A groundbreaking study at the University of Tokyo introduces a system capable of accelerating changes in bacterial genome structure, focusing on insertion sequences (ISs). By increasing the activity of these "jumping genes" in Escherichia coli (E. coli), researchers have been able to observe large-scale evolutionary changes within just 10 weeks, a process that typically takes decades in natural conditions. This innovation not only sheds light on how ISs influence genome evolution but also provides insights into the mechanisms behind genome reduction and expansion. The findings pave the way for further exploration of evolutionary processes and the potential applications in biotechnology and synthetic biology.
Inspired by insect-associated bacteria with significantly smaller genomes, the research team led by Yuki Kanai sought to simulate DNA reshuffling using transposons. Typically, IS transposition in E. coli occurs infrequently, about once per year or every few thousand generations. However, by introducing multiple copies of highly active ISs, the team managed to dramatically increase the rate of genetic change. Over the course of their experiments, test organisms exhibited approximately 25 new insertions of mobile genetic elements and experienced fluctuations in genome size by over 5%. This rapid accumulation of changes allowed scientists to directly observe and analyze the interplay between small deletions and large duplications.
The accelerated evolution revealed a more nuanced understanding of genome reduction, moving beyond the simplistic notion of deletion bias. Structural variants emerged as a result of high IS activity, leading to the formation of composite transposons. These discoveries illuminate possible evolutionary pathways for both ISs and composite transposons, offering valuable references for future laboratory experiments. Furthermore, the study unexpectedly highlighted the evolutionary behavior of transposons themselves, an area that has received limited attention despite their significant role in shaping bacterial genomes.
Kanai expressed enthusiasm about the implications of this research, suggesting its application to broader questions such as the evolution of cooperation between bacteria or between bacteria and their hosts. Such inquiries align with his long-term aspiration to uncover the principles driving biological complexity. By building and evolving simple organisms, there is potential to develop advanced organic materials through evolutionary fine-tuning, achieving functions that are challenging to design directly.
This innovative approach not only enhances our understanding of bacterial genome evolution but also opens doors to novel applications in various scientific fields. The ability to accelerate genome evolution in a controlled environment offers unprecedented opportunities to explore complex biological processes and engineer sophisticated solutions to pressing challenges.