Effect of ldhA gene deletion on the metabolism of Escherichia coli based on gene expression, enzyme activities, intracellular metabolite concentrations, and metabolic flux distribution

Abstract

To investigate how the central metabolism of Escherichia coli changes with the deletion of ldhA (lactate dehydrogenase gene), an integrated study was made by combining the information of cultivation characteristics, gene expressions, enzyme activities, intracellular metabolite concentrations, and metabolic flux distribution. The deletion of ldhA gene reduced the specific growth rate and the specific glucose consumption rate. The production rates of acetate, ethanol, and formate were all higher for the ldhA mutant as compared with those of the parent strain. The anaplerotic enzyme phosphoenol pyruvate carboxylase (Ppc), which is also known to be contributed to catabolic succinate formation under anaerobic condition, was downregulated in the ldhA mutant compared to the parent strain. On the other hand, phosphoenol pyruvate carboxykinase (Pck) that catalyzes the opposite reaction to Ppc was upregulated significantly in the mutant. This was mainly due to the shortage of phosphoenol pyruvate (PEP) in the ldhA mutant as was evidenced by the measurement of intracellular PEP concentration. Interestingly, two other catabolic enzymes, NAD +- and NADP +-specific malic enzymes, were both shown to be present in the parent E. coli but regulated differently in ldhA mutant. The activity of NADP +-specific malic enzyme encoded by maeB remained unchanged, whereas NAD +-specific malic enzyme encoded by sfcA was found to be upregulated significantly in the ldhA mutant compared to those in the parent strain implying that the inactivation of ldhA gene leads to the production of malate from pyruvate. Moreover, it was found that ldhA gene deletion induced a stress response as was evidenced by the significant upregulation of the genes dnaJ, grpE, groS, and fkpA involved in the heat shock response.