Spirochetes are bacteria responsible for several serious diseases that include Lyme disease ( Borrelia burgdorferi), syphilis ( Treponema pallidum), leptospirosis ( Leptospira interrogans), and contribute to periodontal diseases ( Treponema denticola) 1 . These spirochetes employ an unusual form of flagella-based motility necessary for pathogenicity; indeed, spirochete flagella (periplasmic flagella, PFs) reside and rotate within the periplasmic space 2– 11 . The universal joint or hook that links the rotary motor to the filament is composed of approximately 120–130 FlgE proteins, which in spirochetes form an unusually stable, high-molecular weight complex (HMWC) 9, 12– 17 . In other bacteria, the hook can be readily dissociated by treatments such as heat 18 . In contrast, spirochete hooks are resistant to these treatments, and several lines of evidence indicate that the HMWC is the consequence of covalent cross-linking 12, 13, 17 . Here we show that T. denticola FlgE self-catalyzes an interpeptide cross-linking reaction between conserved lysine and cysteine resulting in the formation of an unusual lysinoalanine adduct that polymerizes the hook subunits. Lysinoalanine cross-links are not needed for flagellar assembly, but they are required for cell motility, and hence infection. The self-catalytic nature of FlgE cross-linking has important implications for protein engineering, and its sensitivity to chemical inhibitors provides a new avenue for the development of antimicrobials targeting spirochetes.