In a significant advance toward creating the first “designer” complex cell, scientists say they are one-third of the way to synthesizing the complete genome of baker's yeast.
In seven studies published Thursday in the journal Science, the researchers describe how they built six of the 16 chromosomes required for the yeast Saccharomyces cerevisiae, altering the genetic material to edit out some genes and write in new characteristics.
“A lot of synthetic biology is motivated by this idea that … you only understand something when you can build it,” said Johns Hopkins computational biologist Joel Bader, one of the leaders of the project. “Well, now we know enough about biological systems that we can design a chromosome on a computer, synthesize it in a laboratory, put it in the cell, and it will work.”
Scientists have built designer cells in the past. In 2010, scientists at the J. Craig Venter Institute created a bacterial cell controlled by a synthesized genome by copying the DNA of one bacterium into another. Last year they took the effort a step further by building the first “minimal cell,” an organism never found in nature that had the smallest number of genes required for life. Several months later, a team led by researchers at Harvard Medical School successfully re-engineered a small fraction of the genes of the bacterium E. coli.
This isn't the first time scientists have written genetic code for yeast. Jef Boeke, director of New York University Langone’s Institute for Systems Genetics and an organizer of the project, and his colleagues synthesized their first chromosome in 2014. They dubbed their project Sc2.0 (“Sc” stands for S. cerevisiae).
The new papers, however, signal an important advance. The chromosomes generated this time represent the largest amount of genetic material ever synthesized, and the new Sc2.0 cells are substantially different from their natural, or “wild type,” relatives. “In addition to building the thing, we’ve really added new features to chromosomes that weren't there before,” said Boeke.
Among the most significant of these new features is a program the scientists called “SCRaMbLE,” or “Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution” (scientists are congenitally disposed toward convoluted acronyms). The program allows scientists to rearrange elements within the genome to generate new and potentially useful permutations.
Whereas many of Boeke's peers labor for years in the lab trying to genetically modify organisms, the SCRaMbLE system “lets the yeast do the work and lets the yeast teach us new biology,” Boeke said. It's like a version of the lottery in which you can continuously and instantaneously roll new numbers until you get a result you want.
Other innovations in the Sc2.0 genome include the removal of duplicate bits of genetic code and the addition of short genetic sequences that distinguish synthetic chromosomes from their natural counterparts.
“By rebuilding chromosomes, these teams are showing that biology can be remade such that it is easier to measure, model and manipulate,” said Andrew Endy, a professor of bioengineering at Stanford University who was not involved in the project. Endy noted that evolution doesn't necessarily favor biological systems that are easy to understand; scientists have been analyzing the human genome for 25 years and still aren't really sure how a lot of it works. If researchers can engineer simpler cells — ones whose DNA the scientists wrote themselves — they will have an easier time harnessing those systems for research, medicine and industry.
Unlike other synthetic organisms, the engineered yeast is a eukaryote — a complex cell with diverse internal structures, just like the cells in the human body. It has more genetic material than the bacteria synthesized by the Venter Institute and Harvard projects.
Yeast is among the most well-studied organisms on Earth, a staple of biology labs, making it extremely useful for research. And it has myriad industrial, medical and scientific applications, from the production of biofuels to the development of vaccines. The Sc2.0 team plans to add a 17th chromosome to the designer cell to improve its protein-making machinery.
Incidentally, S. cerevisiae is the same yeast that bakers use to make bread. Some of the undergraduates working on the Sc2.0 project crafted a gene that would cause the yeast to produce beta carotene, the molecule that gives carrots their vitamin A and orange coloring, and baked a loaf with it. The bread came out of the oven with a lovely orange color, but Boeke wouldn't let them eat it. (They didn't have approval from their Institutional Review Board, which oversees research safety and ethics.)
Culinary misadventures aside, the new papers illustrate “a major milestone,” said Huimin Zhao, a synthetic biologist at the University of Illinois at Urbana-Champaign. Though the Sc2.0 team still has several chromosomes left to generate, the new research provides proof of concept for future genome synthesis projects, and the system has become radically more efficient.
It took nearly 10 years for the researchers to build their first chromosome — even though they were working on the shortest one in the yeast's genome. But they needed less than three years to generate the next five chromosomes, which include some of the genome's longest, and Boeke said the team will complete the full genome by the end of next year.
Though the process has gotten faster, each synthesized chromosome still requires a herculean effort on the part of more than 100 collaborators working across three continents. The blueprints for the chromosomes are written via a computer program and then analyzed by biologists to see if they will work. These are then broken into short, manageable segments and shipped off to commercial DNA synthesis labs. The short chunks are then stitched together using a technique developed by Boeke and undergraduate students who took his “build-a-genome” course at Johns Hopkins, and then injected into the cell.
The compliant yeast cells make it easy to swap in the fabricated material for the DNA that's already there. And in many cases the new genetic material has no effect on the organisms' growth. The data for the entire Sc2.0 project is open-source, so anyone can borrow from or contribute to the research.
“This is a progress report, it is not a final product,” said Harvard geneticist George Church, who led the research on engineered E. coli. “But the fact that there are so many teams involved indicates this is a generalizable and adoptable strategy. It's not a one-off stunt.”
Church speculated that scientists could be heading toward “a post-CRISPR world,” in which, instead of using the heralded gene editing technology to modify chromosomes, scientists will simply synthesize entire new ones. “We’re seeing something that goes far beyond editing,” he said.
Church and Boeke are organizers of the Genome Project-write, an heir to the Human Genome Project that aims to develop the tools needed to engineer and test genomes on a large scale, dramatically reducing the cost of such efforts. The initiative drew criticism from many in the scientific community when it was formally launched last year. Francis Collins, head of the National Institutes of Health and an organizer of the earlier Human Genome Project, told The Washington Post at the time that “whole-genome, whole-organism synthesis projects extend far beyond current scientific capabilities, and immediately raise numerous ethical and philosophical red flags.”
Endy of Stanford also urged caution: “Do we wish to be operating in a world where people are capable of organizing themselves to make human genomes? Should we pause and reflect on that question before we launch into doing it?” he told The Post. “They’re talking about making real the capacity to make the thing that defines humanity — the human genome.”
Boeke acknowledged that there are serious ethical considerations to be made when it comes to synthesizing the genomes of humans and even other animals. But he doesn't worry too much about the safety profile of Sc2.0.
“Let's say for the sake of argument there could be the yeast that ate Manhattan,” he said. “If such a yeast could arise in nature it probably already would have.”
In other words, nature has had billions of years to perfect the process of synthesizing genomes. Humans may have crafted a handful of sequences for a few single-cell organisms, but if our dreams — and our nightmares — involve someday mastering evolution, we've still got a long way to go.