Chemical proteomics inside us: Using chemical tools to decipher coexistence between bacteria and humans

最近的研究表明，将人体视为大约100万亿个细胞的静态集合的传统观点是错误的。不仅这个集合的构成高度多样化，不同个体之间的组成也非常不同，而且不同细菌和真菌物种的种群(它们加在一起占我们身体中的大多数细胞)在一个人的生命周期中不断变化。我们认为，细菌物种之间的化学串扰以及细菌与宿主细胞之间的串扰都对细菌的定植和毒力进行了严格的调控。了解这些分子接触背后的化学原理将有助于我们回答以下开创性的问题：当一群病原体开始在健康的菌群中增长到超过它们的“自然”极限时会发生什么？具体地说，共生物种如何对特定信号分子的突然上升做出反应，以及它们如何感知它们？是什么阻止了健康菌群的成员被根除，我们如何利用这些信息来预防或治疗生物失调？我们的目标是通过使用一个先进的化学蛋白质组学平台，在两个不同但相关的环境中揭开这些类型的化学串扰背后的分子细节：人类呼吸道(目标2)和人类肠道(目标3)。该平台基于可光激活的无标签分子探针(目标1)。我们的总体目标是识别和详细研究已知病原体中的小分子和蛋白质，这些小分子和蛋白质是它们彼此之间以及与人类宿主关系的主要调节因素，以及来自已知和未知肠道细菌的小分子和蛋白质，它们调节肠道健康和失调之间的平衡。我们的长期目标是回答以下基本问题：共生体和病原体如何评估其环境的确切化学状态？特定的病原体是如何成功地控制某些特定的生态位的？我们的微生物群在防止这种情况下起到了什么作用？这个团队恰好汇集了有效解决这些开创性问题所需的学科。Meijler团队在合成和应用基于细菌信号分子的探针方面拥有丰富的化学和微生物学经验，最近他的团队利用这个化学蛋白质组平台成功地阐明了铜绿假单胞菌4-烷基-喹诺酮受体网络的一部分。Elinav小组利用他们在下一代测序、免疫学和先进的无菌小鼠模型方面的丰富专业知识，揭示了微生物区系如何改变宿主的生理和行为。Mann团队通过开发多肽序列标签、纳米电喷雾离子源、MaxQuant和细胞培养中氨基酸的稳定同位素标记(SILAC)等工具，使蛋白质组学在宽度、深度和精确度方面实现了前所未有的分析，从而使蛋白质组学发生了革命性的变化。

Recent studies have shown that the traditional view of the human body as a static collection of roughly 100 trillion cells is misguided. Not only is the makeup of this collection highly diverse and strongly dissimilar between different individuals, but also the populations of different bacterial and fungal species (which together account for the majority of cells in our bodies) are in constant flux during the life cycle of an individual human being. We propose that both colonization and virulence are meticulously regulated by chemical crosstalk between bacterial species as well as by crosstalk between bacterial and host cells. Understanding thechemistry underlying these molecular encounters will help us to answer the following seminal questions: What happens when a population of pathogens starts to grow among healthy flora beyond their 'natural' limit?Specifically, how do the commensal species react to a sudden rise in specific signaling molecules, and how do they sense them? What prevents members of the healthy flora from being eradicated, and how can we use this information to prevent or treat dysbiosis? We aim to unravel the molecular details behind these types of chemical crosstalk by using an advanced chemical proteomics platform, based on the development of photoactivatable tag-free molecular probes (aim 1), in two distinct yet related settings: the human airways (aim 2) and the human gut (aim 3). Our overall objective is to identify and examine in detail thesmall molecules and proteins from known pathogens which serve as primary regulators of their relationship with each other and with the human host, and the small molecules and proteins from known and unknown gut bacteria that regulate the balance between intestinal health and dysbiosis. Our long-term objective is to answer the following fundamental questions: How do commensals and pathogens assess the exact chemical state of their environment? How do specific pathogens succeed in dominating certain niches and what is the role of our microbiome in preventing this? This team brings together precisely the disciplines required to effectively approach these seminal questions. The Meijler group has ample chemical and microbiological experience in the synthesis and application of probes based on bacterial signaling molecules and recently his group used this chemical proteomics platform successfully to elucidate part of the network of 4-alkyl-quinolone receptors in P. aeruginosa. The Elinav group has used their strong expertise in next-generation sequencing, immunology, and advanced germ-free mousemodels to reveal how microbiota alter host physiology and behaviour. The Mann group has revolutionized proteomics through the development of tools such as peptide sequence tags, the nano-electrospray ion source, MaxQuant, and stable isotope labeling of amino acids in cell culture (SILAC), that enable unprecedented analyses of proteomes in terms of width, depth and precision.