Previous analysis of a Corynebacterium glutamicum Delta mtrAB mutant showed that the MtrAB two-component signal transduction system influences the expression of genes involved in cell wall metabolism or osmoregulation, but it remained unknown whether this influence is direct or indirect. In order to identify the direct target genes of the response regulator MtrA, chromatin immunoprecipitation as a genome-wide approach and DNA affinity chromatography as a gene-specific approach were used. The results indicate that mepA and nlpC, both encoding putative cell wall peptidases, are directly repressed by MtrA, whereas proP and betP, both encoding carriers for compatible solutes, are directly activated by MtrA.