Electron micrograph of a cluster of minimal cells magnified 15,000 times. The synthetically streamlined bacterium, Mycoplasma mycoides, contains less than 500 genes. (Image by Tom Deerinck and Mark Ellisman of the National Center for Imaging and Microscopy Research at the University of California at San Diego)

The Unexpected Evolution of Minimalist Synthetic Microbes

Researchers at Indiana University Bloomington found that minimal synthetic cells can evolve just as fast as normal cells—demonstrating the capacity for organisms to adapt, even with a non-natural genome
Emerging Technologies
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July 6, 2023

In the iconic 1993 science fiction film Jurassic Park, Ian Malcolm, portrayed by Jeff Goldblum, famously muses, "Listen, if there's one thing the history of evolution has taught us is that life will not be contained. Life breaks free. It expands to new territories, and it crashes through barriers painfully, maybe even dangerously, but... life finds a way."

Jurassic Park may be a universe away from the evolutionary biology lab of Jay T. Lennon at Indiana University Bloomington, but the central theme of life's tenacity and adaptability rings true here too. In the absence of fantastical Velociraptors, Lennon's team grapples with life's mysteries, not at the macro level of dinosaurs but at the micro level of synthetic cells. Their recent findings illuminate that life indeed finds a way even when pared down to its most basic elements. His laboratory’s work was published in Nature

“There’s something about life that’s really robust,” Lennon states. “We can simplify it down to just the bare essentials, but that doesn’t stop evolution from going to work.”

Working with a streamlined organism, Mycoplasma mycoides JCVI-syn3B—a laboratory-constructed version of a bacterium commonly found in goat guts, Lennon and his colleagues observed the organism's remarkable capacity for evolution. Despite a genetically sparse structure, it proved as adaptive as its fuller-genome counterparts, challenging established evolutionary assumptions.

“We report on how an engineered minimal cell contends with the forces of evolution compared with the Mycoplasma mycoides non-minimal cell from which it was synthetically derived. Mutation rates were the highest among all reported bacteria but were not affected by genome minimization,” the authors wrote. “Genome streamlining was costly, leading to a decrease in fitness of greater than 50%, but this deficit was regained during 2,000 generations of evolution.”

The authors continued stating that “despite selection acting on distinct genetic targets, increases in the maximum growth rate of the synthetic cells were comparable. Moreover, when performance was assessed by relative fitness, the minimal cell evolved 39% faster than the non-minimal cell. The only apparent constraint involved the evolution of cell size. The size of the non-minimal cell increased by 80%, whereas the minimal cell remained the same.”

In the world of evolutionary biology, simplicity comes with a perceived genetic bottleneck. A pared-down genome, offering fewer targets for positive selection, should theoretically restrict its adaptability. The researchers embarked on a mission to test these principles using the stripped-down bacterium, which carried just 493 essential genes, compared to the 20,000+ genes commonly found in animals and plants.

“Every single gene in its genome is essential,” explains Lennon, hinting at the supposed evolutionary constraints of M. mycoides JCVI-syn3B.

Yet, the Lennon lab's research, detailed in a recent Nature publication, revealed surprising outcomes. After letting the minimal bacterium evolve in a lab for an equivalent of 40,000 years in human terms, the microbe displayed not just survival but significant evolutionary progress. It held its own against non-minimal versions of the bacterium and even recovered fitness lost due to its minimalist genetic makeup.

These findings shatter conventional views on evolutionary limitations, providing profound insights into the resilience of life in its most elementary form. Understanding this adaptability could reshape how we approach various biological challenges—from tackling clinical pathogens and sustaining symbiotic organisms to refining bio-engineered microbes and pondering the origins of life itself.

In demonstrating the ability of the simplest autonomous organism to adapt and thrive, Lennon's research encapsulates the essence of life's evolutionary power. Seemingly, life, no matter how stripped back, will find a way.

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