Analyzing the role of DNA methylation in a bioremediation bacterium

Researchers studied the role of DNA methylation on gene expression and other processes in the heavy-metal reducing bacterium Shewanella oneidensis MR-1 with the help of next-generation Single-Molecule Real Time (SMRT) sequencers from Pacific Biosciences.

The study is thought to be the first to look at DNA methylation and gene expression in a wild-type bacterium. The findings suggest all Shewanella microbes, and many members of the Gammaproteobacteria family, use DNA methylation to regulate genome replication.

DNA methylation is a common signaling tool cells use to tell genes if they should be "on" or "off." However, its role is poorly understood for the vast majority of prokaryotes and needs to be characterized. In the study published online ahead of print August 30, 2013 in the Journal of Bacteriology, DOE JGI researchers used next-generation sequencers from Pacific Biosciences to gain insights into the role of DNA methylation in Shewanella bacteria.

Shewanella bacteria grow naturally almost everywhere and play key roles in global carbon and nitrogen cycles. They are also major microbial players in cleaning up environments contaminated with toxic metals and radioactive waste, and are capable of using contaminants such as uranium, chromium and technetium as energy sources and then expelling them in a less toxic form. For example, S. oneidensis is capable of breaking down carbon tetrachloride, a drinking water contaminant. Their potentials for multiple biogeochemical applications are the reason the DOE Joint Genome Institute has sequenced several Shewanella strains to date.

The team relied on PacBio instruments for their study because these sequencers can automatically detect DNA base modifications without altering the DNA, affording researchers more insights into biological functions. They identified methylated sites within the bacterium's genome and also measured the DNA methylation levels in cultures grown under various conditions. Their results indicated that DNA methylation regulates a number of processes in S. oneidensis MR-1, including genome replication and DNA mismatch repair. Additionally, they reported that "while methylation may impact the expression of a few genes, our data suggest that methylation does not play a large and direct role in regulating gene expression in S. oneidensis MR-1, at least not under the conditions we tested."