Genomic DNA is modified by chemical markers, which can change gene expression without altering the underlying genetic code. These so-called epigenetic tags (described in the videos) can also mark DNA to distinguish old strands from those that are freshly made, or can be used by the cell to identify foreign DNA. One of these epigenetic modifications is the addition of a methyl group to the DNA molecule; this methylation process is carried out by enzymes called methyltransferases. Different methyltransferase enzymes create different methyl tag patterns, and now scientists reporting in Nature Communications have learned more about linking methyltransferases to their methylation scheme.
If researchers attempt to introduce foreign DNA into an organism, such as when the genes required for manufacturing some important chemical are introduced into bacteria that are supposed to start making that chemical. Often, a host will reject this foreign DNA. The methylation patterns on the DNA molecule indicate that it's not native, and the host cell will destroy it. Bacteria that are commonly used in the lab, like E. coli, can usually withstand the introduction of foreign DNA and won't chop it up, but many other microbes will, impeding research.
"Knowing which enzyme does what opens up to a lot of applications. With this knowledge, you can construct model organisms with artificial methylomes, mimicking the methylation pattern of the strain you want to introduce DNA to. In this way you can ensure [the] survival of introduced DNA," said the first author of the study, Specialist Torbjørn Ølshøj Jensen of The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) at the Technical University of Denmark (TUM).
"Working in other bacteria than E. coli, you often have to do a lot of trial and error when it comes to DNA transformation, but that's just not good enough. You need knowledge and tools. With this, you have a systematic and rational way of fixing the problems," explained Jensen.
Working towards that goal, the researchers aimed to find what enzyme was creating which methylation pattern. They created circular strands of DNA (plasmids) that carried a methyltransferase gene. These were coupled with multiple copies of a specific DNA sequence, which were intended to be targets for the methyltransferase enzymes encoded by the plasmid. The team repeated this study for every methyltransferase.
The researchers could then observe the specific impact of individual methyltransferases by detecting the methyl groups on the target DNA sequences.
The scientists confirmed their results by assessing the genomes of two microbes used in manufacturing. Together, they carry 23 genes for methyltransferases, with twelve methylation patterns on their DNA. This suggested that not all their methyltrasnferases were at work, so the scientists looked for active methyltransferase genes in the bacterial genomes. After investigating the methylation patterns, they traced eleven of the twelve back to specific genes.
This work can help create clearly defined 'methylomes' that describe methylation patterns in hosts, and make adding foreign DNA to these hosts easier.