International scientists have teamed up to combine seven synthetic chromosomes synthesized in the laboratory into a single cell, producing yeast strains with more than 50 percent of synthetic DNA.The strain survived and was able to replicate like a wild strain.The semi-synthetic yeast study was published in Cells Nov. 9.
The study is part of the results of the Synthetic Yeast Genome Project (Sc2.0).This is a global coalition dedicated to developing the first synthetic eukaryotic genome from scratch.The team has now synthesized and adapted all 16 yeast chromosomes.
"We want to understand the fundamentals of the genome by building synthetic genomes.Co-author Patrick Yizhi Cai, a synthetic biologist at the University of Manchester in the UK, said: "The team has now rewritten the germ yeast gene operating system, opening a new era in engineering biology.”
Although bacterial and viral genomes have been synthesized, this will be the first synthetic eukaryotic genome, involving the complexity of polychromosomes.Synthetic yeast is also a "design" genome, which is very different from the natural yeast genome.
"Our primary goal is to build a yeast that will teach us new biology."Jef Boeke, a synthetic biologist at New York University's Langney Health Center and a leader in Sc2.0, said the paper's correspondent.
To this end, researchers removed non-coding DNA fragments and duplicates that could be "junk," added new DNA fragments to make it easier to distinguish genes from natural ones, and introduced a built-in diversity generator called SCRaMbLE.
To increase the stability of the genome, the team also removed many genes encoding transfer RNA (tRNA) and relocated them to a new "new chromosome" composed entirely of tRNA genes."It's the first chromosome in the world to be synthesized entirely from scratch, something that doesn't exist in nature."Cai said.
Since the yeast genome consists of 16 chromosomes, researchers began to assemble each chromosome independently, creating 16 partially synthesized yeast strains, each containing 15 natural and one synthetic chromosome.The next challenge is to start combining these synthetic chromosomes into a yeast cell.
Boeke's team used a Mendelian pea-like approach: hybridizing different partially synthetic yeast strains and then looking for individuals in offspring carrying both synthetic chromosomes.Although effective, the method is slow, even though the team gradually integrates all synthetic chromosomes—six complete chromosomes and one chromosome arm—into one cell.Finally, the synthesis rate of yeast strains was over 31%, the morphology was normal, and there was only a slight growth defect compared with wild yeast.
To more effectively transfer specific chromosomes between yeast strains, researchers have developed a new method called chromosome substitution.They used chromosome substitution to transfer a newly synthesized chromosome (chromosome IV, the largest of all synthesized chromosomes), resulting in a yeast cell with 7.5 synthesized chromosomes, more than 50%.
When synthetic chromosomes were integrated into a single yeast strain, the team discovered several genetic defects that were invisible to yeast strains carrying only one synthetic chromosome."We know this can happen - there can be a lot of things, each with a small impact, and when you put them together it can be fatal." said Boeke.
Some of these errors are due only to the superimposition of many minor defects in the genome, while others involve genetic interactions between genes on different synthetic chromosomes.By using CRISPR/Cas9-based methods, researchers were able to fix several of these errors and improve synthetic yeast.
"We've shown that basically half of the synthetic genome can be integrated, and the resulting yeast is still well-adapted."We can learn a new twist in the rules of life," Boeke said.”
Next, the researchers will integrate the remaining synthetic chromosomes."We are only so far from the end of a single cell with 16 synthetic chromosomes."I like to call full synthesis the beginning, not the end, because that's when we can really start shuffling and producing yeast and do things that we haven't done before," Boeke said.