Evolution is the right of all life forms – even synthetic ones

When forced to evolve or die, genomes edited down to the bare minimum compatible with life didn’t give up.

July 16, 2023 10:30 am | Updated 07:27 pm IST

A representative illustration of a DNA double helix.

A representative illustration of a DNA double helix. | Photo Credit: Getty Images/iStockphoto

Our ability to sequence genomes and genomic research more broadly have significantly enriched our understanding of the genome of humans as well as the many life forms around us. Yet researchers have always been curious about what really constitutes the minimal requirement for a genome compatible with an organism’s ability to live freely and replicate.

Concurrent advancements in not just reading the genome sequence (sequencing) but also our ability to write (synthesise) genome sequences has sparked the human imagination, and has provided impetus to a new field of research called synthetic biology.

What we can build

An early attempt in this direction was led by researchers at the J. Craig Venter Institute (JCVI) in Maryland, U.S.. In 2008, they attempted to synthesise a small bacterial genome, but at the time were unable to put it back into the cell and give it a spark of life.

Finally, in 2010, researchers at JCVI were able to synthesise a complete genome of around 1 million base-pairs of a modified genome of a free-living organism called Mycoplasma mycoides. They named it JCVI-syn1.0. This genome could be introduced into a cell and could replicate, thus becoming one of the first synthetic life-forms. This was a culmination of efforts spanning over 15 years, which included attempts to redesign the genome by assembling small fragments of artificially synthesised 1,000-odd base pairs and systematically assembled in the lab using molecular tools.

The paper for this effort was published in Science and was hailed as a landmark – not just as a technological feat, but also vis-à-vis our understanding of the molecular mechanisms of life. As the famous physicist Richard Feynman stated, “What I cannot build, I cannot understand.” This was also why this effort was seen as humankind’s baby steps towards engineering life-forms based on evidence, technologies, and an understanding of the fundamental rules of the molecular mechanisms that govern life.

Meet syn3.B

Attempts to modify genomes continued. In 2016, researchers at JCVI and a California-based company named Synthetic Genomics, Inc. (since changed to Viridos) attempted to create a minimal genome by further systematically deleting parts of the genome of Mycoplasma mycoides, publishing the results in Science. The researchers’ idea was to create a ‘bare-minimum’ genome and cell that was compatible with life as well as with the possibility that the genome could be used as a bare-bones framework for synthetic biology.

They succeeded in creating a minimal cell deleting with around 45% of the genes in the genome of the organism. Specifically, the edited genome had 531,000 base pairs and just 473 genes. This newer modified synthetic version was named JCVI-syn3.0.

Additional modifications to the genome resulted in two more versions, dubbed JCVI-syn3.A and JCVI-syn3.B. These versions differed from JCVI-syn3.0 by the addition of 19 non-essential genes, making the two newer versions more optimised for laboratory conditions.

JCVI-syn3.B in particular had an additional genomic locus (a location on the genome) where the researchers could insert new gene fragments and antigens. This is required to allow the genome to bind to a lineage of human cells called the HeLa cell lines, which researchers use widely in laboratory studies. As a result, JCVI-syn3.B could be cultured with human cells.

The barebones genome had the absolute minimum number of genes to be compatible with life. At the same time, it was widely believed that the resulting organism would be constrained and unlikely to evolve because it had very little wiggle room to adapt to environmental conditions.

But a recent report in Nature suggested that this conclusion could be mistaken.

A minimal genome evolves

Researchers led by Jay T. Lennon at Indiana University in Bloomington, U.S., attempted to understand how a synthetic life-form would adapt or evolve over time, especially in situations where the raw materials required to do so could be limited, forcing the genome to die or adapt through evolution.

To understand this, the researchers cultured a bacterial organism in the laboratory for over 300 days, corresponding roughly to 2,000 rounds of replication. The researchers established that this life-form’s synthetic genome – which was also minimal – had a robust potential to develop genetic variations.

Now, the researchers conducted an experiment. They mixed the bacteria with a separate bacterial culture in equal numbers, checked whether either population went on to make up more than 50% of the total over time as they varied the environmental conditions. If the minimal bacteria could optimise themselves for the condition, they would out-compete the others that were suboptimal.

As the team expected, the minimal genome was inferior in its ability to compete with the native, non-synthetic Mycoplasma. However, to their surprise, the researchers found that the synthetic bacteria that had evolved through 300 days could significantly out-compete the non-evolved minimal version of the organism.

Its own path

The study suggested that synthetic life-forms could evolve through natural processes of evolution and adapt themselves to the environment. The minimisation of the genome didn’t constraint natural adaptation.

Additionally, using genome-sequencing, the researchers were able to identify specific genes and regions on the genome that had accumulated genetic variants associated with the adaptation. They also found that the adaptation of the minimal genome took distinctly different steps and paths from that of the native/non-adapted organism, as evidenced by the different genomic regions and genes where the genetic variants accumulated during the process of adaptation.

The findings have enormous implications – not just for our ability to understand the natural evolutionary processes of synthetic life but also for the practical applications of synthetic genomes for the industrial-scale production of chemicals and biologicals.

Insights into the evolutionary processes of organisms also open big windows into understanding how antimicrobial resistance emerges, how pathogens evade immune systems, and, possibly, new opportunities to prevent them or be prepared for them.

Sridhar Sivasubbu and Vinod Scaria are scientists at the CSIR Institute of Genomics and Integrative Biology. All opinions expressed are personal.

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