DNA methylation by DNA methyltransferases (MTases) is an epigenetic strategy for gene regulation that has been detected in all domains of life. However, detailed studies of MTases have been performed in very few bacterial species, and the targets and cellular roles for a majority of bacterial MTases-an extremely diverse family of enzymes with representatives in almost all sequenced bacteria-remain completely uncharacterized. Furthermore, studies of the roles of MTases genome-wide are rare, and we lack any systematic understanding of the regulatory contributions of these enzymes. In this study, I propose comprehensive analyses of the extent and consequences of DNA methylation in the cholera pathogen, Vibrio cholerae, a genetically tractable bacterial species that encodes a diverse subset of the MTases found in the bacterial kingdom. Until recently, such methylome analyses were not technically feasible;however, the advent of single molecule real time (SMRT) DNA sequencing enables quantitative genome-wide mapping of methylation sites in bacteria. Comparative methylome and transcriptomic analyses, using wt and MTase-deficient V. cholerae grown under a variety of conditions, will be used to define the extent to which methylation varies in response to environmental conditions (a largely unexplored question to date) and the overall impact of such methylation on gene expression. My preliminary analyses have already demonstrated that V. cholerae encodes two MTases, HsdM and VCA0198, that have notable effects upon bacterial gene expression and growth. Planned mechanistic analyses focused on individual regulated genes will define the means by which such methylation governs gene expression, including identification of methyladenine and methylcytosine-sensitive DNA binding proteins. In particular, I plan to i) determine the mechanisms of HsdM-mediated repression of gene expression, ii) interrogate the role of 5mC in the growth and environmental adaptation of V. cholerae, and iii) identify and characterize the effects of novel methylation sensitive DNA-binding proteins on gene expression. Overall, this work will help decipher the epigenetic roles and molecular mechanisms behind methylation mediated gene regulation. This work will likely be extrapolateable to other species, and thus will provide us with a deeper understanding of how DNA methylation functions as a universal mechanism for regulating cellular processes across the bacterial kingdom.

Public Health Relevance

We have used a revolutionary new DNA sequencing approach to decipher the complete set of methylated bases in the genome of the cholera pathogen. The fundamental aim of the proposed studies is to define the mechanisms by which DNA methylation controls cell processes in this important human pathogen. These studies will expand our knowledge of how bacterial pathogens utilize DNA methylation to regulate gene expression and virulence, and may lead to new approaches for novel therapeutics for cholera.

Agency
National Institute of Health (NIH)
Type
Postdoctoral Individual National Research Service Award (F32)
Project #
5F32GM108355-02
Application #
8680035
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Hoodbhoy, Tanya
Project Start
Project End
Budget Start
Budget End
Support Year
2
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Brigham and Women's Hospital
Department
Type
DUNS #
City
Boston
State
MA
Country
United States
Zip Code
02115
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Möll, Andrea; Dörr, Tobias; Alvarez, Laura et al. (2014) Cell separation in Vibrio cholerae is mediated by a single amidase whose action is modulated by two nonredundant activators. J Bacteriol 196:3937-48
Pritchard, Justin R; Chao, Michael C; Abel, Sören et al. (2014) ARTIST: high-resolution genome-wide assessment of fitness using transposon-insertion sequencing. PLoS Genet 10:e1004782
Chao, Michael C; Pritchard, Justin R; Zhang, Yanjia J et al. (2013) High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data. Nucleic Acids Res 41:9033-48