Diversification and functional expansion of archaeal TFF machineries

Archaea have several cell surface structures that belong to the type 4 filament (TFF) superfamily. What all have in common is the presence of core minimal assembly systems consisting of an ATPase, a platform protein, a filament forming protein and a class III signal peptidase. Here we generated novel MacSyFinder2 models to identify and classify archaeal TFF systems. Our analysis revealed a vast diversity of archaeal TFF with several members harboring one or more TFF assembly machineries. Structure-based phylogenetic analyses revealed that the variable N-terminal domain of TFF-related ATPases reflects the subsystem clustering. This indicates a diversification of the core machinery components within the archaeal secretion ATPase family driven through structural innovation. Genome-wide screening of SP-III containing proteins revealed the widespread presence of substrate binding proteins with SPIII. We hypothesize that these binding proteins with canonical SPIII cleavage sites are used to functionalize TFF machineries for efficient substrate scavenging, expanding the functional repertoire of archaeal TFF systems beyond currently characterized roles. Author SummaryThe type IV filament superfamily (TFF) comprises a broad group of surface structures that are widespread across both Archaea and Bacteria. While most well-characterized members originate from bacteria, only a limited number of archaeal TFF systems have been experimentally studied so far. Here, we expand the known diversity of archaeal TFF loci through bioinformatic and comparative genomic analyses. Our results show that these systems are far more diverse and versatile than previously appreciated, often exhibiting specialized functions. The structural diversification of the ATPase machinery likely played a key role in driving the functional diversification of TFF systems in Archaea. Overall, these findings deepen our understanding of how archaea adapt and persist in diverse environments, highlighting their surface structures as essential tools for communication, adhesion, and nutrient acquisition.