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

Date Published: July 4, 2013

Publisher: Public Library of Science

Author(s): Scarlet S. Shell, Erin G. Prestwich, Seung-Hun Baek, Rupal R. Shah, Christopher M. Sassetti, Peter C. Dedon, Sarah M. Fortune, William R. Bishai.

http://doi.org/10.1371/journal.ppat.1003419

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.

Partial Text

Mycobacterium tuberculosis is a pathogen of tremendous global significance, causing 9 million cases of tuberculosis annually and latently infecting up to a third of the world’s population [1]. Untreated, M. tuberculosis can persist for decades in the infected host. Over such timescales, the bacterium must tune gene expression patterns to match conditions in the host environment, including hypoxia, nutrient deprivation, and low pH, and maintain these adaptations over long periods of time.

In this work we demonstrate that Rv3263 encodes an adenine methyltransferase, MamA, which is responsible for all detectable DNA methylation in the Euro-American lineage strain of M. tuberculosis, H37Rv. By deleting mamA, we show that in M. tuberculosis, adenine methylation alters gene expression. Furthermore, mamA is required for optimal bacterial survival in a hypoxic environment. The expression changes mediated by MamA appear subtle in the bulk assays we used. One possible explanation is that methylation may direct greater expression differences in a subpopulation of cells. Single-cell methods will be required to explore this possibility and to determine whether DNA methylation allows heritable (epigenetic) regulation of gene expression in M. tuberculosis.

 

Source:

http://doi.org/10.1371/journal.ppat.1003419

 

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