Molecular structure of the bacterial chemotaxis apparatus

细菌趋化性是研究得最好的信号转导途径之一，几十年来对信号传导的结构、生化、遗传和生理成分的分析有助于对整个信号传导过程的广泛理解。在过去的一年里，我们在完整细菌细胞的结构成像和预测计算模型的发展方面取得了重大进展，这些模型可以捕捉细胞对环境变化的反应，从而为现代细胞生物学的中心目标做出贡献。细菌通过配体与一系列趋化受体的结合来感知局部化学环境的许多变化，进而触发信号通路的激活，最终调节鞭毛马达的旋转。详细了解细菌趋化装置的时空结构是一个基本的问题，因为它将提供一个框架来整合这一过程的广泛的遗传、生理、生化和结构分析。随着先进的成像方法的出现，可以在细胞内对特定蛋白质复合物进行空间定位，在分子水平上对整个细菌细胞进行综合结构理解的前景是可能的。化学趋向性是一种特别容易处理的信号通路，因为它涉及的成分很少，而且我们知道信号转导级联前端的空间定位。在过去的几年里，我们已经采取了系统的步骤来弥合从结构到生理学的差距，因为它涉及到导出趋化性的定量模型，该模型考虑了信号通路中蛋白质成分的空间和分子组织。我们首先建立了在细菌细胞中定位受体的可行性，然后建立了在完整细菌中获得受体蛋白3D结构的可能性。这反过来又导致了受体在膜平面上部分有序的六边形排列的发现。我们现在已经扩展了这些基础，将受体的结构、空间分布和生长介质的丰富程度等信息转化为可测试的、可预测的趋化性信号的计算模型。过去一年的进展亮点包括：(i)发现多种革兰氏阴性细菌中化学受体阵列的部分有序排列；（ii）在分离的受体组合中存在三聚体-二聚体组织的明确证据；（iii）将冷冻电子层析研究扩展到类核，以建立类核结构与受体组织之间的联系；（iv）开发计算模型，正确预测培养基中营养条件变化时受体排列和密度的变化；(v)在将EM/SIMS联合成像应用于完整细菌细胞方面取得进展。

Bacterial chemotaxis is among the best-studied signal transduction pathways, where decades of analysis of structural, biochemical, genetic and physiological components of signaling have contributed to a broad understanding of the overall signaling process. We have taken significant steps over the last year both in structural imaging of intact bacterial cells and in the development of predictive computational models that capture cellular responses to changes in their environment, thus contributing to a central goal of modern cellular biology. Bacteria sense many of the changes in their local chemical environment by the binding of ligands to a family of chemotaxis receptors, which in turn trigger the activation of a signaling pathway that ultimately regulates the rotation of the flagellar motor. A detailed understanding of the spatial and temporal architecture of the bacterial apparatus for chemotaxis is a problem of fundamental interest because it will provide a framework to integrate the extensive genetic, physiological, biochemical and structural analyses of this process. With the advent of advanced imaging methods that allow spatial localization of specific protein complexes within the cell, the prospect of developing an integrated structural understanding of whole bacterial cells at the molecular level is potentially within range. Chemotaxis is a particularly tractable signaling pathway given the small number of components involved and the knowledge of the spatial localization of the front end of the signal transduction cascade. Over the last few years, we have taken systematic steps to bridge the gap from structure to physiology as it relates to deriving a quantitative model for chemotaxis that takes into account the spatial and molecular organization of the protein components in the signaling pathway. We began with first establishing the feasibility of localizing the receptors in the bacterial cell, and moved on to establishing the possibility of obtaining 3D structures of receptor proteins when they are still in an intact bacterium. This in turn, led to the discovery of the partially ordered hexagonal arrangement of receptors in the plane of the membrane. We have now extended these foundations to translating the information on the structure of the receptors, their spatial distribution, and richness of the growth medium into a testable, predictive computational model for chemotaxis signaling. Highlights of progress over the last year include (i) discovery of the partially ordered arrangement of chemoreceptor arrays in multiple gram-negative bacteria; (ii) definitive evidence of the trimer-of-dimer organization in isolated receptor assemblies; (iii) extension of cryo-electron tomographic studies to the nucleoid to establish the connection between nucleoid structure and receptor organization; (iv) development of computational models that correctly predict the changes in receptor arrangement and density with changing nutrient conditions in the medium and (v) progress towards applying combined EM/SIMS imaging to intact bacterial cells.