Recombinant alkaline polygalacturonate lyase (PGL) production by recombinant Pichia pastoris GS115 was selected as a model to study as a continuous culture strategy for enhancing heterologous protein production based on controlling methanol feeding (CCCM culture) or on dual carbon source feeding (CCCD culture). Using the CCCM process with a dry cell weight of 75 g/L regulated by controlling methanol concentration in the induction media, the final PGL activity was 441.9 U/mL. The PGL productivity (Q(v)) and the average specific enzyme production rate (Q(x)) were 4.65 U mL(-1) h(-1) and 84.5 U g(-1) 11(-1), an increase of 42.1% and 191.2%, respectively, over what was achieved with traditional fed-batch culture with high cell density. The control strategies also reduced proteolytic degradation by 84.1% in the fermentation broth and increased cell viability by 12.2%. (C) 2012 Elsevier Ltd. All rights reserved.