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Related Experiment Video

Updated: May 16, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Laboratory evolution of the bacterial genome structure through insertion sequence activation.

Yuki Kanai¹, Atsushi Shibai², Naomi Yokoi²

¹Department of Biological Sciences, The University of Tokyo, 7-3-1 Hongo, 113-0033 Tokyo, Japan.

Nucleic Acids Research

|May 10, 2025

Summary

Accelerated evolution in Escherichia coli using insertion sequences (IS) revealed rapid genome structure changes. This system simulates IS expansion in pathogens, offering insights into bacterial evolution and mobile element dynamics.

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Area of Science:

Microbiology
Bacterial Genetics
Evolutionary Biology

Background:

Bacterial genome structure influences physiology, ecology, and evolution.
Insertion sequences (IS) drive genome evolution but are slow to observe.
Understanding IS-mediated evolution is crucial for bacterial adaptation.

Purpose of the Study:

To develop a system for accelerated IS-mediated genome evolution in Escherichia coli.
To simulate IS expansion under conditions found in host-restricted bacteria.
To investigate the impact of high IS activity on bacterial genome structure and evolution.

Main Methods:

Introduction of multiple high-activity IS copies into Escherichia coli.
Evolution of bacterial strains under relaxed neutral conditions.
Analysis of genome structure changes, including IS insertions, deletions, and duplications.

Main Results:

Strains accumulated a median of 24.5 IS insertions within ten weeks.
Over 5% genome size changes were observed, comparable to decades of wild-type evolution.
Frequent small deletions and rare large duplications were detected, updating views on genome reduction.
High IS activity led to IS structural variants and composite transposon emergence.

Conclusions:

The developed system effectively accelerates IS-mediated genome evolution.
Observed genome dynamics provide a baseline for assessing fitness effects of IS activity.
This study advances understanding of how mobile elements shape bacterial genomes and evolution.