The membrane-bound H+-ATPase plays a key role in free-energy transduction of biological systems. We report how the carbon and energy metabolism of Escherichia coli changes in response to deletion of the atp operon that encodes this enzyme. Compared with the isogenic wild-type strain, the growth rate and growth yield were decreased less than expected for a shift from oxidative phosphorylation to glycolysis alone as a source of ATP. Moreover, the respiration rate of a atp deletion strain was increased by 40% compared with the wild-type strain. This result is surprising, since the atp deletion strain is not able to utilize the resulting proton motive force for ATP synthesis. Indeed, the ratio of ATP concentration to ADP concentration was decreased from 19 in the wild type to 7 in the atp mutant, and the membrane potential of the atp deletion strain was increased by 20%o, confirming that the respiration rate was not controlled by the magnitude of the opposing membrane potential. The level of type b cytochromes in the mutant cells was 80%o higher than the level in the wild-type cells, suggesting that the increased respiration was caused by an increase in the expression of the respiratory genes. The atp deletion strain produced twice as much by-product (acetate) and exhibited increased flow through the tricarboxylic acid cycle and the glycolytic pathway. These three changes all lead to an increase in substrate level phosphorylation; the first two changes also lead to increased production of reducing equivalents. We interpret these data as indicating that E. colh makes use of its ability to respire even if it cannot directly couple this ability to ATP synthesis; by respiring away excess reducing equivalents E. coli enhances substrate level ATP synthesis.The membrane-bound ATP synthase of Escherichia coli has a central role in free-energy transduction under aerobic and anaerobic growth conditions. Under aerobic conditions, the proton motive force generated by the respiratory chain is utilized by the ATP synthase to drive ATP synthesis and to maintain solute gradients. Under anaerobic conditions, the proton motive force can be generated by the ATP synthase through hydrolysis of ATP. The atp operon, which encodes the ATP synthase, consists of nine genes in the following order: atpIBEFHAGDC (12,19,20). atpI encodes a 14-kDa protein of unknown function and has been shown to be dispensable (28). atpBEF encodes the three subunits that form the membrane-integrated Fo part (the proton channel), whereas atpHAGDC encodes the five subunits that form the cytoplasmic F, part (the ATPase) (12,20).von Meyenburg et al. (27) analyzed the growth of strains that lack an intact ATP synthase. These strains are not able to grow on nonfermentative carbon sources, such as acetate or succinate. The growth rate and growth yield in aerobic minimal glucose medium were reduced to 75 and 55% of the wild-type levels, respectively. Mutant strains with Tn1O insertions in the promoter region of the atp operon also exhibited a reduced growth yield that ...