Potato proteinase inhibitor II (PI-2) is composed of two sequence repeats. It contains two reactive site domains. We developed an improved protocol for the production of PI-2 using the yeast Pichia pastoris as the expression host. We then assessed the role of its two reactive sites in the inhibition of trypsin and chymotrypsin by mutating each of the two reactive sites in various ways. From these studies it appears that the second reactive site strongly inhibits both trypsin (K i 0.4 nm) and chymotrypsin (K i 0.9 nm), and is quite robust towards mutations at positions P2 or P1H . In contrast, the first reactive site inhibits only chymotrypsin (K i 2 nm), and this activity is very sensitive to mutations. Remarkably, replacing the reactive site amino acids of domain I with those of domain II did not result in inhibitory activities similar to domain II. The fitness for protein engineering of each domain is discussed.Keywords: mutational analysis; Pichia pastoris; serine proteinase inhibitor; Solanum tuberosum.Protease inhibitors are abundant proteins in the storage organs and seeds of plants [1]. In addition, their synthesis is induced to high levels in response to stress, infection and wounding [2]. Potato expresses many different proteinase inhibitors belonging to a wide range of inhibitor families. Members of the potato proteinase inhibitor II (PI-2) family have been shown to inhibit serine proteases, such as trypsin, chymotrypsin, subtilisin, oryzin and elastase [3,4]. Until now, they have been found only among the Solanaceae. Proteins and messenger RNAs have been identified in potato tubers [5,6], wounded tomato and tobacco leaves [4,7], eggplant fruits [8], green tomatoes [9] and ornamental tobacco flower stigma [10]. There is medical interest in the properties of PI-2. It has been shown to have anticarcinogenic properties, protecting mouse embryo fibroblasts from radiation-induced transformation [11]. Although the mechanism underlying this effect is poorly understood, it is correlated to the capacity of PI-2 to inhibit chymotrypsin-like enzymes [12].Plant protease inhibitors such as PI-2 have been proposed to function as part of the plant defense system [13]. The plant defense role is deduced from observations that proteinase inhibitors in leaves are synthesized in response to wounding [2,14,15] or viral infection [2,16]. In addition, direct evidence for a protective role has been obtained; it was shown that transgenic tobacco plants over-expressing potato PI-2 gained resistance against the tobacco hornworm Manduca sexta [17]. Also, when the PI-2 gene was introduced into rice under its own wound-inducible promoter, plants were protected from the major lepidopteran rice pest, Sesamia inferens [18]. PI-2 probably acts by inhibiting digestive proteases from the insects, thereby restricting the availability of amino acids [13].The anti-nutrient activity of PI-2 has been shown to be overcome by pest insects like Spodoptera exigua [19]. When these larvae are reared on tobacco leaves expressing potato PI-2, the spe...