panel D. The R-2 pyocin is largely comprised of the contractile sheath and the inner needle. They are connected by a six-stranded collar at the top of the pyocin. However, the most complex part of the system is the baseplate, which is located at the bottom of the pyocin and is composed of eight different proteins. Among them, six copies of the triplex (two PA0618 and one PA0619) form an iris-like ring by lateral dimerization of two adjacent PA0618 proteins in the precontraction state (Figure 1A,C). The iris-like ring appears to be essential for stabilizing the baseplate and maintaining the precontraction state. When the R-2 pyocin encounters a target cell, it lands on the cell surface and the tail fibers bind to specific receptors. Remarkably, a binding signal from the tail fibers appears to be sufficient for breaking the lateral dimer of PA0618 and the iris-like ring. Consequently, the baseplate expands and morphs into a hexamer (Figure 1C). This conformational change of the baseplate further triggers a cascade of irreversible events, including sheath contraction and penetration of the needle into the target cell (Figure 1B). This latest study provides the most detailed information required for understanding the mechanical action of a molecular syringe. Given that the model of action for CISs is believed to be highly conserved, it is expected that the mechanistic insights derived from the R-2 pyocin will have a profound impact on our understanding of other CISs. Nevertheless, further investigation of other CISs will surely help to distinguish common and specialized features of each system. Importantly, the advanced cryo-EM techniques used in this study of R2 pyocin proved to be essential for the tremendous progress in the field; they will be certainly deployed to visualize other CISs in different conformational states, enabling a better understanding of these contractile nanomachines and their action at the atomic level. Due to their sophisticated mechanisms of action, high bactericidal potency, and focused spectrum, pyocins could be potentially developed as novel antibacterial agents. In particular, the tail fibers of pyocins are essential for their specificity on pathogen recognition, making it possible to engineer pyocins into precision antibiotics. Compared to broad-spectrum synthetic antibiotics, engineered pyocins have an advantage in killing specific pathogenic microbes without limiting or disturbing other microbes in a complex bacterial ecosystem like the gut microbiota. This study of near-atomic-resolution structures of the complete R-2 pyocin will surely inspire further exploitation of these types of nanomachines as precision antimicrobials. Q.G. and J.L. were supported by grants from the National Institutes of Health (AI087946, GM124378, and GM110243). The authors declare no competing financial interest. The authors thank Ian Molineux for critical reading and suggestions. This article references 5 other publications.

中文翻译：

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看到收缩的杀菌纳米机正在以接近原子的分辨率起作用。

R型囊球蛋白是可收缩的分子注射器，可刺穿靶细胞的细胞膜并诱导细胞死亡。最近的一项研究（1）描述了在收缩前和收缩后两种状态下完整R-2霉素的第一个近原子结构，为对其作为分子注射器的作用机理进行机械理解以及利用这些类型的杀菌纳米机械奠定了基础。作为精密抗菌剂。R型脓单胞菌是由细菌物种（如铜绿假单胞菌）产生的大分子细菌素。众所周知，R型囊球蛋白在附着于靶细胞后会发生重大收缩，类似于注射器的作用。它们属于一种进化上相关家族收缩喷射系统（CISS），其中包括R型pyocins，收缩噬菌体，细菌VI型分泌系统，和毒力暗盒光杆状。尽管CIS由保守的核心组件组成，包括针，可收缩的鞘和基板，但它们是将蛋白质和/或DNA传递到细菌或真核细胞中的最多样化和用途最广泛的纳米机器。鉴于CIS的普遍性及其对细菌进化和发病机理的深远影响，人们对其进行了广泛的分析以破译其组装和功能。[2-5]但是，仍然存在两个基本问题：（1）收缩的分子机制是什么？（2）收缩是如何在分子水平上激活或引发的？为了解决这些问题，Ge及其同事结合了X射线晶体学，低温电子显微镜（cryo-EM），以及最先进的单颗粒分析方法，以测定收缩前和收缩后两种状态下完整R-2霉素的近原子结构。他们总共解析了10种不同基因产物的384个亚基，这些亚基直接参与了收缩机四个不同组件的组装：衣领，收缩鞘，内管或针以及带有六根尾纤维的底板（图1A） 。重要的是，在两个不同状态下比较R-2霉素的原子结构对于揭示收缩及其激活的分子机制至关重要。图1. R-2霉素和T4噬菌体的收缩前和收缩后状态。（A）收缩前和收缩后状态的R2霉素模型。（B）在收缩前和收缩后状态下的T4噬菌体模型。收缩后 针头会弹出目标细胞膜，包括外膜（OM）和肽聚糖（PG）。R-2霉素和T4噬菌体的底色为黄色和橙色。它们通过横向二聚化形成了虹膜状环，如面板C所示。尾部纤维与宿主受体之间的相互作用传递了导致虹膜环断裂和基板构象变化的信号，如面板D所示。 -2霉素主要由可收缩的鞘和内针组成。它们通过pyocin顶部的六链项圈连接。但是，系统中最复杂的部分是底板，该底板位于pyocin的底部，由八种不同的蛋白质组成。其中，三倍体的六个副本（两个PA0618和一个PA0619）通过在收缩前状态下两个相邻PA0618蛋白的横向二聚化形成虹膜状环（图1A，C）。虹膜状的环似乎对于稳定基板和保持预收缩状态至关重要。当R-2霉素遇到目标细胞时，它会落在细胞表面，并且尾纤维会与特定受体结合。值得注意的是，来自尾纤维的结合信号似乎足以破坏PA0618的横向二聚体和虹膜状环。因此，底板会膨胀并变形为六聚体（图1C）。底板的这种构象变化进一步触发了一系列不可逆事件，包括鞘收缩和针头刺入靶细胞（图1B）。这项最新研究提供了了解分子注射器的机械作用所需的最详细的信息。鉴于CIS的作用模型被认为是高度保守的，因此可以预期，从R-2霉素中获得的机理见解将对我们对其他CIS的理解产生深远的影响。尽管如此，对其他CIS的进一步调查肯定会有助于区分每个系统的共同和专业特征。重要的是，在R2霉素的这项研究中使用的先进的cryo-EM技术被证明对该领域的巨大进步至关重要。当然，它们将被部署为可视化处于不同构象状态的其他CIS，从而更好地了解这些可收缩的纳米机器及其在原子级的作用。由于其复杂的作用机制，杀菌素具有很高的杀菌力和集中的光谱，可潜在地开发为新型抗菌剂。特别是，对于特定的病原体识别而言，凸突霉素的尾巴纤维是必不可少的，这使得将凸突霉素改造成精密抗生素成为可能。与广谱合成抗生素相比，工程化的球菌蛋白酶在杀死特定的病原微生物方面具有优势，而不会限制或干扰肠道菌群等复杂细菌生态系统中的其他微生物。完整的R-2霉素的近原子拆分结构的这项研究必将激发这些类型的纳米机器作为精密抗菌剂的进一步开发。QG和JL得到了美国国立卫生研究院（AI087946，GM124378和GM110243）的资助。作者宣称没有竞争性的经济利益。作者感谢Ian Molineux的批评阅读和建议。本文引用了其他5个出版物。