The first synthetic chromosome for a creature with complex cells, designed on a computer and made from scratch in a laboratory, is being put through its paces

THE science of synthetic biology took an important step forward this week with the announcement in Science, by a team from Jef Boeke’s laboratory at Johns Hopkins University, in Baltimore, of the first completely synthetic yeast chromosome. This takes the field from the bacterial realm to that of creatures like man.

That fungi and people are closely related may not be obvious to the average human being. But biologically it is true, because both are eukaryotes, meaning that they have proper cell nuclei with several linear chromosomes in them, and also lots of other complex and well-defined cellular structures, called organelles. Bacteria, in contrast, are prokaryotes—meaning their DNA is arranged in small, circular chromosomes which float around in more or less organelleless cells.

Dr Boeke and his colleagues have taken advantage of the falling price of DNA synthesis, and an army of willing undergraduates who did the grunt work, to make a molecule more than 270,000 base pairs (genetic “letters”) long. This forms the basis of the new chromosome, which is similar to yeast’s third-smallest chromosome (out of 16), but has some important differences from the natural version.

First, it has been cleaned up. The team have removed genetic parasites called transposons, which use a cell’s DNA-replication machinery without contributing anything to an organism’s well-being. They have also tidied places near the chromosome’s ends, where the genetic letters repeat for no apparent reason, and chopped out regions called introns that break up the business parts of genes. Eleven entire genes for molecules called transfer RNAs are out, too. Transfer RNAs are important (they carry the components of proteins, known as amino acids, to protein factories), but yeast has 275 genes for them, and there are only 42 types of transfer RNA in yeast cells. Since transfer-RNA genes are often sites of chromosomal instability, excising a few of them seemed to the team like a good idea.

Gene genie, let yourself go

All this was done, as the paper puts it, “in silico”—in other words, on a computer before the chromosome was made. The team also tinkered in ways that will let them modify it subsequently, in vivo. They have added 98 pieces of DNA called loxPsym sequences, which mark individual genes and allow those genes, by the application of an appropriate enzyme, to be excised. This is part of a plan to find out which genes are necessary to yeast’s survival, and which merely desirable, by knocking them out. Until now, that has had to be done one gene at a time. Using a synthetic chromosome modified in this way means it will be easier to execute multiple, simultaneous gene knockouts.

The team have also fitted their new chromosome with the potential to make proteins that contain unnatural amino acids which might thus have entirely new properties. They did this by replacing some of the chromosome’s stop codons.

Codons are three-letter DNA words. Most represent specific amino acids, and indicate where these should fit into a protein. Stop codons, by contrast, tell gene-reading enzymes that they have got to the end of the message. In gene-speak, a stop codon can be either TAG or TAA. In the artificial chromosome they have all been converted to TAA. That leaves TAG free to be used, after further appropriate tinkering, as the codon for a 21st amino acid, in addition to the 20 natural ones.

All these changes risk destabilising the new chromosome. But that does not seem to have happened. The team have run it through 125 generations in 30 different sets of yeast without it coming to any apparent harm. They thus seem to have created a robust demonstration that a synthetic eukaryotic chromosome can work.

The next step is to make more yeast chromosomes—eventually creating a completely synthetic genome. This is the goal of the Synthetic Yeast Genome Project, of which Dr Boeke is head. That will have practical applications, since yeast is both a model for the biochemistry of more complex eukaryotes, including people, and an industrially important organism. It has been used for thousands of years to make ethanol, of course. But these days researchers are extending its chemical portfolio. The ability to design its chromosomes in silico will make that easier to do.

In the longer term, other eukaryotes will no doubt be treated likewise. The day of designer plants and animals, then, is getting closer. And so too, for those who worry about such things, is the day when designer humans might be possible.

Clarification: The Synthetic Yeast Genome Project, though based at Johns Hopkins University when this work was carried out, has now moved, along with Dr Boeke, to the Langone Medical Centre at New York University.