To explore systemic effects of mutations in the UDP-N-acetylmuramoylalanyl-d-glutamate 2,6-diaminopimelate ligase (MurE) of Corynebacterium glutamicum, that leads to extracellular l-lysine accumulation by this bacterium. The analysis of a mutant cohort of C. glutamicum strains carrying all possible 20 amino acids at position 81 of MurE revealed unexpected effects on cellular properties. With increasing l-lysine accumulation the growth rate of the producing strain is reduced. A dynamic flux balance analysis including the flux over MurE fully supports this finding and suggests that further reductions at this flux control point would enhance l-lysine accumulation even further. The strain carrying the best MurE variant MurE-G81K produces 37 mM l-lysine with a yield of 0.17 g/g (l-lysine center dot HCl/glucose center dot H2O), bearing no other genetic modification. Interestingly, among the strains with high l-lysine titers, strain variants occur which, despite possessing the desired amino acid substitutions in MurE, have regained close to normal growth and correspondingly lower l-lysine accumulation. Genome analyses of such variants revealed the transposition of mobile genetic elements which apparently annulled the favorable consequences of the MurE mutations on l-lysine formation. MurE is an attractive target to achieve high l-lysine accumulation, and product formation is inversely related to the specific growth rate. Moreover, single point mutations leading to elevated l-lysine titers may cause systemic effects on different levels comprising also major genome modifications. The latter caused by the activity of mobile genetic elements, most likely due to the stress conditions being characteristic for microbial metabolite producers.