A three-compartment structured model is proposed for simulating batch cultivation of growth, substrate utilization and intracellular EcoRI endonuclease production by E. coli 294, an overproducing recombinant strain containing plasmid pPG430. Model development and verification are based on the dynamic changes in biomass formation and production of intracellular components such as total protein, total RNA, plasmid DNA and EcoRI endonuclease in supplemented minimal media with glucose as the carbon source. The three compartment model presented here has potential for evolutionary modelling work because of its simplicity and can easily be applied to other recombinant microorganisms and to industrial fermentations using complex media. (C) 2001 Published by Elsevier Science Ltd. All rights reserved.