title: 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.
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Scarlet S
authors.initials: SS
authors.lastname: Shell
authors.forename: Erin G
authors.initials: EG
authors.lastname: Prestwich
authors.forename: Seung-Hun
authors.initials: SH
authors.lastname: Baek
authors.forename: Rupal R
authors.initials: RR
authors.lastname: Shah
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Sassetti
authors.forename: Peter C
authors.initials: PC
authors.lastname: Dedon
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Fortune
mesh_terms: D000818:Animals; D058491:Bacterial Load; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D018387:Codon, Initiator; D019175:DNA Methylation; D004269:DNA, Bacterial / Q000378:metabolism*; D005260:Female; D017353:Gene Deletion; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D006801:Humans; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D008168:Lung / Q000382:microbiology; D051379:Mice; D008810:Mice, Inbred C57BL; D050296:Microbial Viability; D009169:Mycobacterium tuberculosis / Q000254:growth & development / Q000302:isolation & purification / Q000378:metabolism*; D017354:Point Mutation; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013312:Stress, Physiological; D013379:Substrate Specificity; D014376:Tuberculosis / Q000382:microbiology
chemical_list: D001426:Bacterial Proteins; D018387:Codon, Initiator; D004269:DNA, Bacterial; D007527:Isoenzymes; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)