Scientists have created the first semi-synthetic living creature

Prof. Floyd Romesberg and his colleagues at the Script Institute have now shown that the single-celled organism they engineered can forever retain the synthetic base pair as it divides

The genetic code of life contains four natural bases. These bases pair up to create two "base pairs" - on either side of the DNA ladder - and are simply rearranged to create different creatures: bacteria and butterflies, penguins and people. Four bases are responsible for all life as we know it.

Scientists at the SCRIPPS Research Institute (TSRI) announce the development of the first semi-stable synthetic organism based on their 2014 research.

In their 2014 study where they succeeded in synthesizing a pair of DNA bases, the researchers created a new bacterium that uses the four natural bases (called: AT, C and G), but also contains a pair of synthetic bases called X and Y in its genetic code.

Prof. Floyd Romesberg and his colleagues at the Script Institute have now shown that the single-celled organism they engineered can forever retain the synthetic base pair when it divides. The study was published on January 23, 2017 in the online version of the journal PNAS.

"We built this organism more like a living organism," says Romesberg, the lead author of the paper. While practical uses for such an organism are still far from being made, the researchers say their work could be used to create new properties in single-celled organisms that will play an important role in drug discovery and other applications.

Building a unique organism

When Romsberg and his colleagues announced the development of X and Y bases in 2014, they also showed that engineered E. coli bacteria could have such a synthetic base pair in their genetic code. What this bacterium could not do was keep the new base pair in its genetic code indefinitely while dividing the cell. The X and Y base pairs have been pushed aside over time which has limited the ways in which the organism can use the extra information found in their DNA.

"Our genome is not supposed to be stable for just one day," Romesberg said. "The genome should be stable throughout life. If a semi-synthetic organism is really going to be a living being, it must be able to maintain this information stably."

Together with research student Yorke Zhang and Brian Lamb, a postdoctoral fellow in Romesberg's lab on behalf of the American Cancer Society at the time, they helped develop the means for a single-celled organism to preserve the artificial base pair.

First, Zhang and Lamb optimized the molecular tool known as a nucleotide transporter that brings the necessary materials to the pair of artificial bases so that they can be copied beyond the cell membrane. "The transporter they used in the 2014 study, but it made the semi-synthetic creature very sick," Zhang explained. The researchers discovered how the transporter could be adapted to overcome the problem and make it easier for the creature to grow and divide while maintaining the X and Y bases.

In addition, the researchers optimized an earlier version of the Y base. The new Y base was a chemically different molecule that the enzymes that synthesize the DNA molecules during replication could recognize. This made it easier for the cells to copy the synthetic base pair.

A new use of CRISPR-Cas9

Finally, the researchers developed a "spell-check" system for the organism using CRISPR-Cas9, an increasingly popular tool also used in human genome editing experiments. But instead of editing a genome, the researchers took advantage of CRISPR-Cas9's original role in bacteria.

The CRISPR-Cas9 genetic tool originated in the immune response of bacteria. When a bacterium encounters a threat, such as a virus, it takes genome fragments of the invading virus and infects them with its own genome. Later, it can use the infected genes to direct an enzyme to attack the invader should it return.

Knowing this, the researchers engineered their organism to recognize a genetic sequence without X and Y as a foreign invader. A cell without X and Y will be destroyed, leaving the scientists with a creature that can hold on to the new bases. Thus they gave the organism immunity against the loss of the base of the unnatural pairs. "We were able to address the problem at a fundamental level," said Lamb, who now serves as a research scientist at Vertex Pharmaceuticals.

The semi-synthetic organism was able to retain the X and Y pairs after 60 divisions, leading the researchers to believe it could hold on to the base pair indefinitely.

According to Romesberg. "Success indicates that all processes of life can be subject to manipulation."

basis for future research

Romesberg emphasizes that the research was only carried out in unicellular organisms and they do not intend to use it in more complex organisms. According to him, the number of current applications for its development is zero at this time. So far, scientists have only been able to cause the organism to store the genetic information. In the next step, the researchers plan to investigate how the new genetic code can be transcribed into RNA, the molecule responsible for translating DNA into proteins. "The research lays the groundwork for what we need to do to move forward," says Zhang.

More of the topic in Hayadan:

• An interview with one of the developers of CRISPR-Cas9
• Advances in the field of synthetic biology and biological computing
• A programming language for building synthetic DNA