The evolution of archaeal flagellar filaments

Eukaryotes, archaea, and bacteria each independently evolved flagellar-based motility systems allowing cells to swim in solution. The two prokaryotic flagellar systems involve the motor-driven rotation of supercoiled flagellar filaments, which function as propellers providing the thrust needed to swim. Despite being unrelated to each other, archaeal and bacterial flagellar filaments have convergently evolved to form similar supercoils with pitches around 1 to 2.5 µm and diameters around 0.2 to 0.6 µm. The recent discovery of 11 protofilament states in the supercoiled bacterial flagella and 10 in archaeal flagella [Kreutzberger et al., Cell (2022)] further highlights the analogous mechanism of supercoiling shared by these two structures. It is known that archaeal flagellar filaments are homologous to archaeal type IV pili (T4P), and the N-terminal domains in these archaeal T4P and flagellar filaments are homologous to the N-terminal domains in bacterial T4P. However, the features which distinguish archaeal flagellar filaments from archaeal T4P remained unclear. Here, we report several new structures of archaeal T4Ps and archaeal flagellar filaments and compare these with existing structures. We find that archaeal T4Ps have highly variable symmetries with nearly all of their helical twists varying by about 1-5 degrees and having either 7 or no protofilaments. All archaeal flagellar filament structures have helical twists within ∼0.2 degrees of each other and have 10 protofilaments. Strikingly, one of our new structures from Pyrobaculum calidifontis is of a flagellar-like filament with a pilin-like sequence which has a symmetry most similar to archaeal flagellar filaments assembling into a 10-protofilament structure. This provides the basis for proposing that archaeal flagellar filaments arose from such P.calidifontis-like T4P with symmetries very similar to those of the extant archaeal flagellar filaments, with supercoiled structures arising following the emergence of the filaments with 10 protofilaments.