Discovery and characterization of peptides that direct communication in phages and bacteria

在每一次感染中，温带噬菌体需要决定是复制和裂解宿主，还是裂解和保持宿主存活。作为当前SPP2002优先计划第一学期的一部分，我们发现感染芽孢杆菌的噬菌体使用小分子通信系统来协调裂解-溶源决定(Erez等人，《自然》2017年；Stokar-Avihail等人，细胞宿主和微生物2019年)。在感染宿主细胞的过程中，噬菌体产生一种短的(6aa-10aa)的通信肽，它由µ-蛋白产生并释放到培养基中。在随后的感染中，后代噬菌体测量这种多肽的浓度，如果浓度足够高，则进行溶原性。我们称这一制度为“仲裁”制度(拉丁语中的“决定”)。我们的结果表明，许多噬菌体都含有编码仲裁蛋白的µ-蛋白，并使用它们来沟通和协调感染决策。然而，到目前为止，所有的仲裁菌同源物都是在分类杆菌科细菌基因组中发现的，目前尚不清楚感染其他分类群细菌的噬菌体是否也利用基于肽的沟通策略来决定裂解/溶源。在目前的项目中，我们将尝试在感染非芽孢杆菌物种的噬菌体中发现额外的类似仲裁的系统。由于仲裁系统的发现形成了病毒之间实际交流的第一个证明，它代表了病毒学中的一种新范式，可能会延伸到原核生物世界之外。了解噬菌体通信系统的多样性和限制条件不仅有助于我们为细菌和噬菌体基因组中的数百种微蛋白分配功能，还可能为未来在感染高等生物的病毒中发现此类蛋白奠定基础。作为SPP2002头3年的一部分，我们开发了一个通用平台，用于在数千个感兴趣的基因组中计算发现和实验验证基于微蛋白的通信系统。结果表明，该平台不仅可以在噬菌体中发现新的通讯系统，还可以在细菌中发现新的通讯系统。在该项目的第二个主要目标中，我们计划将我们的平台应用于公共数据库中可用的数千个革兰氏阳性细菌，试图大规模发现和验证指导细菌交流的新的微蛋白。

In every infection, temperate phages need to decide whether to replicate and lyse their host or to lysogenize and keep the host viable. As part of the first term of the current SPP2002 Priority Programme, we discovered that phages infecting Bacillus bacteria use a small-molecule communication system to coordinate lysis-lysogeny decisions (Erez et al., Nature 2017; Stokar-Avihail et al, Cell Host & Microbe 2019). During infection of its host cell, the phage produces a short (6aa-10aa) communication peptide that is produced by a µ-protein and released to the medium. In subsequent infections, progeny phages measure the concentration of this peptide and lysogenize if the concentration is sufficiently high. We termed this system the “arbitrium” system (“decision” in Latin). Our results showed that many phages harbor arbitrium-encoding µ-proteins and use them in order to communicate and coordinate infection decisions. However, so far all arbitrium homologs were found in prophages residing in bacterial genomes belonging to the taxonomic family Bacillaceae, and it is currently unknown whether phages infecting bacteria of other taxonomic groups also utilize peptide-based communication strategies for lysis/lysogeny decisions. In the current project we will attempt to discover additional, arbitrium-like systems in phages infecting non-bacillus species. As the discovery of the arbitrium system forms the first demonstration of actual communication between viruses, it represents a new paradigm in virology that may extend beyond the prokaryotic world. Understanding the diversity and constraints of phage communication systems will not only help us to assign function to hundreds of µ-proteins in bacterial and phage genomes, but may also set the stage for future such discoveries in viruses that infect higher organisms.As part of the first 3 years of SPP2002 we developed a general platform for the computational discovery and experimental validation of µ-proteins-based communication systems across thousands of genomes of interest. We showed that this platform could be used for discovery of new communication systems not only in phages, but also in bacteria. In the second major aim of this project, we plan to apply our platform on the thousands of Gram positive bacteria available in the public databases in attempt to massively uncover and validate new µ-proteins that direct bacterial communication.