The precursor of aqualysin I, a subtilisin-type protease secreted by Thermus aquaticus, consists of four domains, an N-terminal signal sequence, an N-terminal pro-sequence, a protease domain, and a C-terminal pro-sequence. A non-covalent N-terminal pro-sequence facilitates the production of active aqualsin I, when the C-terminal pro-sequence is deleted. The role of the C-terminal pro-sequence in protein secretion was analyzed using a Saccharomyces cerevisiae expression system. Deletion of the C-terminal pro-sequence resulted in increased secretion of aqualysin I, i.e., about three times as much as that in the case of the wild type. In the case of the wild-type precursor, non-secreted aqualysin I with the C-terminal pro-sequence was retained in the endoplasmic reticulum in an inactive form, suggesting that the C-terminal pro-sequence prevents the protease domain from taking on a properly folded structure, unlike the N-terminal pro-sequence.