The effect of polypeptide fractions of proteose peptone on the induction of cloned gene expression of rice alpha-amylase in recombinant Yarrowia lipolytica which is under the control of its XPR2 promoter, was studied. Gel-filtration chromatography with Sephacryl S-100 and Sephadex G-25 (coarse) gels was used to fractionate the active polypeptide fractions from the proteose peptone. The polypeptide size fractions that were effective for the induction of cloned gene expression ranged between mol wt of 1.0 and 6.0 kDa. The fed-batch culture experiments with active polypeptide fractions were performed in a 6-L fermenter. The specific productivity of alpha-amylase and the enzyme yield based on nitrogen source increased from 25.7 to 33.0 U/g cell.h and 4.96 to 6.73 U/(mg nitrogen consumed), respectively, when proteose peptone was replaced by active polypeptide fractions in production medium. The specific productivity of alpha-amylase and the enzyme yield further improved to 36.2 U/g cell.h and 8.14 U/(mg nitrogen consumed), respectively, when the glutamic acid-enriched active polypeptide fractions in the production medium was used. The specific productivity of alpha-amylase and the enzyme yield were improved by 41 and 64%, respectively, as compared with the results obtained with the medium containing proteose peptone. Through medium design, a bioprocess strategy for heterologous protein production was developed and a significant productivity improvement achieved.