Accelerating bacterial evolution in the laboratory

The genome structure — how genes are organized within DNA sequences in an organism — is fundamental to the processes and functions of organisms. A team at the University of Tokyo has developed a system to control and accelerate the evolution of changes in bacterial genome structure, targeting small “jumping genes,” or DNA sequences known as insertion sequences.

“Most of what we know about evolution comes from studying the past. But some events, like the origin of mitochondria or other organelles, leave few traces, making it hard to reconstruct how they happened,” explained Yuki Kanai. “On the other hand, experiments that evolve organisms in the lab typically involve only small genetic changes. Our research bridges this gap by accelerating genome evolution in bacteria, allowing us to directly observe large-scale changes in genome structure.”

Researchers often study bacterial genomes, with their relatively small size and consistency, useful for modeling changes in physiology, ecology and evolution. Insertion sequences (ISs) are known to “jump” or change its position within a genome, and are drastic drivers of evolutionary change in bacterial genome structure. Such changes can result in mutations or their reversal, and alter the identity or size of the genome.

Under ordinary conditions, the slow pace and changing environmental conditions place limitations on isolating the precise role of ISs in evolution. In Escherichia coli (E. coli), a widely studied model organism important to biotechnology and microbiology, IS transposition occurs typically once per year (or every few thousand generations). Kanai and the team came up with a way to accelerate the changes by introducing multiple copies of high-activity ISs in E. coli.

The source of inspiration for their method came from a chance collaboration with researchers investigating insect evolution, Kanai relates. “Some insect-associated bacteria have tiny genomes, one-tenth the size of their free-living relatives, containing many ‘jumping genes’ called transposons. These transposons may have helped shrink the genome by cutting and reshuffling DNA. This left us wondering whether we could use transposons to rapidly simulate DNA reshuffling in nature.”

In the experiments, the test organisms quickly accumulated changes in their DNA — about 25 new insertions of mobile genetic elements and over a 5% increase or decrease in genome size — within just 10 weeks, a rate similar to what usually happens over decades in nature. The detected interplay of frequent small deletions and rare large duplications updates the view of genome reduction as a simple consequence of deletion bias to a more nuanced picture that takes into account transient expansions. The high IS activity resulted in structural variants and the emergence of composite transposons, illuminating potential evolutionary pathways for ISs and composite transposons.

The results provide a remarkable reference for studying fitness effects of IS insertions, genome size changes and rearrangements in future laboratory experiments. “Unexpectedly,” Kanai remarked, “our study also shed light on the evolution of transposons themselves. These mobile genetic elements are well known for shaping bacterial genomes, yet their own evolutionary behavior has received little attention — and clearly deserves more study.”

Excited by the future possibilities, Kanai said, “Now that we’ve shown it’s possible to accelerate genome evolution in the lab, we’re eager to apply this system to broader questions. For instance, under what conditions does cooperation evolve — either between bacteria or between bacteria and their hosts?”

For Kanai, such answers form part of a long-term dream to understand the principles behind nature’s process to drive biological complexity. “I hope to one day build and evolve simple organisms to uncover how life becomes complex. This could also enable the engineering of highly sophisticated organic materials that are difficult to design directly, requiring evolutionary fine-tuning to achieve desired functions.”

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Journal article: Yuki Kanai, Atsushi Shibai, Naomi Yokoi, Saburo Tsuru, Chikara Furusawa, “Laboratory evolution of the bacterial genome structure through insertion sequence activation”, Nucleic Acids Research, https://doi.org/10.1093/nar/gkaf331

Funding: This work was supported by the Japan Society for the Promotion of Science [21J20693 to Y.K., 18H02427 to S.T., 24K21985 to S.T., 22K21344 to C.F, 23K27164 to C.F, 24H01798 to C.F]; the Japan Science and Technology Agency [JPMJER1902 to C.F]; the Japan Agency for Medical Research and Development [JP223fa627001 to Y.K.]; and a Grant-in-Aid from the Institute for Fermentation, Osaka [G-2025-2-046].

Useful links:

Universal Biology Institute - https://park.itc.u-tokyo.ac.jp/UBI/index_e.html
Graduate School of Science - https://www.s.u-tokyo.ac.jp/en/

Research contact:
Professor Chikara Furusawa
Universal Biology Institute, The University of Tokyo,

7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

furusawa@phys.s.u-tokyo.ac.jp

Press contact:
Mr. Rohan Mehra
Public Relations Group, The University of Tokyo,
7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
press-releases.adm@gs.mail.u-tokyo.ac.jp
 

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