Scientists develop new technique for analyzing the epigenetics of bacteria

June 15, 2015
Helicobacter pylori
Histopathology of Helicobacter pylori infection in a gastric foveolar pit demonstrated in endoscopic gastric biopsy. Credit: Wikipedia.

Scientists from the Icahn School of Medicine at Mount Sinai have developed a new technique to more precisely analyze bacterial populations, to reveal epigenetic mechanisms that can drive virulence. The new methods hold the promise of a potent new tool to offset the growing challenge of antibiotic resistance by bacterial pathogens. The research was published today in the journal Nature Communications, and conducted in collaboration with New York University Langone Medical Center and Brigham and Women's Hospital of Harvard Medical School.

The information content of the genetic code in DNA is not limited to the primary nucleotide sequence of A's, G's, C's and T's. Individual DNA bases can be chemically modified, with significant functional consequences. In the bacterial kingdom, the most prevalent base modifications are in the form of DNA methylations, specifically to adenine and cytosine residuals. Beyond their participation in host defense, increasing evidence suggests that these modifications also play important roles in the regulation of gene expression, virulence and antibiotic resistance.

The research team employed the PacBio RS II system from Pacific Biosciences, which can collect data on base modifications simultaneously as it collects DNA sequence data. PacBio's single molecule, real-time sequencing enables the detection of N6-methyladenine and 4-methylcytosine, two major types of DNA modifications comprising the bacterial methylome. However, existing methods for studying bacterial methylomes rely on a population-level consensus that lack the single-cell resolution required to observe epigenetic heterogeneity.

'We created a technique for the detection and phasing of DNA methylation at the single molecule level. We found that a typical clonal bacterial population that would otherwise be considered homogeneous using conventional techniques has epigenetically distinct subpopulations with different gene expression patterns' said Gang Fang, Ph.D., assistant professor of genetics and genomics at the Icahn School of Medicine at Mount Sinai and senior author of the study. 'Given that phenotypic heterogeneity within a bacterial population can increase its advantage of survival under stress conditions such as antibiotic treatment, this new technique is quite promising for future treatment of bacterial pathogens, as it enables de novo detection and characterization of epigenetic heterogeneity in a bacterial population.'

The researchers studied seven bacterial strains, demonstrating the new technique reveals distinct types of epigenetic heterogeneity. For Helicobacter pylori, a pathogenic bacterium that colonizes over 40 percent of the world population and is associated with gastric cancer, the team discovered that epigenetic heterogeneity can quickly emerge as a single cell divides, and different subpopulations with distinct methylation patterns have distinct gene expressions patterns. This may have contributed to the increasing rate of of Helicobacter pylori.

'The application of this will enable a more comprehensive characterization of the functions of DNA methylation and their impact on bacterial physiology. Resolving nucleotide modifications at the single molecule, single nucleotide level, especially when integrated with other single molecule- or single cell-level data, such as RNA and protein expression, will help resolve regulatory relationships that govern higher order phenotypes such as drug resistance' said Eric Schadt, Ph.D., founding director of the Icahn Institute and professor of genomics at the Icahn School of Medicine at Mount Sinai. 'The approach we developed can also be used to analyze DNA viruses and human mitochondrial DNA, both of which present significant epigenetic heterogeneity.'

Explore further: Genome-wide methylation map of disease-causing E. coli reveals surprises

More information: John Beaulaurier, Xue-Song Zhang, Shijia Zhu, Robert Sebra, Chaggai Rosenbluh, Gintaras Deikus, Nan Shen, Diana Munera, Matthew K. Waldor, Andrew Chess, Martin J. Blaser, Eric E. Schadt, and Gang Fang. 'Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.' Nature Communications. DOI: 10.1038/ncomms8438

Related Stories

Genetic guides to epigenetics

February 10, 2015

Dirk Schübeler and his group at the Friedrich Miescher Institute for Biomedical Research (FMI) identify determinants that set epigenetic marks along the genome. The new study, published in Nature, shows that genetic activity ...

Recommended for you

Finding a lethal parasite's vulnerabilities

December 15, 2017

An estimated 100 million people around the world are infected with Strongyloides stercoralis, a parasitic nematode, yet it's likely that many don't know it. The infection can persist for years, usually only causing mild symptoms. ...

1 comment

Adjust slider to filter visible comments by rank

Display comments: newest first

JVK
1 / 5 (1) Jun 29, 2015
Journal article excerpt:

"...applicable outside the bacterial kingdom, such as in the analysis of human mitochondrial
DNA or DNA viruses..."

The link from virus-induced entropic elasticity and the anti-entropic epigenetic effects of nutrients is clear. It's the nutrient-dependent production of pheromones that control the physiology of reproduction in species from microbes to humans.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.