Cardosins are model plant aspartic proteases, a group of proteases that are involved in cell death events associated with plant senescence and stress responses. They are synthesized as single-chain zymogens, and subsequent conversion into two-chain mature enzymes is a crucial step in the regulation of their activity. Here we describe the activation and proteolytic processing of recombinant procardosin A. The cleavage sites involved in this multi-step autocatalytic process were determined, some of them using a novel method for C-terminal sequence analysis. Even though the two-chain recombinant enzyme displayed similar properties as natural cardosin A, a single-chain mutant form was engineered based on the processing results and produced in Escherichia coli. Determination of its primary specificity using two combinatorial peptide libraries revealed that this mutant form behaved like the natural enzyme. The primary specificity of the enzyme closely resembles those of cathepsin D and plasmepsins, suggesting that cardosin A shares the same peptide scissile bond preferences of its vacuolar/lysosomal mammalian and protozoan homologues.Sequencing of the Arabidopsis genome unveiled over 50 genes coding for aspartic proteases of the pepsin type (1, 2). These genes have been assigned to three different categories: typical, nucellin-like, and atypical proteases (2). With the exception of the products of cnd41 (3-5) and cdr1 (6) genes, very little is known about the nucellin and the atypical subgroups. In fact, most of the knowledge acquired during the last decade relates to the typical subgroup of plant aspartic proteases and has been generated predominantly from the study of phytepsin from barley seeds and cardosins from the flowers of cardoon (7).Typical plant aspartic proteases constitute a set of enzymes that share many structural and functional features not only among them but also with some of their mammalian and microbial homologues. They display activity at acidic pH and are inhibited by pepstatin A, a natural hexapeptide from Streptomyces. Common features also include the overall three-dimensional structure of mature enzymes, the catalytic apparatus, and a conserved DT/SG motif. A distinguishing feature of typical plant aspartic proteases is the occurrence of an extra 100-amino acid-long internal segment, known as the plant-specific insert (PSI), in the sequence of their precursors. This domain displays structural and functional similarities to saposins (8, 9), sphingolipid-activating proteins from animals, and some antimicrobial peptides such as NK-lysin, granulysin, and amoebapores (10); it folds as an independent domain in the precursor form (11) and is subsequently excised to generate the mature two-chain form (7). Even though the function of PSI 1 is not yet fully elucidated, it seems to play an important role in targeting plant aspartic protease precursors to the vacuole (11,12).Little is known regarding the function of typical plant aspartic proteases. Colocalization studies with putative substrates and thei...