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At ASM, Pioneering Scientists Presented Bacterial Methylome Highlights

Thursday, May 22, 2014

This week’s annual meeting of the American Society for Microbiology was every bit as interesting, data-rich, and jam-packed as promised. We’re grateful to everyone who stopped by our booth and got to know more about Single Molecule, Real-Time (SMRT®) Sequencing.

Our favorite session, “Bacterial Methylomes,” took place on the last day of the conference and was organized by Rich Roberts, Nobel laureate and Chief Scientific Officer at New England Biolabs. The session highlighted several projects analyzing genome-wide methylation states of bacteria, a task which has been all but impossible due to the technical inability to detect such base modifications. As Roberts kicked off the event, he noted that until recently, most scientists avoided this area of study — until, he said, the PacBio® technology came along.

Because SMRT Sequencing can differentiate methylated bases from unmethylated ones as the polymerase processes the DNA strand, our platform can detect base modifications across an entire genome. In the past couple of years, the community has gone from the very first papers making use of this capability to many labs deploying this kind of data. At ASM, we got to see some cutting-edge work utilizing methylome data, often integrated with other kinds of ’omics information, to get a better understanding of bacterial strains.

Matthew Blow from the Joint Genome Institute spoke about the need to characterize genome-wide methylation in bacteria more thoroughly, along the lines of the studies that have been done in eukaryotes. With SMRT Sequencing’s ability to spot 4mC and 6mA, the most common types of methylation in bacteria, he said, “there’s no excuse for neglecting prokaryotic methylomes anymore.” JGI has sequenced some 300 bacterial methylomes, finding that almost all have detectable methyltransferase activity and many have novel specificities of methyltransferases. Blow noted that much of the evidence points to regulatory roles of methyltransferases in bacteria in addition to restriction modification functions, and additional studies are ongoing.

From the Icahn School of Medicine at Mount Sinai in New York City, Gang Fang and his student Shijia Zhu both gave talks. Fang spoke about the need to understand the diversity, complexity, and function of bacterial methylomes, noting that his lab has looked at de novo motif mapping and methyltransferase mapping. His team is also studying heterogeneity of methylation by comparing base modifications at the same site in different cells. Zhu presented results from integrating gene expression, transcription factor regulatory network, and other data sets. He is perturbing methyltransferases to look at the effect on global gene expression to determine whether that would explain differential expression seen among transcription factors.

Maria Hoffman from the US Food and Drug Administration spoke about methylome studies for various strains of Salmonella, one of the leading causes of foodborne illness. She said her team first used the PacBio platform to deliver a fully closed Salmonella genome in 2012, and that the instrument’s ability to detect modified bases has been critical as the group tries to figure out how methylation relates to outbreak transmission among strains. A study of methylomes across 30 Salmonella isolates found some motifs conserved across the species, as well as some serovar-specific motifs.

Another talk came from Scarlet Shell at Harvard School of Public Health. Her work focuses on Mycoplasma tuberculosis and how the organism responds to environmental stress. The team switched from originally using mass spec for methylation studies to SMRT Sequencing. In one project, they found that knocking out a particular methylase in the bacterium caused it to die faster in a hypoxic environment.

Juliane Krebes from Hannover Medical School presented on Helicobacter pylori, which has tremendous genetic diversity as well as a very high number of restriction modification systems. A comparison of H. pylori strains found that few recognition sites were shared across strains, suggesting there is not a large core methylome for this organism.

Finally, Richard Morgan from New England Biolabs spoke about new restriction modification systems known as type IIG, which are characterized by a specificity unit shared by both the endonuclease and the modification system. These type IIG systems have been underrepresented in traditional screening discovery, Morgan said, but they can be spotted by SMRT Sequencing. Because this type of system changes faster, studying it allows scientists to see evolution in action, he added.

It was really an honor to see so many compelling studies using SMRT Sequencing that offer progress in this exciting new area of science. Congratulations to all of the speakers on their fascinating work!

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