A micrograph of one of Jef Boeke’s yeast strains with a partially synthetic genome (Credit: Yu Zhao, NYU Langone Health)
November 9, 2023 07:11 AM EST R&DDiscoveryIn Focus
Fully synthetic genome nears completion in a step toward unraveling genetic mysteries
Ryan Cross
Senior Science Correspondent
An international effort to create yeast cells with a fully synthetic genome is nearing completion, with the eventual aim of unraveling the mysteries of genomes and ushering in a tool for producing complex medicines.
Scientists hope to create the synthetic organism by stitching together small pieces of DNA into artificial chromosomes and trimming out some genetic fat in the process.
The Synthetic Yeast Genome Project — abbreviated Sc2.0 — dates back more than 15 years. Now, in the consortium’s biggest update since revealing five synthetic chromosomes in 2017, its scientists published 10 papers describing the creation of most of the remaining chromosomes, along with a wholly new one that does not exist in nature.
Jef Boeke
“We’ve got all 16 chromosomes completely synthesized,” Jef Boeke, a synthetic biologist at NYU Langone Health and leader of the project, told Endpoints News. The group is still working on bringing those chromosomes, each in different yeast strains, together into a single organism. “We’re about a year or two away from completing that whole thing,” Boeke said.
Scientists at the J. Craig Venter Institute, led by the eponymous geneticist who rose to fame as a leader of the Human Genome Project, have previously built viruses and bacteria from synthetic DNA. But the Sc2.0 yeast would be the most complex synthetic organism yet. And since yeast is more closely related to animals than bacteria, it’s a better stepping stone for answering questions about how human genomes work.
“This is a gargantuan task,” J. Craig Venter, whose institute was not involved in Sc2.0, said in an interview. “Having a completely synthetic yeast would be a major milestone. I can’t say how impressed I am with what they’ve managed to pull off,” he said.
J. Craig Venter
Making a synthetic genome is not as simple as creating a carbon copy of what nature has already produced. The project is partly motivated by the belief that scientists can improve upon what nature has created.
“These synthetic yeast cells allow us to think about how the genome could have been organized,” Patrick Cai, a synthetic biologist at the University of Manchester, said in an email. “Our understanding of genomes is largely based on the observation of these natural genomes. The ability to build synthetic genomes will lead us to a much deeper understanding of the first principles of life.”
Patrick Cai
So far, the scientists have brought seven and a half synthetic chromosomes together under one Baker’s yeast cell, accounting for 54% of the organism’s DNA. That process of consolidation has proven trickier than expected, but scientists are already envisioning future uses for the completed cell.
“Baker’s yeast has always been the world’s number one microbe for making things for humans,” said Tom Ellis, a synthetic biologist at Imperial College London whose lab constructed one of the yeast chromosomes. “And with a finished synthetic cell, it opens up the possibility of making those products — biochemicals, drugs, antibodies, vaccines, biomaterials — in more optimal ways and with more diverse chemistry too.”
Decluttering and debugging a genome
Dreams of writing genomes, rather than just reading them, took hold at the turn of the century soon after scientists finished sequencing the first human genome. Researchers at Venter’s institute “booted up” the first bacteria with a synthetic genome in 2010 and refined and minimized its code in subsequent years.
Tom Ellis
For Boeke, creating a synthetic yeast genome was the natural next step. Yet, as simple as a yeast cell is compared to a human, its genome is still much larger than that of bacteria. It took about eight years before the first synthetic yeast chromosome was finished in 2014. In the years since, with the help of labs around the world and armies of undergrads, the Sc2.0 consortium has finally finished constructing the chromosomes.
One of the surprises that the group faced was that while the yeast was often healthy with one synthetic chromosome, the cells sometimes got sick when multiple synthetic chromosomes were added, sending the scientists back to the drawing board to figure out what went wrong and debug the design.
“It indicates that there are more mysteries within the genomic sequences than we thought,” said Junbiao Dai, deputy director of the Shenzhen Institute of Synthetic Biology, whose lab made one of the chromosomes. “Debugging is a really big time-consuming process.”
Junbiao Dai
The Sc2.0 project shows that “you have to build it to understand it,” Venter said. “Every time we or somebody else tries to make something, we find out that there are huge gaps in our knowledge.”
The synthetic yeast genome has thousands of changes, reducing its length by about 10% compared to a natural genome, Boeke said. Some of those changes include stripping out repetitive DNA sequences that the scientists believe have accumulated over time and are unnecessary. So far, removing ones called transposons hasn’t had a negative effect on the cells.
The team also did some reorganizing. Hundreds of genes encoding tRNA molecules — which are crucial for protein production — are normally scattered across the yeast’s chromosomes. Cai’s lab took those genes and put them all together on a synthetic tRNA neochromosome.
Repetitive regions and tRNA genes are both hotspots for genetic mishaps that damage DNA. While clumping the tRNA genes together “could really create a nightmare,” some additional tinkering to reduce their liabilities seems to have worked, Boeke said. “We’re seeing if we can build a more stable genome than the natural genome.”
Jay Keasling
They also installed tidbits of DNA throughout the genome that they can use to easily add, remove, or rearrange genes. That technique, called Scramble, allows scientists to rapidly generate thousands to millions of genetic variants of yeast. Boeke compares the approach to shuffling a massive deck of cards, each representing a gene, over and over.
“One of those hands is going to give you a royal flush, the best possible hand in poker. And another one’s going to give you the best hand in gin rummy,” Boeke said, with different “winning hands” for researchers making antibodies, biofuels, or vaccine antigens. “It’s going to be a very practical tool for biotech companies that are trying to optimize yeast to produce useful products.”
“It’s such a cool project, and coordinating all these institutions and investigators is a herculean task,” said Jay Keasling, a bioengineer at the University of California, Berkeley, who was not involved in the effort. “It’s a stepping stone to what comes next, and just like DNA sequencing got cheaper and cheaper, doing this will get easier and easier.”
Designer genomes for making drugs
Scientists are already envisioning a new project, Sc3.0, to dramatically shrink the size of the yeast genome, only retaining genes that are absolutely vital to life.
“Imagine stripping back your smartphone to the most basic functions and having everything else as an optional app — its battery life would probably be a lot better. We’d like to try to do that for cells,” Ellis said.
Shen Yue
Shen Yue, chief scientist of synthetic biology at BGI-Research in China, is excited to expand the genetic code of the synthetic yeast, allowing the cells to incorporate new amino acids beyond the standard twenty building blocks used to make peptides and proteins. Those new amino acids could grant new footholds for making antibody-drug conjugates, she said, or creating protein therapies with improved properties, like less frequent dosing.
Sc2.0 was once viewed as a stepping stone towards creating a fully synthetic human genome. Boeke was previously among the leaders of a grassroots effort called Human Genome Project-Write, announced in 2016. Yet, without concerted funding, the goal of synthesizing a human genome remains far off.
“The human genome is 200 times larger, not to mention a lot more complicated and difficult to work with,” Boeke said. “It’s just not practical.”
Boeke said he withdrew from the group during the pandemic because his lab was busy helping with Covid-19 testing for New York City. But he also thinks that the time it would take to synthesize a full human genome poses a challenge. The cost of synthesizing DNA is another barrier.
Joel Bader
“I’m surprised that the cost of the raw starting materials hasn’t come down more,” said Joel Bader, professor of biomedical engineering at Johns Hopkins University who was part of Sc2.0.
Several biotech companies are working on new methods for making DNA in the lab cheaper and faster. It’s too soon to say if they will succeed, but the value of making fully synthetic genomes could soon be put to the test when the synthetic yeast is complete. “When all of those chromosomes are consolidated, that’s when the power of Sc2.0 is really going to take off,” Boeke said.
“I have a bet on a case of very good wine with a colleague who thinks we won’t be able to do it,” he said. “But I’m pretty confident I’m going to be drinking some good wine.”
AUTHOR
Ryan Cross
Senior Science Correspondent
[email protected]
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