Exploring the role of signaling secondary metabolites in bacterial communications

Abstract

Throughout their lifespan, bacteria generate diverse natural products postulated to serve as chemical signal mediators and defensive weaponry. However, although enormous natural products have been identified, elucidating their ecological functions, such as antibacterial, antifungal, and quorum sensing (QS) induction properties, remains limited. This study focuses on exploring novel molecules that function as QS autoinducers or inhibitors. Chapter 1 comprehensively reviews the latest advancements in these fields. Several major families of QS autoinducers are discussed, including N-acyl-homoserine lactones (AHL), autoinducer-2 (AI-2), RRNPP peptides, autoinducing peptides (AIP), and N-heterocycles. Additionally, the principles, examples, screening models, and applications of QS inhibitors are introduced. Following the review, Chapter 2 delves deeper into the genome mining-guided discovery of QS molecules, leading to the discovery of new N-heterocycles as QS inhibitors. We next examined the corresponding biosynthetic enzymes, focusing on the CAR enzyme family due to their diversity, prevalence, and untapped enzymatic potential in N-heterocycle biosynthesis. Further enzyme characterization and in vitro product reconstruction revealed that a single CAR enzyme can produce hundreds of N-heterocycles, with a series of pyrazine molecules identified as QS inhibitors. Considering the widespread occurrence of N-heterocycles, particularly pyrazine molecules, this study provides novel insights into the ecological functions of these ubiquitous molecules. The comparative metabolome analysis conducted in the last chapter suggested the presence of the signaling molecule that potentially influences secondary metabolite production in Paenibacillus. Consequently, Chapter 3 conducted a comprehensive exploration of this signaling molecule, which has been identified as a novel group of AIPs, belonging to QS autoinducers. The discovery of Pp-AIPs was led by a bioactivity-guided search. Notably, these AIPs represent the first known instance of regulating secondary metabolite production, distinguishing them from previously reported AIPs with different functions. Consequently, they offer a novel mode of communication with host plants, as the AIPs may assist Paenibacillus in shaping the root microbiome. This study broadens the diversity of AIPs and their ecological significance in complex bacteria-microbiome-plant biosystems. In summary, this study establishes novel links between natural products and bacterial communications, particularly within the N-heterocycle and AIP families. These findings serve as inspiration for future investigations into genomic-guided and bioactivity-guided explorations of novel chemical families as potential QS inhibitors or autoinducers. These studies hold the potential to elucidate the ecological functions of abundant secondary metabolites produced by bacteria and guide their applications in areas such as human health and agriculture. (391 word)