Purification and characterization of an arginyl peptidase from the chloroplast stroma of pea seedlings

Stromal extract of pea (Pisum sativum var. Alaska) chloroplasts was fractionated by column chromatography, using the cleavage of benzoyl-arginine p-nitroanilide (BAPNA) as an assay for peptidase activity. We purified an arginyl peptidase 168-fold, with a yield of 37%. SDS-PAGE of the purified fraction revealed a major band of 79 kDa and a fainter one of 41 kDa. N-terminal amino-acid sequencing identified the smaller protein as aldolase, while the N-terminus of the larger protein was blocked. Activity assay identified the larger protein as the active peptidase. Fractionation of the peptidase on a sizing column suggested a size of 188 kDa for the native protein. Only Arg-containing peptides were cleaved by the peptidase, and it was found most sensitive to the inhibitors 3,4-dichloroisocoumarin and antipain. This peptidase could not cleave stromal or thylakoid proteins, suggesting that its activity is limited to later stages of the protein degradation process in chloroplasts, in which short peptides are further cleaved to ultimately yield free amino acids.