How a University of Tokyo Team is Rapidly Advancing Bacterial Genome Evolution in the Lab

The structure of genomes—the way genes are organized within DNA—is vital to how organisms function. Researchers at the University of Tokyo have developed a method to speed up changes in bacterial genomes by focusing on small “jumping genes,” known as insertion sequences.

“Most of our knowledge about evolution comes from the past. Some events, like the rise of mitochondria, leave few clues behind, making them tough to study. Our research fills this gap by fast-tracking genome evolution in bacteria, so we can observe large changes directly.”

Yuki Kanai, University of Tokyo

Bacterial genomes are a popular focus for research because they are small and consistent, making it easier to study changes in physiology and evolution. Insertion sequences have the ability to “jump” around the genome, driving significant evolutionary changes. These changes can lead to mutations that modify the genome’s size or identity.

Normally, the evolution of these sequences occurs slowly, often just once a year in organisms like Escherichia coli (E. coli), a model organism in microbiology. Kanai and his team introduced multiple copies of highly active insertion sequences into E. coli to accelerate this process.

Their method was inspired by collaboration with researchers studying insect evolution. Some bacteria associated with insects have much smaller genomes containing many jumping genes called transposons. These transposons can cut and rearrange DNA, prompting the team to consider if they could mimic this rapid reshuffling in lab settings.

In their experiments, they observed that the bacteria accumulated significant DNA changes—about 25 new insertions and variations in genome size—within just ten weeks. This is astonishingly rapid compared to the natural timeline, where such changes could take decades. Their findings showed that frequent small deletions and occasional large duplications paint a more complex picture of genome evolution than previously thought.

These results are important for future studies on how insertion sequences impact genome fitness and size. Interestingly, Kanai also noted, “Our research highlighted how transposons themselves evolve, an area that has often been overlooked.”

Looking forward, Kanai is eager to explore bigger questions, such as how cooperation evolves between bacteria or between bacteria and their hosts. “I aspire to understand how simple organisms can evolve into complex life forms. This knowledge could also lead to engineering advanced organic materials through evolutionary tuning.”

This innovative work opens up a pathway for a deeper understanding of genome evolution, adeptly shedding light on the fascinating interplay between genetic elements in nature. For further insights into related research, you can check [this article from Nature](https://www.nature.com/articles/s41598-020-70429-9).

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Bacterial, Evolution, Genes, Laboratory, Bacteria, DNA, E. coli, Genetic, Genome, Mitochondria