Chromosome by chromosome, researchers have artificially recreated the genome of baker's yeast and created a yeast strain whose genome is more than half synthetic. The semi-synthetic strain survives and grows as well as natural yeast. On the one hand, the research helps to better understand the basics of the genome. On the other hand, they can help create optimized strains for industrial use. The goal is a completely synthetic organism whose properties can be adjusted as needed.
People have been using the yeast Saccharomyces cerevisiae for thousands of years to bake bread, brew beer or ferment juice into wine. In modern biotechnology, yeast is now also used to produce fuels, medicines or fragrances, and it is a common model organism in medical research. Their genome is therefore well known and has been modified many times, at least in part.
Variations on the natural model
A team led by Yu Zhao from New York University has now created a yeast strain for the first time whose genome is more than half synthetic. The research is part of the large-scale international research project Synthetic Yeast Genome Project, which is working to develop a completely synthetic yeast. While the genomes of some viruses and bacteria have already been fully synthesized, yeast would be the first eukaryote with a designer genome.
In order to actually create something new, the researchers did not simply recreate the natural chromosomes, but varied them. They left out numerous non-coding regions and added new DNA sections instead. The researchers removed all areas that coded for so-called transfer RNAs, which are needed to assemble new proteins, from the original chromosomes and relocated them to a completely new chromosome, which they gave the name tRNA neochromosome. “The tRNA neochromosome is the world’s first completely synthetic chromosome,” says co-author Yizhi Cai from the University of Manchester. “There is nothing like this in nature.”
Synthetic chromosomes crossed in
Towards a fully synthetic yeast, the team synthesized artificial variants of all sixteen of the yeast's chromosomes in the laboratory and inserted each one individually into a yeast strain in which the remaining 15 chromosomes were of natural origin. Through trial and error, they discovered which variants each made possible a viable organism. “Our motivation is to understand the fundamental principles of the genome by building synthetic genomes,” explains Cai.
The researchers crossed the functioning strains, each with one synthetic chromosome, and selected the offspring with several synthetic chromosomes. They continued to cross these together until they had combined six complete synthetic chromosomes and one chromosome arm into a single strain. They then inserted the largest of all synthetic chromosomes using a newly developed method called chromosome substitution. The genetic makeup of the strain created in this way is more than 50 percent synthetic.
To learn from mistakes
However, this strain showed growth deficits compared to wild-type yeast. The researchers identified several small genetic errors in the synthetic DNA sections that were not noticeable as long as only a single chromosome was replaced. “We knew in principle that something like this could happen - that we could have a huge number of tiny effects that, when you put them all together, can add up and magnify,” says Zhao's colleague Jef Boeke. Using genetic engineering methods, the researchers were able to find and correct some of these errors, thereby increasing the survival and reproduction of the semi-synthetic yeast. “We have now shown that we can essentially consolidate half of the genome with good fitness,” says Boeke. “And through troubleshooting we learn new things about the rules of life.”
In the next step, the scientists plan to also integrate the remaining synthetic chromosomes. “This is an exciting milestone in engineering biology,” says Cai. “While we have been able to edit genes for some time, we have never been able to rewrite a eukaryote genome from scratch. This work is fundamental to our understanding of the building blocks of life and has the potential to revolutionize synthetic biology.”
Sources: Yu Zhao (New York University) et al., Cell, doi: 10.1016/j.cell.2023.09.025; Daniel Schindler (University of Manchester) et al., Cell, doi: 10.1016/j.cell.2023.10.015