The jump genes accelerate bacterial evolution in the laboratory

The structure of the genome – How the genes are organized in DNA sequences in an organism – is fundamental for the processes and functions of organisms.

A team from the University of Tokyo has developed a system to control and accelerate the evolution of changes in the structure of the bacterial genome, targeting small “jump genes” or DNA sequences called insertion sequences. The study is published in the journal Nucleic acid search.

“Most of what we know about evolution comes from the study of the past. But certain events, such as the origin of mitochondria or other organelles, leave few traces, which makes it difficult to reconstruct the way they occurred,” said Yuki Kanai.

“On the other hand, the experiences that evolve laboratory organizations generally imply only small genetic changes. Our research fills this gap by accelerating the evolution of genome in bacteria, allowing us to directly observe changes on a large scale in the structure of the genome.”

Researchers often study bacterial genomes, with their relatively low size and coherence, useful for modeling changes in physiology, ecology and evolution. The insertion sequences (ISS) are known to “jump” or change their position in a genome and are drastic engines of evolutionary changes in the structure of the bacterial genome. Such changes can lead to mutations or their inversion and modify the identity or size of the genome.

Under ordinary conditions, the slow pace and the evolution of environmental conditions give limits to the isolation of the precise role of the ISS in evolution.

In Escherichia coli (E. coli), a largely studied model organism important for biotechnology and microbiology, transposition generally occurs once a year (or all thousands of generations). Kanai and the team found a way to accelerate changes by introducing several copies of high activity ISS in E. coli.

The source of inspiration for their method came from a fortuitous collaboration with researchers investigating in the evolution of insects, says Kanai.

“Some bacteria associated with insects have tiny genomes, a tenth of the size of their free parents, containing many jump genes called transposons. These transposons may have helped to shrink the genome by cutting and reworking DNA.

In experiments, test organizations quickly accumulated changes in their DNA – around 25 new insertions of mobile genetic elements and more than one increase or decrease in the size of the genome by 5% – in just 10 weeks, a rate similar to what is usually happening over the decades in nature.

The interaction detected of small frequent deletions and large rare duplications updates the view of the reduction of the genome as a simple consequence of the abolition bias in a more nuanced image which takes into account transitional extensions.

High activity has led to structural variants and the emergence of composite transposons, illuminating the potential evolutionary pathways for the ISS and composite transposons.

The results provide a remarkable reference to study the fitness effects of insertions, changes in the genome size and rearrangements in future laboratory experiences.

“Unexpectedly, our study also highlighted the evolution of the transposons themselves,” said Kanai. “These mobile genetic elements are well known to shape bacterial genomes, but their own evolutionary behavior has received little attention and clearly deserves more study.”

Excited by future possibilities, Kanai said: “Now that we have shown that it is possible to accelerate the evolution of the genome in the laboratory, we are impatient to apply this system to broader questions. For example, under what conditions does cooperation evolve, either between bacteria or between bacteria and their hosts?”

For Kanai, these responses are part of a long -term dream to understand the principles of the process of nature to stimulate biological complexity.

“I hope one day to build and develop simple organizations to discover how life becomes complex.