Upregulation of MetC Is Essential for d-Alanine-Independent Growth of an alr/dadX-Deficient Escherichia coli Strain

d-Alanine is a central component of the cell wall in most prokaryotes. d-Alanine synthesis in Escherichia coli is carried out by two different alanine racemases encoded by the alr and dadX genes. Deletion of alr and dadX from the E. coli genome results in a d-alanine auxotrophic phenotype. However, we have observed growth of prototrophic phenotypic revertants during routine culturing of a d-alanine auxotrophic strain. We present a detailed comparison of the proteome and transcriptome profiles of the d-alanine auxotroph and a prototrophic revertant strain. Most noticeably, a general upregulation of genes involved in methionine synthesis in the revertant strain was detected. The appearance of the revertant phenotype was genetically linked to point mutations in the methionine repressor gene (metJ). Our results reveal an alternative metabolic pathway which can supply essential d-alanine for peptidoglycan synthesis of alr- and dadX-deficient E. coli mutants and provide evidence for significant alanine racemase coactivity of the E. coli cystathionine beta-lyase (MetC).