Genome-wide analysis of the biogenesis and function of surface structures involved in interbacterial interactions

细菌是生活在群落中的社会有机体。因此，感知环境并与环境相互作用对于细菌来说至关重要，并且为了这些目的，细菌细胞表面展示了各种各样的结构。外膜使得分子在表面的移位对于革兰氏阴性细菌特别具有挑战性，为此，它们使用不同的复杂系统，从简单的T5 SS（用于5型分泌系统）到复杂的多亚基纳米机器，如T4 SS或T6 SS。这些系统涉及毒力和/或微生物-微生物相互作用，因此，破译其生物起源和功能的全球要求对于了解细菌如何引起感染特别重要。 传统上，这些表面结构已经使用简化的方法进行了研究，该方法简化了细菌的复杂性，以便专注于系统本身。虽然这种策略已经产生了大量关于它们的结构和功能的信息，但它们的组装如何整合到细胞生理学中仍然是未知的。因此，需要新的方法来充分了解这些多亚基复合物的生物起源和功能。这项研究的目的是探索复杂表面结构的生物起源和功能。特别是，该提案旨在开发新的方法来研究生物起源和表面结构的功能，如T4 SS，T5 SS和T6 SS使用全基因组的方法。作为第一步，我们将询问模型细菌大肠杆菌和相关病原体鼠伤寒沙门氏菌的完整基因组，以确定参与这些系统的生物发生和功能的所有基因，并表征有助于这些系统的组装和功能的新型遗传相互作用。我们还将在这些分泌系统的生物发生的关键步骤中产生缺失，以确定这些复杂结构的组装如何整合到细菌生理学中。 总的来说，该提案包含了几项技术创新，将为系统生物学作为研究细菌生理学和毒力的工具提供新的可能性。此外，所获得的结果将使我们更好地了解细菌如何组装大型蛋白质复合物，并为不同分泌系统的生物起源和功能提供见解。最后，这项提议将为研究细菌如何与环境相互作用带来新的思路。

Bacteria are social organisms that live in communities. Accordingly, sensing and interacting with the environment is of critical importance for bacteria, and a wide array of structures are displayed at the bacterial cell surface for these purposes. The outer membrane makes the translocation of molecules at the surface particularly challenging for Gram-negative bacteria, and to this end, they use different systems that range in complexity, from the simple T5SS (for Type 5 Secretion System) to complex, multi-subunit nanomachines like the T4SS or T6SS. These systems are involved in virulence and/or microbe-microbe interactions, and thus, deciphering the global requirements for their biogenesis and function is particularly important to understand how bacteria cause infections. Traditionally, these surface structures have been studied using a reductionist approach that simplifies the bacterial complexity in order to focus on the system itself. While this strategy has generated a great amount of information on their structure and function, how their assembly is integrated within the cell physiology remains mostly unknown. Thus, new approaches are required to fully understand the biogenesis and function of these multi-subunit complexes. The goal of this research proposal is to explore the biogenesis and function of complex surface structures. In particular, this proposal aims at developing new methodologies to study the biogenesis and the function of surface structures such as the T4SS, T5SS, and T6SS using genome-wide approaches. As a first step, we will interrogate the complete genome of the model bacterium Escherichia coli and the related pathogen Salmonella Typhimurium to identify all the genes involved in the biogenesis and function of these systems, and characterize novel genetic interactions that contribute to the assembly and function of these systems. We will also generate deletions at key steps in the biogenesis of these secretion systems to determine how the assembly of these complex structures integrates into bacterial physiology. Overall, this proposal contains several technical innovations that will offer new possibilities for systems biology as a tool to study bacterial physiology and virulence. Furthermore, the results obtained will give us a better understanding of how bacteria assemble large protein complexes and provide insights into the biogenesis and the function of different secretion systems. Finally, this proposal will lead to new ideas to study how bacteria interact with their environment.