BACKGROUND Whole-cell catalysis has been widely used because the steps of extracting pure enzyme are omitted and the cost would be greatly saved. However, the efficiency of the whole-cell catalyst can be limited by the existence of the cell membrane. In the present study, to enhance the binding between an intracellular enzyme and a substrate, ionic liquids (ILs) and deep eutectic solvents (DESs) were used to treat Escherichia coli BL21-pET21a-rhaB1 cells for isoquercitrin production by the biotransformation of rutin. RESULTS The whole-cell catalyst exhibited the highest catalytic activity with 6% choline chloride-urea (ChCl/U) after treatment with different concentrations. The ChCl/U-treated whole-cell catalyst was more stable than the crude rhaB1, because its optimum pH was closer to neutral and it demonstrated higher temperature tolerance. Under the best conditions of rutin concentration 0.05 g L-1, pH 6.5 and 40 degrees C, the isoquercitrin yield reached a maximum of 93.05 +/- 1.3%. Additionally, the whole-cell catalyst retained >52% enzyme activity after five repeated uses. CONCLUSION These results show that using ChCl/U to increase cell permeability improves the catalytic performance of the whole-cell catalyst of E. coli BL21-pET21a-rhaB1. This approach has promising potential for the utilization of natural flavonoids. (c) 2019 Society of Chemical Industry