Streptococcus pneumoniae synchronizes the states of cell wall peptidoglycan acetylation and genome methylation by programmed DNA inversions

Bacterial cell wall peptidoglycan (PG) consists of alternating β-(1,4) linked N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG). The C-6 hydroxyl group of NAM is acetylated by transmembrane O-acetyltransferases post PG biosynthesis in many pathogenic bacteria. This modification is important for bacterial resistance to lysozyme. It is also known that the extent of NAM O-acetylation varies greatly, depending on genetic background and growth phase. However, it remains unclear if the fluctuation of NAM O-acetylation has any function. In this study, we show that NAM O-acetylation functions as a potential extracellular signal of cellular metabolism for epigenetic response to nutrient conditions in human pathogen Streptococcus pneumoniae (pneumococcus). The O-acetylation was found to control reversible switch between opaque and transparent colony phases by modulating inversion reactions of DNA methyltransferase hsdS genes in the colony opacity determinant (cod) locus, and thereby phase-defining genome methylation pattern. The NAM O-acetylation made S. pneumoniae adopt the HsdSA1 methylome and opaque colony phase, whereas the lack of this modification favored the HsdSA3 methylome and transparent colony phenotype. Further analysis revealed that the major autolysin LytA and multiple other proteins are required for the O-acetylation-dependent control of epigenetic machinery. Lastly, the extent of NAM O-acetylation was found to correlate with the cellular level of the acetyl donor acetyl-CoA and glucose. These data support the postulation that S. pneumoniae uses NAM O-acetylation as an extracellular marker of cellular acetyl-CoA to synchronize nutrient availability with bacterial lifestyle by epigenetic modulation of cellular metabolism.