Decoding the chemical language from the untapped domain of archaea

Abstract

Microorganisms are renowned for producing diverse secondary metabolites (SMs), such as signaling molecules and antimicrobials. These SMs function as "chemical languages", playing a pivotal role in the intricate social interactions of microorganisms, from facilitating symbiotic relationships to engaging in competitive battles. As one of the three domains of life, Archaea constitute a vast and diverse group widely distributed across various environments on Earth. Nevertheless, our understanding of archaeal chemical languages, especially regarding their SM structural diversity and ecological functions, remains severely limited compared to the well-studied bacterial domain. As the most recently discovered life domain, archaea represent a largely unexplored reservoir of biosynthetic potential, characterized by unique metabolic pathways and lineage-specific enzymes. Chapter 1 reviews the progress in characterizing archaeal SMs. Despite limited reported structures and bioinformatic predictions, novel structural features have been identified, confirming the existence of unique SMs and biosynthetic pathways in archaea. However, significant limitations remain. The historical challenges in cultivating archaea constrain fermentation-based metabolic investigations. Advanced technologies are now required to identify low-abundance SMs produced by encoded biosynthetic gene clusters (BGCs), especially those from uncultivated archaea. Chapter 2 employs a systematic genomic approach to explore the biosynthetic potential of archaeal SMs, uncovering numerous novel BGCs with unprecedented architectures. Genomic and metabolic analyses guided the discovery of two novel lanthipeptides with different ring topologies from haloarchaea. Notably, archalan α exhibits anti-archaeal activity against haloarchaea, potentially mediating antagonistic interactions within the halophilic niche. This discovery establishes archalan α as the first structurally validated archaeal ribosomally synthesized and post-translationally modified peptides (RiPPs). It confirms the functional production of SMs predicted from genomic data and addresses gaps in our understanding of archaeal SM diversity and ecological function. Chapter 3 presents a large-scale genome-mining analysis that uncovers an unexpected diversity of archaeal RiPP families. Among these, lanthipeptides exhibit enzyme-precursor co-evolution with distinct amino acid biases compared to their bacterial counterparts, potentially representing an adaptive response to halophilic conditions. Furthermore, the validation of classic and noncanonical lanthipeptides by combining the first archaeal heterologous expression system with rule-based metabolomic analysis highlights their unique chemical characteristics and biosynthetic pathways. Moreover, archaeal RiPPs play a novel ecological role in enhancing host motility by inducing rod-shaped cell morphology and upregulating archaellin gene transcription, thereby facilitating archaeal interactions with abiotic environments and improving competition for nutrients and space. This thesis integrates genome mining, metabolomics, synthetic biology, morphology, and transcriptomics to systematically investigate the landscapes and ecological functions of archaeal SMs. It reports extensive BGCs and experimentally verifies archaeal SMs, positioning archaea as a novel source for compound discovery. The identification of noncanonical lanthipeptides highlights the chemical and enzymatic uniqueness of archaeal SMs. Additionally, this work elucidates the ecological roles of archaeal RiPPs, from anti-archaeal activity to behavior regulation. These findings address gaps in our understanding of archaeal SM diversity, biosynthesis, and ecology, while laying a robust foundation for exploring SM-mediated interactions within archaeal ecosystems. This research advances archaeal chemical and cell biology and holds promise for discovering bioactive SMs with potential applications in medicine, industry, and agriculture.