New Artificial Chromosomes Set Stage for First Complex Synthetic Genome

Jef Boeke discusses the construction of five new synthetic yeast chromosomes as part of the long-term goal to build a completely synthetic genome.  / NYU Langone Medical Center

In seven new studies, scientists of the Synthetic Yeast Genome Project (Sc2.0) who previously constructed a single yeast chromosome now report constructing five more chromosomes — representing more than one-third of yeast's entire genome.

The results , published in the 10 March issue of Science, are major progress on the road to building the first fully synthetic eukaryotic — or nucleus-containing — organism, which the Sc2.0 consortium hopes to complete in the next two years by swapping all 16 yeast chromosomes for engineered ones. Such a genome, equipped with a full set of chromosomes that could be engineered to give new properties to yeast, would be ripe for customization.

"Natural yeast is a major organism for making products like bread, beer and biofuel, as well as those used in biotechnology, such as enzymes or antibiotics, but currently, optimizing it for new products is inefficient," said Joel Bader, a Sc2.0 project leader and professor of biomedical engineering at the Johns Hopkins University. "Our synthetic chromosomes permit the yeast genome to overcome this problem."

Once equipped with a full set of synthetic and changeable chromosomes, baker's yeast could produce better versions of the important commodities it already delivers, including new antibiotics or more environmentally friendly biofuels. It could also help scientists understand more about the underlying drivers of certain human diseases, and render gene therapy more powerful.

In addition to serving as a highly versatile industrial chemical factory, a fully synthetic eukaryotic yeast genome also could help researchers learn more about how genomes are built and organized. It may even assist them in answering some long-standing evolutionary questions, like determining the maximum number of nonessential genes that can be deleted in an organism without a catastrophic loss of fitness.

"It's also going to be a powerful tool for understanding gene function not just for yeast but for humans," Bader added, noting that many human genes share a common ancestor with their yeast counterparts.

In March 2014, researchers led by Bader built the first synthetic yeast eukaryotic chromosome, synIII. "The Sc2.0 project started as a coffee break and became a breakthrough," Bader said.

To expedite the work of building synthetic yeast chromosomes, Bader and colleagues set up a summer class at Johns Hopkins called Build-A- Genome. It involved almost 50 students working 24 hours a day, seven days a week, for a year and a half, to put together parts for the synthetic genome.

But even that wasn't enough. "Very soon," Bader said, "we realized no single lab could do this project. It was simply too large."

Bader and colleagues teamed with different collaborating labs across the globe, in Britain, China, Australia and Singapore, with each one adopting a chromosome to synthesize. "Working with international teams has been a delight," Bader said.

Now, he and colleagues have described the assembly of five more synthetic chromosomes: synII, synV, synVI, synX, and synXII, which correspond to the smaller yeast chromosomes.

The chromosome-building work involved first using specially designed software to carefully design the chromosomes of interest. This included making conservative changes, such as removing some of the repetitive and less used regions of DNA between genes.

Once equipped with a full set of synthetic and changeable chromosomes, baker's yeast could produce better versions of the important commodities it already delivers, including new antibiotics or more environmentally friendly biofuels.

"Genomes are in constant flux… prone to deletions, duplications, and insertions," Science editors Laura Zahn and Guy Riddihough note in an introduction to the papers. "These many changes are subject to the vagaries of natural selection, resulting in a genome organization not based on principles of efficiency or economy of space ... Sc2.0 has set out to untangle, streamline and reorganize the genetic blueprint of one of the most studied of all eukaryotic genomes."

In certain cases, the researchers did move especially large swaths of DNA from one chromosome to another. Despite such changes, Bader and colleagues report, once the altered chromosomes were chemically synthesized — a process that involved stringing together individual DNA building blocks and placing the resulting chromosomes in living yeast cells — the cells grew normally.

"The plasticity we are seeing when we make these big changes without much or any penalty," said New York University geneticist Jef Boeke, another Sc2.0 project leader, "suggests that we can continue to be even bolder in our future designs … and make more dramatic changes to have the yeast do our bidding, resulting in even more useful products."

Now that six complete synthetic chromosomes have already been integrated into different living cells, the remaining chromosomes are progressing rapidly, and the final phase of the project will be to integrate all of the synthetic chromosomes into a single yeast cell. Bader said he is hopeful that within two years, every synthetic chromosome will be inserted into yeast.

Among other applications, the approach outlined here paves the way for a new era of gene manipulation. Gene therapy is currently limited to a delivery of a single gene, but could be expanded to allow for delivery of gene networks or pathways, or even multiple genes.

"We are excited about engineering yeast as models for human disease," said Boeke. "Right now we are rebuilding a network of human genes inside of yeast. We hope to use this system to learn more about human metabolic diseases underlying certain neurologic diseases, and forms of mental retardation, autism and cancer."

"One of the other exciting areas that synthetic biology is moving towards is synthetic biology for more complex organisms, like mammals," Bader added. "Even if we wanted to make a mammalian synthetic chromosome that would let us do things like create more organs for organ transplantation or create synthetic skins so that people with horrible burns are able to recover, we need a platform to be able to put together mammalian chromosomes that encode genetic material in a designable way. Yeast is likely going to be the most important organism where that work will be done."