Genomic Adaptations to the Loss of a Conserved Bacterial DNA

ABSTRACT CcrM is an orphan DNAmethyltransferase nearly universally conserved in a vast group of Alphaproteobacteria. In Caulobacter crescentus, it controls the expression of key genes involved in the regulation of the cell cycle and cell division. Here, we demonstrate, using an experimental evolution approach, that C. crescentus can significantly compensate, through easily ac-cessible genetic changes like point mutations, the severe loss in fitness due to the absence of CcrM, quickly improving its growth rate and cell morphology in rich medium. By analyzing the compensatory mutations genome-wide in 12 clones sampled from independentccrM populations evolved for ~300 generations, we demonstrated that each of the twelve clones carried at least one mutation that potentially stimulated ftsZ expression, suggesting that the low intracellular levels of FtsZ are the major bur-den ofccrMmutants. In addition, we demonstrate that the phosphoenolpyruvate-carbohydrate phosphotransfer system (PTS) actually modulates ftsZ andmipZ transcription, uncovering a previously unsuspected link betweenmetabolic regulation and cell division in Alphaproteobacteria. We present evidence that point mutations found in genes encoding proteins of the PTS provide the strongest fitness advantage toccrM cells cultivated in rich medium despite being disadvantageous in minimal medium. This environmental sign epistasis might prevent suchmutations from getting fixed under changing natural conditions, adding a plausible explanation for the broad conservation of CcrM. IMPORTANCE In bacteria, DNAmethylation has a variety of functions, including the control of DNA replication and/or gene expression. The cell cycle-regulated DNAmethyltransferase CcrMmodulates the transcription of many genes and is critical fo