A novel rutin-␣-L-rhamnosidase hydrolyzing ␣-L-rhamnoside of rutin, naringin, and hesperidin was purified and characterized from Aspergillus niger DLFCC-90, and the gene encoding this enzyme, which is highly homologous to the ␣-amylase gene, was cloned and expressed in Pichia pastoris GS115. The novel enzyme was classified in glycoside-hydrolase (GH) family 13. ␣ -L-Rhamnosidase (EC 3.2.1.40) cleaves terminal ␣-L-rhamnose from a large number of natural products, such as flavonoids, saponins, and many other natural glycosides, and this enzyme has been used in the food industry for eliminating the naringin bitterness of citrus juices (4,20,25,26), removing hesperidin crystals from orange juices and releasing 7-O--D-glucoside-hesperetin, an important precursor in sweetener production (17,24), and enhancing wine aromas (7,6,22). In addition, the deglycosylation of flavonoids in vitro by ␣-L-rhamnosidase has ushered in a new era of drug development (5,8,19,27). Hitherto, ␣-L-rhamnosidases from fungi, bacteria, and animals have been purified and characterized (29), and several genes encoding ␣-Lrhamnosidases have also been cloned (1, 2, 3, 9, 16). Thus far, the ␣-L-rhamnosidases are categorized into four glycoside-hydrolase (GH) families, 28, 78, 106, and NC (nonclassified), in the CAZy (carbohydrate-active enzymes) database based on amino acid sequence similarities (10, 11).In this paper, a novel rutin-␣-L-rhamnosidase was purified and characterized from Aspergillus niger DLFCC-90, and the gene (rhaR) encoding this enzyme was also cloned and expressed in Pichia pastoris GS115.The strain A. niger DLFCC-90, obtained from the Culture Collection of Biotechnology Engineering of Dalian Polytechnic University (Dalian, China), was cultured with shaking at 28 to 30°C for 72 to 96 h in a wort medium of 5.0 Baume degrees containing 2% extract from flowers of Sophora japonica (Huai Hua in Chinese). To obtain pure enzyme, the cell-free culture was treated by a 3-step method, i.e., ammonium sulfate precipitation (75% saturation), a Sephadex G-75 column (Amersham Pharmacia) eluted with 0.02 M acetate buffer (pH 5.0), and a DEAE 52-cellulose column (Amersham Pharmacia) eluted with a linear gradient of KCl (0.0 to 0.5 M) in 0.02 M acetate buffer (pH 5.0). The determination of the protein concentration was performed as described in reference 13. The enzymatic activity was measured using 2.0 mg/ml rutin (Sigma) in 0.02 M acetate buffer (pH 5.0) as a substrate after a reaction at 50°C for 18 h, and products of rhamnose and isoquercitrin from the enzyme reaction were detected to calculate the enzyme activity (18, 28). After the above-described 3 steps of purification, the enzyme's specific activity was increased 5.3-fold. The purified enzyme migrated as a single band on the 12% SDS-PAGE gel (12) with an apparent molecular mass of about 66 kDa (Fig. 1A), which was similar to those for the previously reported ␣-L-rhamnosidase from Curvularia lunata (6) and naringinase from Aspergillus sojae (5). The 3-step-purified enzyme gave one major p...