BioEd Online

Researchers have equipped yeast cells with semi-synthetic chromosomes. It is the first such achievement in eukaryotic, or complex-celled, organisms, and marks a step towards large-scale genome engineering in these cells.

The team publishes its results today in Nature¹. The study suggests that the engineered yeast strains are as healthy as natural yeast.

"It appears to be fantastically stable," says Andy Ellington, a biochemist at The University of Texas at Austin, who was not involved in the work. "At least some of us thought that it would fall flat on its face or would mutate quite readily."

The engineered strains also have a built-in 'scrambling' system that deletes and shuffles random genes on demand — a feature that could prove useful for developing yeast optimized for the production of fuel, drugs or other valuable chemicals. The team's eventual goal is to synthesize the entire yeast genome.

Scientists have previously built and engineered entire genomes, but generally in simpler organisms, such as bacteria.

The biggest genome synthesized so far is that of the bacterium Mycoplasma mycoides, the roughly 1 million base pairs of which were mostly a replica of the natural sequence in a study published last year². Scientists have also made genome-scale changes to viruses³, and have removed unnecessary genetic elements⁴ and replaced sequences⁵ across bacterial genomes.

Yeast, re-programmed

In the latest study, Jef Boeke, a yeast biologist at the Johns Hopkins University School of Medicine in Baltimore, Maryland, and his colleagues tackled two chromosome segments that together represent about 1% of the 12-million-base-pair genome of the yeast Saccharomyces cerevisiae. The researchers designed the synthetic segments with the help of genome-editing software, incorporating several types of changes.

These changes included removing repetitive sequences that could destabilize the genome, and adding tags to distinguish synthetic segments from natural ones. To create the genetic scrambling system, the team inserted short sequences that act as binding sites for a specific enzyme, which can delete or rearrange genes if activated. Overall, the researchers changed about 17% of the sequence in the targeted segments.

The edited segments were then synthesized and introduced into yeast cells, replacing the corresponding natural segments. Tests showed that the resultant semi-synthetic strains had apparently normal growth rates, colony appearance and gene expression. When the researchers turned on the scrambling system by activating the necessary enzyme, they were able to generate mutant strains with varying growth rates, drug sensitivity, temperature sensitivity, use of carbon sources and stress responses.

Scaling up

Boeke says that when more of the yeast genome is synthesized, researchers will be able to use the system to study evolution and speciation. For example, they could delete genes to determine how much of the genome is needed for survival, or see how much genome scrambling it takes to produce a new species.

Ham Smith, a molecular biologist at the J. Craig Venter Institute in San Diego, California, who was involved in the synthesis of the M. mycoides genome, said in a statement that Boeke's work is "another remarkable example of how synthetic biology can be used to rewrite chromosome sequences at a sizable scale".

However, Smith noted that it is unlikely that any cells would survive if the scrambling system were extended over substantially larger parts of the genome. Boeke says that this problem could be addressed by reducing the length of time for which the scrambling system is activated, and weakening the enzyme's expression.

The team has enlisted undergraduate students in Baltimore to construct pieces of the rest of the yeast genome. Students and researchers in China might also join the effort, says Boeke, although it will take several years to build the whole synthetic genome. Boeke estimates that so far, the team has synthesized the DNA pieces for about 10% of the genome, and about 2% have been tested in yeast.