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

细菌是生活在社区中的社会有机体。因此，感知和与环境的相互作用对细菌至关重要，为了这些目的，细菌细胞表面显示了广泛的结构。外膜使分子在表面的移位对革兰氏阴性细菌来说尤其具有挑战性，为此，他们使用了复杂程度不同的不同系统，从简单的T5SS(用于5型分泌系统)到复杂的多亚单位纳米机器，如T4SS或T6SS。这些系统参与毒力和/或微生物-微生物的相互作用，因此，破译它们的生物发生和功能的全球要求对于了解细菌如何导致感染尤为重要。*传统上，这些表面结构是使用简化论的方法来研究的，这种方法简化了细菌的复杂性，以便专注于系统本身。虽然这一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单位复合体的生物发生和功能。*本研究计划的目标是探索复杂表面结构的生物发生和功能。特别是，这项建议旨在开发新的方法来研究生物发生和表面结构的功能，如T4SS、T5SS和T6SS，使用全基因组方法。作为第一步，我们将询问模式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组装和功能的新的遗传相互作用。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中。*总的来说，这项提案包含几项技术创新，这些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体，并为不同分泌系统的生物发生和功能提供见解。最后，这项提议将带来研究细菌如何与环境相互作用的新想法。

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.**