Baker's Yeast Gets a Genetic Makeover

An army of undergraduates built a synthetic chromosome with cheap DNA-making technology

SYNTHETIC CHROMOSOME: The yeast chromosome is represented snake-like, with the positions of "designer changes" indicated by pins and white diamonds, and the deleted segments indicated in yellow, using the native chromosome sequence as a reference.
Illustration by Lucy Reading-Ikkanda

The humble baker's yeast has been enlisted to serve the needs of humanity, responsible for beer, wine and bread, among other staples. A domesticated servant for at least millennia, the microscopic fungus has now had one of its chromosomes swapped out by a host of undergraduate students in favor of a pared-down, synthetic version.
A chromosome is a twisted strand of DNA, the genetic code that tells an organism's cellular machinery what proteins to produce, among other vital functions. There are 16 in baker's yeast (compared to 23 in humans), and the so-called Synthetic Yeast 2.0 project focused on chromosome number three, a "sentimental favorite of yeast geneticists," according to biologist Jef Boeke of the NYU Langone Medical Center, who helped lead the research. That's because it contains the genetics that control the yeast's sexual behavior. As a fungus, Saccharomyces cerevisiae can reproduce both sexually and asexually, and the genes in chromosome number three control mating, which makes it easy to track through the generations. It was also the first chromosome to have its code fully transcribed by scientists and happens to be third shortest of the yeast's 16 chromosomes.
In the early years of the 21st century, Boeke and his colleagues were musing over coffee at a Johns Hopkins University café and hatched a scheme that became Synthetic Yeast 2.0, a full-fledged effort to build a synthetic genome for yeast that would allow near complete control of the organism, whether to boost biofuel production or air pockets in bread. By 2011, Boeke and his colleagues could report success in building one arm of a chromosome, chromosome number nine. That required meticulously synthesizing some 90,000 pairs of the letters of DNA—A for adenine, G for guanine, C for cytosine and T for thymine—that make up the genetic code.
But that effort proved too slow. So Boeke and his colleagues enlisted what he called "an army of undergrads in our 'Build a Genome' course" to build a yeast chromosome—the entirety of baker's yeast chromosome number three, which contains more than 316,000 base pairs. Fortunately, there was a shortcut: synthesizing only those sections considered essential or non-repetitive and cutting down the chromosome to a more manageable 272,871 pairs.
"The organism itself is the workhorse of modern biotechnology and biomanufacturing," says biological engineer Drew Endy of Stanford University, who was not involved in the research or the Synthetic Yeast 2.0 project. "It's a great example of 'do it together' biotechnology."
The undergrads synthesized the DNA—thanks to the ever-decreasing costs of DNA manufacturing enabled by new technology—in roughly 750 pair chunks. The yeast's cellular machinery viewed those chunks as strand breaks in the DNA, so it knit the new, synthetic code in with the old. Over time, the entire chromosome was replaced with the new, pared-down, synthetic version.
This marks the first time scientists have synthesized the genetics of a complex organism, a landmark achievement in the field of synthetic biology, and given the college kids involved, a triumph for the new movement known as "DIY biology." Prior specialist work had succeeded in synthesizing the entire genetic code of simpler microbes, such as the goat pathogen Mycoplasma mycoides, renamed JCVI-syn1.0 by its creators, which has been lying dormant in a freezer since 2010. The new results from the Synthetic Yeast 2.0 team were published online in Science on March 27.


Not everything went smoothly. Occasionally, "unexpected arrangements" occurred as the yeast incorporated the new code, which is shorter by more than 43,000 pairs and has engineered differences in more than 5,000 pairs. But by breeding the yeast containing the synthetic code with one of its parents, a technique known as backcrossing, the project produced an orderly genome. The yeast with the synthetic code thrived, showing no inhibition in growth, size, shape or ability to tolerate normal yeast conditions.

"This is significant as an example of synthetic genomics aimed well beyond making mere copies of chromosomes—the new trend being making significant functional changes, ideally changes useful for biotech productivity and safety," says geneticist George Church of Harvard Medical School, who was not involved in the effort but is a technology developer for synthetic biology.
This partially synthetic strain itself will not find use in ethanol vats or bakeries, largely because it turns out to be even more vulnerable to high concentrations of alcohol than traditional yeast, a flaw that keeps brewery vats from growing too large in an industrial setting. But it will allow for the testing of specific individual genes as well as their interactions, which could lead to yeasts that are much tougher. "They are going strong," Boeke says of the synthetic strains. "We intend to grow them for thousands of generations in chemostats to see if we can evolve yeasts that do better in high ethanol or other special conditions."
"The prospect of being able to design, synthesize and insert entire pathways into industrial organisms is compelling," notes molecular biologist Carsten Hjort, senior director of production strain technology for Novozymes, a company that uses yeast to produce human proteins for medical purposes, among other pursuits. "This is an astonishing achievement that takes DNA synthesis to the next level."
In the meantime, the synthetic yeast will allow novel research into questions such as, what controls yeast division, whether a genome function with just one chromosome, or with 100, and the role of "junk DNA"—perhaps better understood as code with as yet unknown, but perhaps vital, functions. "The questions are endless," Boeke says.
And then there's the task of synthesizing the other 15 chromosomes—not to mention the other cellular machinery, like histones, required for proper function—and creating a fully synthetic yeast genome, a task that will require designing and making as much as 12 million working pairs of DNA's letters. The current work is just 3 percent of the way towards that goal. "We think it will take us a few more years to finish the job," Boeke says. "Then the fruit fly? The worm? We're not sure what will be next."

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