DNA Methylation Impacts Gene Expression and Ensures Hypoxic Survival of Mycobacterium tuberculosis

Abstract

DNA methylation regulates gene expression in many organisms. In eukaryotes, DNA methylation is associated with gene repression, while it exerts both activating and repressive effects in the Proteobacteria through largely locus-specific mechanisms. Here, we identify a critical DNA methyltransferase in M. tuberculosis, which we term MamA. MamA creates N6-methyladenine in a six base pair recognition sequence present in approximately 2,000 copies on each strand of the genome. Loss of MamA reduces the expression of a number of genes. Each has a MamA site located at a conserved position relative to the sigma factor −10 binding site and transcriptional start site, suggesting that MamA modulates their expression through a shared, not locus-specific, mechanism. While strains lacking MamA grow normally in vitro, they are attenuated in hypoxic conditions, suggesting that methylation promotes survival in discrete host microenvironments. Interestingly, we demonstrate strikingly different patterns of DNA methyltransferase activity in different lineages of M. tuberculosis, which have been associated with preferences for distinct host environments and different disease courses in humans. Thus, MamA is the major functional adenine methyltransferase in M. tuberculosis strains of the Euro-American lineage while strains of the Beijing lineage harbor a point mutation that largely inactivates MamA but possess a second functional DNA methyltransferase. Our results indicate that MamA influences gene expression in M. tuberculosis and plays an important but strain-specific role in fitness during hypoxia.

Essential roles of methionine and S -adenosylmethionine in the autarkic lifestyle of Mycobacterium tuberculosis

“…SMRT-sequencing records the replication of individual DNA molecules and can detect methylation through a characteristic slowdown of the polymerase at methylated sites (22). The results supported previous data showing that only a single DNA methylase is active in H37Rv [Rv3263, which methylates the adenines in CTGGAG/CACCAG to form N6-methyladenine (23)]. The interpulse duration (IPD) ratio (Methods) represents the proportion of molecules in a population that are methylated at each site (24), and the mean IPD ratio summarizes this value across the genome.…”

Genomic Characterization of a Pattern D Streptococcus pyogenes emm53 Isolate Reveals a Genetic Rationale for Invasive Skin Tropicity

“…In addition to genetic factors, it should also be noted that epigenetic factors may also play important roles in fitness and pathogenesis. The influence of DNA adenine methylation on virulence has been demonstrated for various pathogens, including Vibrio cholerae (45), Salmonella enterica (46), Yersinia pestis (47), and Mycobacterium tuberculosis (48). The methylation of DNA at specific sites may exert influences through the regulation of chromosome replication, transcriptional regulation, and mismatch repair in response to various environmental stimuli (49,50).…”

WhiB7, an Fe-S-dependent Transcription Factor That Activates Species-specific Repertoires of Drug Resistance Determinants in Actinobacteria

“…Although WhiB7 recognizes an AT-rich motif, recognition sequences for other Wbl proteins are not defined. In the case of WhiB7, there is evidence that other regulators are involved (9,60).…”