DNA adenine hypomethylation leads to metabolic rewiring in Deinococcus radiodurans

•DR_0643 from D. radiodurans encodes functional N-6 adenine-specific DNA methylase.•DR_0643 knockout mutant loses 60% DNA adenine methylation and is defective in growth.•DNA adenine hypomethylation de-represses expression of pyruvate dehydrogenase E1.•De-repression of pyruvate dehydrogenase E1 leads to metabolic rewiring.•Degradation of fatty acids and amino acids restores glycolysis–TCA cycle axis.

The protein encoded by DR_0643 gene from Deinococcus radiodurans was shown to be an active N-6 adenine-specific DNA methyltransferase (Dam). Deletion of corresponding protein reduced adenine methylation in the genome by 60% and resulted in slow-growth phenotype. Proteomic changes induced by DNA adenine hypomethylation were mapped by two-dimensional protein electrophoresis coupled with mass spectrometry. As compared to wild type D. radiodurans cells, at least 54 proteins were differentially expressed in Δdam mutant. Among these, 39 metabolic enzymes were differentially expressed in Δdam mutant. The most prominent change was DNA adenine hypomethylation induced de-repression of pyruvate dehydrogenase complex, E1 component (aceE) gene resulting in 10 fold increase in the abundance of corresponding protein. The observed differential expression profile of metabolic enzymes included increased abundance of enzymes involved in fatty acid and amino acid degradation to replenish acetyl Co-A and TCA cycle intermediates and diversion of phosphoenolpyruvate and pyruvate into amino acid biosynthesis, a metabolic rewiring attempt by Δdam mutant to restore energy generation via glycolysis–TCA cycle axis. This is the first report of DNA adenine hypomethylation mediated rewiring of metabolic pathways in prokaryotes.

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