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First chromosome made synthetically from yeast

Work is major step toward lab-created eukaryotic life-form

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2:05pm, March 27, 2014

RISE UP  Baker’s yeast, Saccharomyces cerevisiae, seen under a microscope, ferment fruit and grain into alcohol and make bread rise. Now researchers have taken the first step toward making a synthetic version of the organism that may perform feats regular yeast never could.

Magazine issue: Vol. 185 No. 8, May 3, 2014
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Designer organisms have crept closer to reality. Scientists have stitched together a version of a yeast chromosome. It is the first synthetic chromosome ever assembled from a eukaryotic organism, the type in which cells store DNA in nuclei.

Other groups have previously synthesized chromosomes from bacteria, but this is the first step in designing synthetic eukaryotes.

Researchers from Johns Hopkins University, including a small army of undergraduate students, and colleagues report the achievement March 27 in Science. The synthetic chromosome is based on chromosome III from the yeast Saccharomyces cerevisiae, but it is not an exact replica.

In creating the synthetic version, researchers jettisoned some of the chromosome’s extra baggage. These parts include gene-interrupting pieces of DNA called introns, genes that produce protein-building molecules called transfer RNAs, repetitive regions near the chromosome ends and remnants of genetic parasites called jumping genes or transposons that can replicate and move to other parts of the genome. In addition to whittling away some DNA, the team endowed the synthetic chromosome with a scrambling system that can reshuffle the chromosome’s genetic deck to produce organisms with new properties. The finished chromosome’s length measures 272,871 base pairs — much shorter than the original chromosome’s 316,617 base pairs. Base pairs are the information-carrying chemical units of DNA.

“What we’re doing is essentially genetic engineering on steroids,” says Jef Boeke, a yeast geneticist now at New York University who helped spearhead the project while at Johns Hopkins University.

He and colleagues created an undergraduate class called Build-A-Genome that aided in the assembly. Students started with single DNA strands that copied yeast chromosome III, 60 to 79 bases at a time, and melded them into 750-base-pair building blocks. Other members of the team snapped those DNA building blocks together to form “minichunks” 2,000 to 4,000 base pairs long.

Then the researchers let the yeast take over. Yeast cells are masters of a process called homologous recombination in which bits of matching DNA can swap with one another. In a series of 11 experiments, the researchers inserted an average of 12 synthetic minichunks into the yeast. The fungi then swapped the synthetic chunks for the matching portion of its native chromosome, eventually creating a fully engineered chromosome. Similar yeast assembly lines might stitch together chromosomes from other eukaryotic organisms, such as humans, fruit flies, mice or plants.

Losing nearly 14 percent of the bases in chromosome III could have crippled the yeast’s ability to compete, but the team found that yeast cells carrying the synthetic chromosome grew as well as ones with the natural version under 20 different conditions. Only one situation, growing with high concentrations of a sugar alcohol called sorbitol, put fungi with the synthetic chromosome at a slight disadvantage compared with normal yeast.  

“The fact that it grows as well as it does is really encouraging,” says Philip Weyman, a synthetic biologist at the J. Craig Venter Institute in La Jolla, Calif. Now the researchers can scramble the chromosome and learn which parts are really important for function and which bits cells can do without. That portion of the research will be the most interesting, but it will also be the most difficult, Weyman says. “Building it, as much of a hurdle as that was, was really the easy part.”

Chromosome III is just one of yeast’s 16 chromosomes, all of which Boeke and his colleagues plan to synthesize. The group hopes to have a completely synthetic yeast genome in three to five years, Boeke says.

He doesn’t expect all of the altered chromosomes to work as well as this one did, but creating one that cripples yeast would be great for learning the rules about how to build a stripped-down genome.

“We aim to fail here,” Boeke says. “We think we know a lot about the biology, but surely we don’t know everything.” Synthetic chromosomes that damage yeast’s evolutionary fitness or fail to produce viable yeast may teach researchers how chromosomes evolved and give clues about the minimal requirements for eukaryotic life, he says.

The scrambling system built into the synthetic yeast may help create fungi that can more efficiently produce chemicals for drug and chemical companies, Boeke says.

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